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- PDB-2c3d: 2.15 Angstrom crystal structure of 2-ketopropyl coenzyme M oxidor... -

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Basic information

Entry
Database: PDB / ID: 2c3d
Title2.15 Angstrom crystal structure of 2-ketopropyl coenzyme M oxidoreductase carboxylase with a coenzyme M disulfide bound at the active site
Components2-OXOPROPYL-COM REDUCTASE
KeywordsOXIDOREDUCTASE / COENZYME M / COM DISULFIDE / REDOX-ACTIVE CENTER / FAD
Function / homology
Function and homology information


2-oxopropyl-CoM reductase (carboxylating) / 2-oxopropyl-CoM reductase (carboxylating) activity / propylene catabolic process / NAD(P)H dehydrogenase (quinone) activity / 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
1-THIOETHANESULFONIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / 2-oxopropyl-CoM reductase, carboxylating
Similarity search - Component
Biological speciesXANTHOBACTER AUTOTROPHICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPandey, A.S. / Nocek, B. / Clark, D.D. / Ensign, S.A. / Peters, J.W.
CitationJournal: Biochemistry / Year: 2006
Title: Mechanistic Implications of the Structure of the Mixed-Disulfide Intermediate of the Disulfide Oxidoreductase, 2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase.
Authors: Pandey, A.S. / Nocek, B. / Clark, D.D. / Ensign, S.A. / Peters, J.W.
History
DepositionOct 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-OXOPROPYL-COM REDUCTASE
B: 2-OXOPROPYL-COM REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9698
Polymers114,8292
Non-polymers2,1406
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.790, 60.050, 105.630
Angle α, β, γ (deg.)90.00, 99.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2-OXOPROPYL-COM REDUCTASE / NADPH\:2-KETOPROPYL COENZYME M CARBOXYLASE/ OXIDOREDUCTASE / 2-KPCC / ALIPHATIC EPOXIDE ...NADPH\:2-KETOPROPYL COENZYME M CARBOXYLASE/ OXIDOREDUCTASE / 2-KPCC / ALIPHATIC EPOXIDE CARBOXYLATION COMPONENT II


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE REDUCTIVE CLEAVAGE OF THE THIOETHER LINKAGE OF 2-KETOPROPYL-COENZYME M, AND THE ...CATALYZES THE REDUCTIVE CLEAVAGE OF THE THIOETHER LINKAGE OF 2-KETOPROPYL-COENZYME M, AND THE SUBSEQUENT CARBOXYLATION OF THE KETOPROPYL CLEAVAGE PRODUCT, YIELDING THE PRODUCTS ACETOACETATE AND FREE COENZYME M.

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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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growDetails: 0.17 M SODIUM ACETATE 0.085M TRIS-HCL PH 8.5 25.5% PEG4000 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 58516 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.8
Reflection shellHighest resolution: 2.2 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M09

1m09


Resolution: 2.15→37.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1257092.13 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2162 1.9 %RANDOM
Rwork0.203 ---
obs0.203 111633 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.0819 Å2 / ksol: 0.375927 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å22.36 Å2
2--1.08 Å20 Å2
3---1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.15→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8046 0 134 654 8834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it3.072
X-RAY DIFFRACTIONc_scangle_it4.262.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 365 2.2 %
Rwork0.248 16521 -
obs--87.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FAD-NEW.PARCOM.TOP
X-RAY DIFFRACTION3COM.PARFAD-NEW.TOP
X-RAY DIFFRACTION4WATER.PAR

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