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- PDB-2h9a: Corrinoid Iron-Sulfur Protein -

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Basic information

Entry
Database: PDB / ID: 2h9a
TitleCorrinoid Iron-Sulfur Protein
Components
  • CO dehydrogenase/acetyl-CoA synthase, iron-sulfur protein
  • Carbon monoxide dehydrogenase corrinoid/iron-sulfur protein, gamma subunit
KeywordsOXIDOREDUCTASE / heterodimer / beta-alpha-barrels
Function / homology
Function and homology information


acetyl-CoA catabolic process / methyltransferase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Rossmann fold - #11600 / CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel / Acetyl-CoA decarbonylase/synthase complex, gamma subunit / : / CO dehydrogenase/acetyl-CoA synthase delta subunit / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / Dihydropteroate synthase-like / Dihydropteroate synthase-like ...Rossmann fold - #11600 / CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel / Acetyl-CoA decarbonylase/synthase complex, gamma subunit / : / CO dehydrogenase/acetyl-CoA synthase delta subunit / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / IODIDE ION / IRON/SULFUR CLUSTER / CO dehydrogenase/acetyl-CoA synthase, iron-sulfur protein / Carbon monoxide dehydrogenase corrinoid/iron-sulfur protein, gamma subunit
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsDobbek, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural insights into methyltransfer reactions of a corrinoid iron-sulfur protein involved in acetyl-CoA synthesis.
Authors: Svetlitchnaia, T. / Svetlitchnyi, V. / Meyer, O. / Dobbek, H.
History
DepositionJun 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase corrinoid/iron-sulfur protein, gamma subunit
B: CO dehydrogenase/acetyl-CoA synthase, iron-sulfur protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,09320
Polymers82,3802
Non-polymers3,71218
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-29 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.030, 44.270, 100.660
Angle α, β, γ (deg.)90.00, 118.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1759-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase corrinoid/iron-sulfur protein, gamma subunit


Mass: 48469.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Carboxydothermus hydrogenoformans (bacteria)
References: UniProt: Q3ACS3
#2: Protein CO dehydrogenase/acetyl-CoA synthase, iron-sulfur protein


Mass: 33910.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Carboxydothermus hydrogenoformans (bacteria)
References: UniProt: Q3ACS0

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Non-polymers , 4 types, 583 molecules

#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, 1mM beta-mercaptoethanol, 100 mM KI, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 11, 2004
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 48806 / Num. obs: 48659 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
SHARPphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 1460 Random
Rwork0.203 --
all0.207 48805 -
obs0.207 48659 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5288 0 115 565 5968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_bond_d0.017

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