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- PDB-2cfc: structural basis for stereo selectivity in the (R)- and (S)- hydr... -

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Basic information

Entry
Database: PDB / ID: 2cfc
Titlestructural basis for stereo selectivity in the (R)- and (S)- hydroxypropylethane thiosulfonate dehydrogenases
Components2-(R)-HYDROXYPROPYL-COM DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD
Function / homology
Function and homology information


2-(R)-hydroxypropyl-CoM dehydrogenase / 2-(R)-hydroxypropyl-CoM dehydrogenase activity / propylene catabolic process
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2-[2-KETOPROPYLTHIO]ETHANESULFONATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-(R)-hydroxypropyl-CoM dehydrogenase
Similarity search - Component
Biological speciesXANTHOBACTER AUTOTROPHICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKrishnakumar, A.M. / Nocek, B.P. / Clark, D.D. / Ensign, S.A. / Peters, J.W.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Basis for Stereoselectivity in the (R)-and (S)-Hydroxypropylthioethanesulfonate Dehydrogenases.
Authors: Krishnakumar, A.M. / Nocek, B.P. / Clark, D.D. / Ensign, S.A. / Peters, J.W.
History
DepositionFeb 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-(R)-HYDROXYPROPYL-COM DEHYDROGENASE
B: 2-(R)-HYDROXYPROPYL-COM DEHYDROGENASE
C: 2-(R)-HYDROXYPROPYL-COM DEHYDROGENASE
D: 2-(R)-HYDROXYPROPYL-COM DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,11012
Polymers104,6634
Non-polymers3,4478
Water16,484915
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.441, 110.280, 68.981
Angle α, β, γ (deg.)90.00, 93.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
2-(R)-HYDROXYPROPYL-COM DEHYDROGENASE / R-HPCD / R-HPCDH / ALIPHATIC EPOXIDE CARBOXYLATION COMPONENT III


Mass: 26165.854 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) XANTHOBACTER AUTOTROPHICUS (bacteria) / Strain: PY2
References: UniProt: Q56840, 2-(R)-hydroxypropyl-CoM dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-KPC / (2-[2-KETOPROPYLTHIO]ETHANESULFONATE


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


Mass: 18.015 Da / Num. of mol.: 915 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growDetails: 15MM NAD, 0.2M MAGNESIUM CHLORIDE, 0.1 M HEPES, PH7.5, 30% W/V PEG400 AND 0.1 SPERMINE TETRACHLORIDE AND 20MM R-HYDROXY PROPYL COM

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.87008,1.00871
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.870081
21.008711
ReflectionResolution: 1.8→20 Å / Num. obs: 149113 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.5
Reflection shellHighest resolution: 1.8 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 5838 3.3 %RANDOM
Rwork0.1974 ---
obs0.1974 133632 76.1 %-
Solvent computationBsol: 78.8068 Å2 / ksol: 0.384731 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.772 Å2
2---3.947 Å20 Å2
3---3.968 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7328 0 220 915 8463
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011661
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_deg1.54661
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3NAD.PAR
X-RAY DIFFRACTION4KETOCOM.PAR
X-RAY DIFFRACTION5R0523.PARAM

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