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- PDB-1c4a: BINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE O... -

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Basic information

Entry
Database: PDB / ID: 1c4a
TitleBINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE OF THE FE-ONLY HYDROGENASE (CPI) FROM CLOSTRIDIUM PASTEURIANUM
ComponentsPROTEIN (FE-ONLY HYDROGENASE)
KeywordsOXIDOREDUCTASE / METALLOPROTEINS / [FES] CLUSTERS / HYDROGEN OXIDATION / PROTON REDUCTION
Function / homology2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-like superfamily / His(Cys)3-ligated-type [4Fe-4S] domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S dicluster domain / Iron only hydrogenase large subunit, C-terminal domain / Iron hydrogenase small subunit / Iron hydrogenase, small subunit superfamily ...2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-like superfamily / His(Cys)3-ligated-type [4Fe-4S] domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S dicluster domain / Iron only hydrogenase large subunit, C-terminal domain / Iron hydrogenase small subunit / Iron hydrogenase, small subunit superfamily / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Iron hydrogenase, subset / Iron hydrogenase / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase, small subunit / 2Fe-2S ferredoxin-type iron-sulfur binding domain / ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / Iron hydrogenase 1
Function and homology information
Specimen sourceClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.4 Å resolution
AuthorsLemon, B.J. / Peters, J.W.
CitationJournal: Biochemistry / Year: 1999
Title: Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum.
Authors: Lemon, B.J. / Peters, J.W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 13, 1999 / Release: Dec 22, 1999
RevisionDateData content typeGroupProviderType
1.0Dec 22, 1999Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FE-ONLY HYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8497
Polyers63,9111
Non-polymers1,9386
Water5,891327
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)133.700, 84.000, 55.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide PROTEIN (FE-ONLY HYDROGENASE) / CPI


Mass: 63911.102 Da / Num. of mol.: 1 / Source: (natural) Clostridium pasteurianum (bacteria) / Genus: Clostridium / Cellular location: CYTOPLASM / References: UniProt: P29166, 1.18.99.1
#2: Chemical ChemComp-HC1 / 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER


Mass: 355.933 Da / Num. of mol.: 1 / Formula: C5H8Fe2O7S2
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Formula: Fe4S4 / Iron–sulfur cluster
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Formula: Fe2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 / Density percent sol: 52.7 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
pH: 4.6 / Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
125 %PEG400011
20.1 Msodium acetate11
30.2 Mammonium acetate11

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Collection date: Jan 15, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2.4 Å / D resolution low: 2 Å / Number obs: 24218 / Observed criterion sigma I: 1 / Rmerge I obs: 0.068 / Redundancy: 7 % / Percent possible obs: 90
Reflection shellRmerge I obs: 0.181 / Highest resolution: 2.4 Å / Lowest resolution: 2.51 Å / Percent possible all: 74.5
Reflection
*PLUS
Number measured all: 176088
Reflection shell
*PLUS
Percent possible obs: 74.5

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.857refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FEH
R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 1
Least-squares processR factor R free: 0.254 / R factor R work: 0.199 / R factor obs: 0.199 / Highest resolution: 2.4 Å / Lowest resolution: 2 Å / Number reflection obs: 23019 / Percent reflection obs: 90.4
Refine hist #LASTHighest resolution: 2.4 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 4461 / Nucleic acid: 0 / Ligand: 52 / Solvent: 327 / Total: 4840
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d2.54
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.010
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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