5LMM

Structure of E coli Hydrogenase Hyd-1 mutant E28Q

• PDB DOI: https://doi.org/10.2210/pdb5LMM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli CFT073, Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2016-08-01 Released: 2017-08-16 
• Deposition Author(s): Carr, S.B., Phillips, S.E.V., Evans, R.M., Brooke, E.J., Armstrong, F.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.146 
• R-Value Work: 0.118 
• R-Value Observed: 0.119 

Starting Model: experimental

Literature

Kinetic consequences of re-engineering the outer shell "canopy" above the active site of a [NiFe]-hydrogenase.

Carr, S.B., Phillips, S.E.V., Evans, R.M., Brooke, E.J., Islam, S.T.A., Roberts, G.M., Wehlin, S.A.M., Armstrong, F.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 207.18 kDa 
• Atom Count: 15,256 
• Modelled Residue Count: 1,690 
• Deposited Residue Count: 1,834 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrogenase-1 small chain	A [auth S], C [auth T]	335	Escherichia coli CFT073	Mutation(s): 0  EC: 1.12.99.6
UniProt
Find proteins for P69739 (Escherichia coli (strain K12)) Explore P69739  Go to UniProtKB:  P69739

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrogenase-1 large chain	B [auth L], D [auth M]	582	Escherichia coli K-12	Mutation(s): 0  EC: 1.12.99.6
UniProt
Find proteins for P0ACD8 (Escherichia coli (strain K12)) Explore P0ACD8  Go to UniProtKB:  P0ACD8

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMT	H [auth S], S [auth T]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
SF4	E [auth S], P [auth T]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SF3	G [auth S], R [auth T]	FE4-S3 CLUSTER Fe4 S3 QQACTBFBZNWJMV-UHFFFAOYSA-N
F3S	F [auth S], Q [auth T]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
FCO	L, W [auth M]	CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N
TRS	BA [auth M]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	J [auth S], K [auth L], V [auth T], Z [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	M [auth L], X [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	I [auth S], T, U [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	N [auth L], Y [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
LI	AA [auth M], O [auth L]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	B [auth L], D [auth M]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.146 
• R-Value Work: 0.118 
• R-Value Observed: 0.119 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.981	α = 90
b = 97.799	β = 90
c = 183.474	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Carr, S.B., Phillips, S.E.V., Evans, R.M., Brooke, E.J., Armstrong, F.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary