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- PDB-4c1n: Corrinoid protein reactivation complex with activator -

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Basic information

Entry
Database: PDB / ID: 4c1n
TitleCorrinoid protein reactivation complex with activator
Components
  • (IRON-SULFUR CLUSTER BINDING ...) x 2
  • CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
  • CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
KeywordsOXIDOREDUCTASE/METAL BINDING PROTEIN / OXIDOREDUCTASE-METAL BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


acetyl-CoA catabolic process / methyltransferase activity / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding
Similarity search - Function
Electron transport complex subunit B, putative Fe-S cluster / Ubiquitin-like (UB roll) - #880 / Domain of unknown function (DUF4445) / RACo, C-terminal / RACo linker region / RACo, middle region / RACo, middle domain superfamily / : / C-terminal domain of RACo the ASKHA domain / RACo linker region ...Electron transport complex subunit B, putative Fe-S cluster / Ubiquitin-like (UB roll) - #880 / Domain of unknown function (DUF4445) / RACo, C-terminal / RACo linker region / RACo, middle region / RACo, middle domain superfamily / : / C-terminal domain of RACo the ASKHA domain / RACo linker region / RACo middle region / Rossmann fold - #11600 / Acetyl-CoA decarbonylase/synthase complex, gamma subunit / CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel / : / CO dehydrogenase/acetyl-CoA synthase delta subunit / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Dihydropteroate synthase-like / Dihydropteroate synthase-like / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / ATPase, nucleotide binding domain / Ubiquitin-like (UB roll) / Nucleotidyltransferase; domain 5 / TIM Barrel / Alpha-Beta Barrel / Roll / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / IRON/SULFUR CLUSTER / CO dehydrogenase/acetyl-CoA synthase, iron-sulfur protein / Iron-sulfur cluster binding protein / Carbon monoxide dehydrogenase corrinoid/iron-sulfur protein, gamma subunit
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.53 Å
AuthorsHennig, S.E. / Goetzl, S. / Jeoung, J.H. / Bommer, M. / Lendzian, F. / Hildebrandt, P. / Dobbek, H.
CitationJournal: Nat.Commun. / Year: 2014
Title: ATP-Induced Electron Transfer by Redox-Selective Partner Recognition
Authors: Hennig, S.E. / Goetzl, S. / Jeoung, J.H. / Bommer, M. / Lendzian, F. / Hildebrandt, P. / Dobbek, H.
History
DepositionAug 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
C: CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
D: CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
E: CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
F: CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
G: CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
H: CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
I: IRON-SULFUR CLUSTER BINDING PROTEIN
J: IRON-SULFUR CLUSTER BINDING PROTEIN
K: IRON-SULFUR CLUSTER BINDING PROTEIN
X: IRON-SULFUR CLUSTER BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)555,64120
Polymers548,91312
Non-polymers6,7288
Water21,5821198
1
C: CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
D: CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
J: IRON-SULFUR CLUSTER BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8785
Polymers137,1963
Non-polymers1,6822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-84.1 kcal/mol
Surface area47120 Å2
MethodPISA
2
G: CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
H: CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
K: IRON-SULFUR CLUSTER BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0075
Polymers137,3253
Non-polymers1,6822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-84.2 kcal/mol
Surface area47320 Å2
MethodPISA
3
A: CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
B: CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
I: IRON-SULFUR CLUSTER BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8785
Polymers137,1963
Non-polymers1,6822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-79.3 kcal/mol
Surface area46870 Å2
MethodPISA
4
E: CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
F: CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
X: IRON-SULFUR CLUSTER BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8785
Polymers137,1963
Non-polymers1,6822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-77.8 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.134, 128.175, 163.366
Angle α, β, γ (deg.)77.61, 82.25, 88.76
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT / BIG SUBUNIT COFESP


Mass: 48125.395 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3ACS3
#2: Protein
CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN / SMALL SUBUNIT COFESP


Mass: 33779.160 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3ACS0

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IRON-SULFUR CLUSTER BINDING ... , 2 types, 4 molecules IJXK

#3: Protein IRON-SULFUR CLUSTER BINDING PROTEIN / RACO


Mass: 55291.496 Da / Num. of mol.: 3 / Fragment: RESIDUES 122-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3ACS2
#4: Protein IRON-SULFUR CLUSTER BINDING PROTEIN / RACO


Mass: 55420.609 Da / Num. of mol.: 1 / Fragment: RESIDUES 121-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3ACS2

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Non-polymers , 3 types, 1206 molecules

#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1198 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.37 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.53→30 Å / Num. obs: 168978 / % possible obs: 96 % / Observed criterion σ(I): 2.6 / Redundancy: 2.74 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 2.53→2.6 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.53→30.631 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 8447 5 %
Rwork0.1908 --
obs0.1934 168947 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→30.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38561 0 396 1198 40155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00339761
X-RAY DIFFRACTIONf_angle_d0.7454107
X-RAY DIFFRACTIONf_dihedral_angle_d13.18314875
X-RAY DIFFRACTIONf_chiral_restr0.0276301
X-RAY DIFFRACTIONf_plane_restr0.0047009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.55870.34832350.26984465X-RAY DIFFRACTION79
2.5587-2.58880.32862600.25254944X-RAY DIFFRACTION89
2.5888-2.62040.3142810.24625335X-RAY DIFFRACTION97
2.6204-2.65350.30562830.24855389X-RAY DIFFRACTION96
2.6535-2.68840.32972840.2415393X-RAY DIFFRACTION96
2.6884-2.72520.27992830.2215371X-RAY DIFFRACTION97
2.7252-2.76410.29972830.22445373X-RAY DIFFRACTION97
2.7641-2.80540.29372890.22855497X-RAY DIFFRACTION97
2.8054-2.84920.28442830.21975369X-RAY DIFFRACTION97
2.8492-2.89580.29852850.22585429X-RAY DIFFRACTION97
2.8958-2.94570.31072850.23165411X-RAY DIFFRACTION98
2.9457-2.99920.29892850.22345405X-RAY DIFFRACTION97
2.9992-3.05690.25762880.21345485X-RAY DIFFRACTION98
3.0569-3.11920.29992830.21425373X-RAY DIFFRACTION97
3.1192-3.1870.27592870.21965457X-RAY DIFFRACTION97
3.187-3.2610.27442850.20995408X-RAY DIFFRACTION98
3.261-3.34250.25042870.20185443X-RAY DIFFRACTION97
3.3425-3.43270.26182800.20245330X-RAY DIFFRACTION97
3.4327-3.53360.25212880.19645480X-RAY DIFFRACTION97
3.5336-3.64750.23472830.18445363X-RAY DIFFRACTION97
3.6475-3.77760.23232840.18435395X-RAY DIFFRACTION97
3.7776-3.92860.23422790.18225311X-RAY DIFFRACTION95
3.9286-4.1070.20982850.16975412X-RAY DIFFRACTION97
4.107-4.3230.2152830.16245380X-RAY DIFFRACTION97
4.323-4.5930.21872850.16415405X-RAY DIFFRACTION97
4.593-4.94620.20562860.16515428X-RAY DIFFRACTION97
4.9462-5.44150.20412840.17325395X-RAY DIFFRACTION97
5.4415-6.22320.22132840.17845408X-RAY DIFFRACTION97
6.2232-7.81890.19982850.16965401X-RAY DIFFRACTION97
7.8189-30.63280.1712750.14255245X-RAY DIFFRACTION94

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