3K1S | pdb_00003k1s

Crystal Structure of the PTS Cellobiose Specific Enzyme IIA from Bacillus anthracis

PDB DOI: https://doi.org/10.2210/pdb3K1S/pdb

Classification: TRANSFERASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-09-28 Released: 2009-10-13
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Kwon, K., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.226 (Depositor), 0.228 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the PTS Cellobiose Specific Enzyme IIA from Bacillus anthracis

Anderson, S.M., Wawrzak, Z., Onopriyenko, O., Kwon, K., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 111.98 kDa
Atom Count: 8,229
Modelled Residue Count: 951
Deposited Residue Count: 981
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system, cellobiose-specific IIA component	A, B, C, D, E A, B, C, D, E, F, G, H, I	109	Bacillus anthracis	Mutation(s): 0 Gene Names: celC-2, celC2, BAS5057, BA_5442, GBAA5442, GBAA_5442 EC: 2.7.1.69
UniProt
Find proteins for A0A6H3A5D1 (Bacillus anthracis) Explore A0A6H3A5D1 Go to UniProtKB: A0A6H3A5D1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6H3A5D1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain O [auth B] SDF format, chain Q [auth C] MOL2 format, chain AA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain AA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C]	AA [auth H], O [auth B], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth H] Focus chain O [auth B] Focus chain Q [auth C] Interactions & Density Focus chain AA [auth H] Focus chain O [auth B] Focus chain Q [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain T [auth E] SDF format, chain Y [auth H] MOL2 format, chain M [auth B] MOL2 format, chain T [auth E] MOL2 format, chain Y [auth H] mmCIF format, chain M [auth B] mmCIF format, chain T [auth E] mmCIF format, chain Y [auth H]	M [auth B], T [auth E], Y [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain T [auth E] Focus chain Y [auth H] Interactions & Density Focus chain M [auth B] Focus chain T [auth E] Focus chain Y [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain CA [auth I] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain BA [auth I] MOL2 format, chain CA [auth I] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain BA [auth I] mmCIF format, chain CA [auth I] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	BA [auth I] CA [auth I] J [auth A] K [auth A] L [auth A] BA [auth I], CA [auth I], J [auth A], K [auth A], L [auth A], N [auth B], P [auth C], R [auth D], S [auth D], U [auth F], V [auth F], W [auth F], X [auth G], Z [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain CA [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain CA [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Z [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.226 (Depositor), 0.228 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33k1s

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.887	α = 90
b = 92.887	β = 90
c = 260.639	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary