5LMM

Structure of E coli Hydrogenase Hyd-1 mutant E28Q


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 

wwPDB Validation 3D Report Full Report



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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 large chain
L, M
582Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hyaBb0973JW0955
EC: 1.12.99.6
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 (periplasmic domain)
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACD8

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 small chain
S, T
335Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: hyaAc1113
EC: 1.12.99.6
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 (periplasmic domain)
Find proteins for P69740 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P69740
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download CCD File 
S, T
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
S, T
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SF3
Query on SF3

Download CCD File 
S, T
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-DXQBTJNKAZ
 Ligand Interaction
F3S
Query on F3S

Download CCD File 
S, T
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download CCD File 
L, M
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download CCD File 
M
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
L, M, S, T
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NI
Query on NI

Download CCD File 
L, M
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
S, T
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
L, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

Download CCD File 
L, M
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
L,M
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
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 = 93.981α = 90
b = 97.799β = 90
c = 183.474γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release