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- PDB-1mo9: NADPH DEPENDENT 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLAS... -

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Basic information

Entry
Database: PDB / ID: 1mo9
TitleNADPH DEPENDENT 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLASE COMPLEXED WITH 2-KETOPROPYL COENZYME M
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 / flavin adenine dinucleotide binding
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-[2-KETOPROPYLTHIO]ETHANESULFONATE / 2-oxopropyl-CoM reductase, carboxylating
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.65 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 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: orf3
B: orf3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7966
Polymers114,8292
Non-polymers1,9684
Water17,727984
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-89 kcal/mol
Surface area34940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.980, 60.120, 105.600
Angle α, β, γ (deg.)90.00, 102.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 57414.348 Da / Num. of mol.: 2 / 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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-KPC / (2-[2-KETOPROPYLTHIO]ETHANESULFONATE


Mass: 198.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O4S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 984 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
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% polyethylene glycol 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: 1.65→20 Å / Num. all: 129754 / Num. obs: 129754 / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.64 Å / Num. obs: 164972 / % possible obs: 98.2 % / Num. measured all: 504165 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
SOLVEphasing
DMmodel building
WARPmodel building
CNS1refinement
CCP4(SCALA)data scaling
DMphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MIRAS / Resolution: 1.65→19.92 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 6219 -Random
Rwork0.188 ---
all0.1892 129754 --
obs0.188 123985 95.6 %-
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20.89 Å21.14 Å2
2--0 Å20.34 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-20 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8046 0 128 984 9158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1
X-RAY DIFFRACTIONc_mcangle_it1.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.08
RfactorNum. reflection% reflection
Rfree0.244 920 -
Rwork0.225 --
obs--90 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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