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- PDB-4udy: NCO- bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic ... -

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Basic information

Entry
Database: PDB / ID: 4udy
TitleNCO- bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic resolution
ComponentsCARBON MONOXIDE DEHYDROGENASE 2
KeywordsOXIDOREDUCTASE / NCO / NI / FE / CODH
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cyanic acid / : / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(3)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsFesseler, J. / Jeoung, J.-H. / Dobbek, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: How the [Nife4 S4 ] Cluster of Co Dehydrogenase Activates Co2 and Nco(.)
Authors: Fesseler, J. / Jeoung, J.H. / Dobbek, H.
History
DepositionDec 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Atomic model
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5May 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9736
Polymers66,9921
Non-polymers9815
Water13,655758
1
X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules

X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,94712
Polymers133,9852
Non-polymers1,96210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9820 Å2
ΔGint-202.1 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.183, 75.008, 71.149
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-2094-

HOH

21X-2347-

HOH

31X-2402-

HOH

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Components

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Protein , 1 types, 1 molecules X

#1: Protein CARBON MONOXIDE DEHYDROGENASE 2 / CODH 2 / NI / FE-CO DEHYDROGENASE


Mass: 66992.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9F8A8, carbon-monoxide dehydrogenase (acceptor)

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Non-polymers , 6 types, 763 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-WCC / FE(3)-NI(1)-S(4) CLUSTER / C CLUSTER CUBANE


Mass: 354.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3NiS4
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-0NM / cyanic acid


Mass: 43.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHNO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / 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: 2.08 Å3/Da / Density % sol: 40.94 % / Description: NONE
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2013 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.09→40.8 Å / Num. obs: 223489 / % possible obs: 98 % / Redundancy: 3.69 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 1.09→1.13 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.77 / % possible all: 94.6

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Processing

Software
NameVersionClassification
SHELXL14refinement
XSCALEdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→33.16 Å / Num. parameters: 50098 / Num. restraintsaints: 62069 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 11175 5.26 %RANDOM
all0.1363 212314 --
obs0.1363 -98.02 %-
Refine analyzeNum. disordered residues: 28 / Occupancy sum hydrogen: 4750 / Occupancy sum non hydrogen: 5408.3
Refinement stepCycle: LAST / Resolution: 1.09→33.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 24 758 5436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0148
X-RAY DIFFRACTIONs_angle_d0.0314
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0049
X-RAY DIFFRACTIONs_zero_chiral_vol0.0788
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0853
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1195
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0454
X-RAY DIFFRACTIONs_approx_iso_adps0.1478

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