4YWH | pdb_00004ywh

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM ACTINOBACILLUS SUCCINOGENES 130Z (Asuc_0499, TARGET EFI-511068) WITH BOUND D-XYLOSE

PDB DOI: https://doi.org/10.2210/pdb4YWH/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Actinobacillus succinogenes 130Z
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-20 Released: 2015-04-15
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM ACTINOBACILLUS SUCCINOGENES 130Z (Asuc_0499, TARGET EFI-511068) WITH BOUND D-XYLOSE

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 73.58 kDa
Atom Count: 4,872
Modeled Residue Count: 617
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC TRANSPORTER SOLUTE BINDING PROTEIN	A, B	332	Actinobacillus succinogenes 130Z	Mutation(s): 0 Gene Names: Asuc_0499 EC: 3.6.3.17
UniProt
Find proteins for A6VLM7 (Actinobacillus succinogenes (strain ATCC 55618 / DSM 22257 / CCUG 43843 / 130Z)) Explore A6VLM7 Go to UniProtKB: A6VLM7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6VLM7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYP Query on XYP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.796	α = 90
b = 37.67	β = 91.5
c = 105.336	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Enzyme Function Initiative (EFI)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM093342

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2023-11-15
Changes: Data collection
Version 2.3: 2024-10-23
Changes: Structure summary