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- PDB-1mok: NADPH DEPENDENT 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLASE -

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Basic information

Entry
Database: PDB / ID: 1mok
TitleNADPH DEPENDENT 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLASE
Componentsorf3
KeywordsOXIDOREDUCTASE / Nucleotide binding motifs / Nucleotide binding domain
Function / homology
Function and homology information


2-oxopropyl-CoM reductase (carboxylating) / 2-oxopropyl-CoM reductase (carboxylating) activity / propylene catabolic process
Similarity search - Function
Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 2-oxopropyl-CoM reductase, carboxylating
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNocek, B. / Jang, S.B. / Jeong, M.S. / Clark, D.D. / Ensign, S.A. / Peters, J.W.
CitationJournal: Biochemistry / Year: 2002
Title: Structural Basis for CO2 Fixation by a Novel Member of the Disulfide Oxidoreductase Family of Enzymes, 2-Ketopropyl Coenzyme M Oxidoreductase/Carboxylase
Authors: Nocek, B. / Jang, S.B. / Jeong, M.S. / Clark, D.D. / Ensign, S.A. / Peters, J.W.
History
DepositionSep 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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: orf3
B: orf3
C: orf3
D: orf3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,8008
Polymers229,6574
Non-polymers3,1424
Water00
1
A: orf3
B: orf3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4004
Polymers114,8292
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-75 kcal/mol
Surface area35220 Å2
MethodPISA
2
C: orf3
D: orf3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4004
Polymers114,8292
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-74 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.600, 87.500, 100.700
Angle α, β, γ (deg.)72.00, 73.40, 69.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
orf3 / 2-Ketopropyl Coenzyme M Oxidoreductase/Carboxylase


Mass: 57414.348 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xanthobacter autotrophicus (bacteria) / Strain: Py2
References: UniProt: Q56839, 2-oxopropyl-CoM reductase (carboxylating)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17M ammonium acetate, 0.085M Tris-HCl pH 8.5, 25.5% PEG 4000, 15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 5.6 / Details: Jang, S.B., (2001) Acta Crystallogr., D57, 445.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 mM2-KPCC1drop
30.17 Mammonium acetate1reservoir
40.085 Mtrisodium citrate dihydrate1reservoirpH5.6
525.5 %(w/v)PEG40001reservoir
615 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 19, 2000 / Details: flat mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 41494 / Num. obs: 41494 / Observed criterion σ(I): 0.5
Reflection
*PLUS
Num. obs: 48234 / % possible obs: 92.1 % / Num. measured all: 213523 / Rmerge(I) obs: 0.098

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
EPMRphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MO9

1mo9


Resolution: 2.8→19.99 Å / Cross valid method: THROUGHOUT / σ(F): 0.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.277 1930 RANDOM
Rwork0.225 --
all0.24 41494 -
obs0.238 38841 -
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.63 Å2-5.7 Å2-2.1 Å2
2---5.16 Å2-4.88 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16092 0 212 0 16304
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.8

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