5LMM | pdb_00005lmm

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.146 (Depositor), 0.152 (DCC)
R-Value Work:
0.118 (Depositor)
R-Value Observed:
0.119 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69739
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ACD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain H [auth S] SDF format, chain S [auth T] MOL2 format, chain H [auth S] MOL2 format, chain S [auth T] mmCIF format, chain H [auth S] mmCIF format, chain S [auth T]	H [auth S], S [auth T]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain H [auth S] Focus chain S [auth T] Interactions & Density Focus chain H [auth S] Focus chain S [auth T]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth S] SDF format, chain P [auth T] MOL2 format, chain E [auth S] MOL2 format, chain P [auth T] mmCIF format, chain E [auth S] mmCIF format, chain P [auth T]	E [auth S], P [auth T]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth S] Focus chain P [auth T] Interactions & Density Focus chain E [auth S] Focus chain P [auth T]
SF3 Query on SF3 Download:Ideal Coordinates CCD File SDF format, chain G [auth S] SDF format, chain R [auth T] MOL2 format, chain G [auth S] MOL2 format, chain R [auth T] mmCIF format, chain G [auth S] mmCIF format, chain R [auth T]	G [auth S], R [auth T]	FE4-S3 CLUSTER Fe₄ S₃ QQACTBFBZNWJMV-UHFFFAOYSA-N		Interactions Focus chain G [auth S] Focus chain R [auth T] Interactions & Density Focus chain G [auth S] Focus chain R [auth T]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain Q [auth T] SDF format, chain F [auth S] MOL2 format, chain Q [auth T] MOL2 format, chain F [auth S] mmCIF format, chain Q [auth T] mmCIF format, chain F [auth S]	F [auth S], Q [auth T]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain F [auth S] Focus chain Q [auth T] Interactions & Density Focus chain F [auth S] Focus chain Q [auth T]
FCO Query on FCO Download:Ideal Coordinates CCD File SDF format, chain L SDF format, chain W [auth M] MOL2 format, chain L MOL2 format, chain W [auth M] mmCIF format, chain L mmCIF format, chain W [auth M]	L, W [auth M]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain L Focus chain W [auth M] Interactions & Density Focus chain L Focus chain W [auth M]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain BA [auth M] MOL2 format, chain BA [auth M] mmCIF format, chain BA [auth M]	BA [auth M]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth M] Interactions & Density Focus chain BA [auth M]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth S] SDF format, chain K [auth L] SDF format, chain V [auth T] SDF format, chain Z [auth M] MOL2 format, chain J [auth S] MOL2 format, chain K [auth L] MOL2 format, chain V [auth T] MOL2 format, chain Z [auth M] mmCIF format, chain J [auth S] mmCIF format, chain K [auth L] mmCIF format, chain V [auth T] mmCIF format, chain Z [auth M]	J [auth S], K [auth L], V [auth T], Z [auth M]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth S] Focus chain K [auth L] Focus chain V [auth T] Focus chain Z [auth M] Interactions & Density Focus chain J [auth S] Focus chain K [auth L] Focus chain V [auth T] Focus chain Z [auth M]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain M [auth L] SDF format, chain X [auth M] MOL2 format, chain M [auth L] MOL2 format, chain X [auth M] mmCIF format, chain M [auth L] mmCIF format, chain X [auth M]	M [auth L], X [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain M [auth L] Focus chain X [auth M] Interactions & Density Focus chain M [auth L] Focus chain X [auth M]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth S] SDF format, chain T SDF format, chain U [auth T] MOL2 format, chain I [auth S] MOL2 format, chain T MOL2 format, chain U [auth T] mmCIF format, chain I [auth S] mmCIF format, chain T mmCIF format, chain U [auth T]	I [auth S], T, U [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth S] Focus chain T Focus chain U [auth T] Interactions & Density Focus chain I [auth S] Focus chain T Focus chain U [auth T]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth L] SDF format, chain Y [auth M] MOL2 format, chain N [auth L] MOL2 format, chain Y [auth M] mmCIF format, chain N [auth L] mmCIF format, chain Y [auth M]	N [auth L], Y [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth L] Focus chain Y [auth M] Interactions & Density Focus chain N [auth L] Focus chain Y [auth M]
LI Query on LI Download:Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain O [auth L] MOL2 format, chain AA [auth M] MOL2 format, chain O [auth L] mmCIF format, chain AA [auth M] mmCIF format, chain O [auth L]	AA [auth M], O [auth L]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain O [auth L] Interactions & Density Focus chain AA [auth M] Focus chain O [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on 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 (Depositor), 0.152 (DCC)
R-Value Work: 0.118 (Depositor)
R-Value Observed: 0.119 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

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

Revision History (Full details and data files)

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