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- PDB-3h7a: CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomo... -

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Basic information

Entry
Database: PDB / ID: 3h7a
TitleCRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomonas palustris
Componentsshort chain dehydrogenase
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Unknown ligand / Possible short chain dehydrogenase
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsPatskovsky, Y. / Toro, R. / Morano, C. / Freeman, J. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomonas palustris
Authors: Patskovsky, Y. / Toro, R. / Morano, C. / Miller, S. / Freeman, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 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: short chain dehydrogenase
B: short chain dehydrogenase
C: short chain dehydrogenase
D: short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)109,6937
Polymers109,6934
Non-polymers03
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-62 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.431, 91.431, 270.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

#1: Protein
short chain dehydrogenase


Mass: 27423.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA0021 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NDT3
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.59 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M CITRIC ACID PH 5.5, 20% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 95778 / % possible obs: 96.7 % / Observed criterion σ(I): -0.5 / Redundancy: 2.9 % / Rsym value: 0.132 / Net I/σ(I): 4.3
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 0.8 / % possible all: 94.4

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Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.3.0034refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.87→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.704 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24148 2830 3 %RANDOM
Rwork0.2055 ---
obs0.20663 91107 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.773 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--1.1 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 1.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 21 425 6980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226723
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9349098
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85522.416298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.325151052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2191561
X-RAY DIFFRACTIONr_chiral_restr0.0860.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025161
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1640.33319
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.54556
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5729
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.324
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.724361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.77936713
X-RAY DIFFRACTIONr_scbond_it6.11532717
X-RAY DIFFRACTIONr_scangle_it8.53552372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1555 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.350.5
medium positional0.330
medium positional0.380
medium positional0.310
medium thermal8.342
medium thermal5.80
medium thermal10.60
medium thermal4.720
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 213 -
Rwork0.374 6549 -
obs--98.21 %

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