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- PDB-4gh5: Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (... -

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Basic information

Entry
Database: PDB / ID: 4gh5
TitleCrystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S-HPCDH)
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


2-(S)-hydroxypropyl-CoM dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / quinone binding / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
PKS_KR / 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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-(S)-hydroxypropyl-CoM dehydrogenase 3
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBakelar, J.W. / Johnson, S.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Crystal structures of S-HPCDH reveal determinants of stereospecificity for R- and S-hydroxypropyl-coenzyme M dehydrogenases.
Authors: Bakelar, J.W. / Sliwa, D.A. / Johnson, S.J.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,34112
Polymers108,4514
Non-polymers2,8908
Water18,5011027
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17630 Å2
ΔGint-126 kcal/mol
Surface area30030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.071, 127.921, 58.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21A-555-

HOH

31B-521-

HOH

41D-648-

HOH

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Components

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 27112.775 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: Py2 / Gene: Xaut_5073 / Plasmid: pET28-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7IQH5
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1027 / 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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.35M ammonium acetate, 27% polyethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 2, 2010 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. all: 113574 / Num. obs: 113574 / % possible obs: 16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Rsym value: 0.046 / Net I/σ(I): 25.75
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.92 / Num. unique all: 9812 / Rsym value: 0.423 / % possible all: 86

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CFC

2cfc


Resolution: 1.6→26.425 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 5687 5.01 %RANDOM
Rwork0.1708 ---
all0.1722 113447 --
obs0.1722 113447 98.22 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.254 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.1666 Å2-0 Å2-0 Å2
2--0.2878 Å20 Å2
3---0.8788 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6895 0 192 1027 8114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067168
X-RAY DIFFRACTIONf_angle_d1.1529731
X-RAY DIFFRACTIONf_dihedral_angle_d15.7542448
X-RAY DIFFRACTIONf_chiral_restr0.0711179
X-RAY DIFFRACTIONf_plane_restr0.0041247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61740.56191620.54872832X-RAY DIFFRACTION78
1.6174-1.63640.52261610.4793103X-RAY DIFFRACTION87
1.6364-1.65630.45232000.42073296X-RAY DIFFRACTION92
1.6563-1.67730.3661720.32243428X-RAY DIFFRACTION94
1.6773-1.69940.32781920.25643542X-RAY DIFFRACTION98
1.6994-1.72260.20661750.17823588X-RAY DIFFRACTION99
1.7226-1.74720.20382010.15973566X-RAY DIFFRACTION100
1.7472-1.77330.20322050.15363647X-RAY DIFFRACTION100
1.7733-1.8010.1961940.14423604X-RAY DIFFRACTION100
1.801-1.83050.17131720.13273651X-RAY DIFFRACTION100
1.8305-1.86210.20331860.13873607X-RAY DIFFRACTION100
1.8621-1.8960.18251690.14073663X-RAY DIFFRACTION100
1.896-1.93240.21241740.14753625X-RAY DIFFRACTION100
1.9324-1.97180.21421850.15493632X-RAY DIFFRACTION100
1.9718-2.01470.20711940.16593646X-RAY DIFFRACTION100
2.0147-2.06150.19291960.16623628X-RAY DIFFRACTION100
2.0615-2.11310.17752010.16013629X-RAY DIFFRACTION100
2.1131-2.17020.17791980.15883673X-RAY DIFFRACTION100
2.1702-2.2340.17941810.15123638X-RAY DIFFRACTION100
2.234-2.30610.17321930.15383656X-RAY DIFFRACTION100
2.3061-2.38850.16121860.15293638X-RAY DIFFRACTION100
2.3885-2.4840.19511870.15783661X-RAY DIFFRACTION100
2.484-2.5970.19411930.16633686X-RAY DIFFRACTION100
2.597-2.73380.19642090.17143640X-RAY DIFFRACTION100
2.7338-2.90480.21842010.16353692X-RAY DIFFRACTION100
2.9048-3.12880.19081960.17063690X-RAY DIFFRACTION100
3.1288-3.44310.16522080.15873713X-RAY DIFFRACTION100
3.4431-3.93990.17132090.15523713X-RAY DIFFRACTION100
3.9399-4.95840.15631940.14063767X-RAY DIFFRACTION100
4.9584-26.4250.19281930.18713906X-RAY DIFFRACTION99

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