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- PDB-4itu: Crystal structure of S-2-HYDROXYPROPYL COENZYME M DEHYDROGENASE (... -

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Basic information

Entry
Database: PDB / ID: 4itu
TitleCrystal structure of S-2-HYDROXYPROPYL COENZYME M DEHYDROGENASE (S-HPCDH) bound to S-HPC AND NADH
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
Chem-1HS / 1,4-DIHYDRONICOTINAMIDE 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
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Sep 20, 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)111,91412
Polymers108,4514
Non-polymers3,4638
Water16,123895
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18500 Å2
ΔGint-133 kcal/mol
Surface area29900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.048, 128.394, 58.394
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-608-

HOH

21B-475-

HOH

31D-582-

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 / Plasmid: PET28-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7IQH5
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-1HS / 2-{[(2S)-2-hydroxypropyl]sulfanyl}ethanesulfonic acid


Mass: 200.276 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / 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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.35 M Ammonium Acetate, 27 % PEG 3350, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 8, 2013 / 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: 108385 / Num. obs: 108385 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 37
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 3.3 / Num. unique all: 7306 / % possible all: 63.9

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Processing

Software
NameVersionClassification
HKL-3000data 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 4GH5

4gh5


Resolution: 1.6→34.649 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 4998 4.99 %random
Rwork0.164 ---
obs0.1655 108385 90.6 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.073 Å2 / ksol: 0.43 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2318 Å20 Å20 Å2
2--0.4345 Å20 Å2
3----0.6663 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6977 0 220 895 8092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077281
X-RAY DIFFRACTIONf_angle_d1.1119890
X-RAY DIFFRACTIONf_dihedral_angle_d12.5062503
X-RAY DIFFRACTIONf_chiral_restr0.0681204
X-RAY DIFFRACTIONf_plane_restr0.0041269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6180.2857870.25551658X-RAY DIFFRACTION23
1.618-1.6370.27041030.2411932X-RAY DIFFRACTION28
1.637-1.6570.24961420.21882239X-RAY DIFFRACTION32
1.657-1.67790.25821260.2042592X-RAY DIFFRACTION37
1.6779-1.70.25421600.19653031X-RAY DIFFRACTION43
1.7-1.72330.23581610.18023396X-RAY DIFFRACTION48
1.7233-1.74790.2181890.18193437X-RAY DIFFRACTION49
1.7479-1.7740.21891920.17713495X-RAY DIFFRACTION49
1.774-1.80170.20961930.17753489X-RAY DIFFRACTION50
1.8017-1.83130.1991660.17063537X-RAY DIFFRACTION50
1.8313-1.86280.21741790.1693507X-RAY DIFFRACTION50
1.8628-1.89670.22561670.17713540X-RAY DIFFRACTION50
1.8967-1.93320.29631690.22483522X-RAY DIFFRACTION50
1.9332-1.97260.20041780.17623555X-RAY DIFFRACTION50
1.9726-2.01550.20221880.17263516X-RAY DIFFRACTION50
2.0155-2.06240.20141990.17393773X-RAY DIFFRACTION54
2.0624-2.1140.18892230.17943900X-RAY DIFFRACTION56
2.114-2.17110.17172540.15694551X-RAY DIFFRACTION64
2.1711-2.2350.17442550.14355045X-RAY DIFFRACTION72
2.235-2.30710.1922740.17295253X-RAY DIFFRACTION75
2.3071-2.38960.17133140.1396053X-RAY DIFFRACTION86
2.3896-2.48520.21043270.14736350X-RAY DIFFRACTION90
2.4852-2.59830.19953310.156555X-RAY DIFFRACTION93
2.5983-2.73520.18553740.15536661X-RAY DIFFRACTION95
2.7352-2.90650.19873750.15726847X-RAY DIFFRACTION97
2.9065-3.13080.18513620.15576934X-RAY DIFFRACTION98
3.1308-3.44560.16683850.14657005X-RAY DIFFRACTION100
3.4456-3.94360.18243920.15616921X-RAY DIFFRACTION99
3.9436-4.96620.18483560.14687021X-RAY DIFFRACTION99
4.9662-34.6490.22083400.22067029X-RAY DIFFRACTION99

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