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- PDB-3o4r: Crystal Structure of Human Dehydrogenase/Reductase (SDR family) m... -

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Basic information

Entry
Database: PDB / ID: 3o4r
TitleCrystal Structure of Human Dehydrogenase/Reductase (SDR family) member 4 (DHRS4)
ComponentsDehydrogenase/reductase SDR family member 4
KeywordsOXIDOREDUCTASE / Structural Genomics / Structural Genomics Consortium / SGC / dehydrogenase/reductase
Function / homology
Function and homology information


3-keto sterol reductase activity / alcohol dehydrogenase [NAD(P)+] activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / protein targeting to peroxisome / alcohol metabolic process / cellular ketone metabolic process / RA biosynthesis pathway / : / peroxisomal membrane ...3-keto sterol reductase activity / alcohol dehydrogenase [NAD(P)+] activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / protein targeting to peroxisome / alcohol metabolic process / cellular ketone metabolic process / RA biosynthesis pathway / : / peroxisomal membrane / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / steroid metabolic process / peroxisomal matrix / Peroxisomal protein import / peroxisome / endoplasmic reticulum membrane / mitochondrion / identical protein binding / nucleus / cytosol
Similarity search - Function
Dehydrogenase/reductase SDR member 4-like / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dehydrogenase/reductase SDR family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUgochukwu, E. / Bhatia, C. / Krojer, T. / Vollmar, M. / Yue, W.W. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. ...Ugochukwu, E. / Bhatia, C. / Krojer, T. / Vollmar, M. / Yue, W.W. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Dehydrogenase/Reductase (SDR family) member 4 (DHRS4)
Authors: Ugochukwu, E. / Bhatia, C. / Krojer, T. / Vollmar, M. / Yue, W.W. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Oppermann, U.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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: Dehydrogenase/reductase SDR family member 4
B: Dehydrogenase/reductase SDR family member 4
C: Dehydrogenase/reductase SDR family member 4
D: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,40815
Polymers110,7634
Non-polymers3,64411
Water10,917606
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20060 Å2
ΔGint-76 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.070, 132.200, 133.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dehydrogenase/reductase SDR family member 4 / Short-chain dehydrogenase/reductase family member 4 / NADPH-dependent carbonyl reductase/NADP- ...Short-chain dehydrogenase/reductase family member 4 / NADPH-dependent carbonyl reductase/NADP-retinol dehydrogenase / PHCR / CR / Peroxisomal short-chain alcohol dehydrogenase / PSCD / NADPH-dependent retinol dehydrogenase/reductase / NRDR / humNRDR / SCAD-SRL


Mass: 27690.865 Da / Num. of mol.: 4 / Fragment: DHRS4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHRS4, UNQ851/PRO1800 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q9BTZ2, carbonyl reductase (NADPH)

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Non-polymers , 5 types, 617 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 277 K / pH: 7
Details: 0.1M KSCN30% mPEG 2K, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: MAR225 / Detector: CCD / Date: Feb 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→29.29 Å / Num. obs: 116449 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 10.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZAT

2zat


Resolution: 1.7→29.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.605 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 5829 5 %RANDOM
Rwork0.21 ---
obs0.212 110448 98.6 %-
all-110448 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.85 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å20 Å20 Å2
2--4.56 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7416 0 235 606 8257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227811
X-RAY DIFFRACTIONr_bond_other_d0.0010.025163
X-RAY DIFFRACTIONr_angle_refined_deg1.3722.0110642
X-RAY DIFFRACTIONr_angle_other_deg0.906312695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54951022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54624.12267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.247151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3081551
X-RAY DIFFRACTIONr_chiral_restr0.0680.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021449
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.91855030
X-RAY DIFFRACTIONr_mcbond_other0.93152068
X-RAY DIFFRACTIONr_mcangle_it2.83878116
X-RAY DIFFRACTIONr_scbond_it3.55492781
X-RAY DIFFRACTIONr_scangle_it5.114112518
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1321medium positional0.10.5
2B1321medium positional0.110.5
3C1321medium positional0.130.5
4D1321medium positional0.120.5
1A1372loose positional0.35
2B1372loose positional0.275
3C1372loose positional0.215
4D1372loose positional0.245
1A1321medium thermal1.012
2B1321medium thermal1.072
3C1321medium thermal1.122
4D1321medium thermal0.882
1A1372loose thermal0.8610
2B1372loose thermal0.8810
3C1372loose thermal0.8810
4D1372loose thermal0.7810
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 451 -
Rwork0.439 8116 -
obs--99.94 %

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