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- PDB-2qq5: Crystal structure of human SDR family member 1 -

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Basic information

Entry
Database: PDB / ID: 2qq5
TitleCrystal structure of human SDR family member 1
ComponentsDehydrogenase/reductase SDR family member 1
KeywordsOXIDOREDUCTASE / DHRS1 / SDR / DEHYDROGENASE / REDUCTASE / SHORT-CHAIN / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


estradiol 17-alpha-dehydrogenase [NAD(P)+] activity / carbonyl reductase (NADPH) activity / testosterone dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / endoplasmic reticulum
Similarity search - Function
short 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
Similarity search - Domain/homology
Dehydrogenase/reductase SDR family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPilka, E.S. / Hozjan, V. / Ugochukwu, E. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of human SDR family member 1.
Authors: Pilka, E.S. / Hozjan, V. / Ugochukwu, E. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydrogenase/reductase SDR family member 1


Theoretical massNumber of molelcules
Total (without water)28,0441
Polymers28,0441
Non-polymers00
Water3,621201
1
A: Dehydrogenase/reductase SDR family member 1

A: Dehydrogenase/reductase SDR family member 1


Theoretical massNumber of molelcules
Total (without water)56,0882
Polymers56,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3500 Å2
MethodPISA
2
A: Dehydrogenase/reductase SDR family member 1

A: Dehydrogenase/reductase SDR family member 1


Theoretical massNumber of molelcules
Total (without water)56,0882
Polymers56,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area1740 Å2
MethodPISA
3
A: Dehydrogenase/reductase SDR family member 1

A: Dehydrogenase/reductase SDR family member 1

A: Dehydrogenase/reductase SDR family member 1

A: Dehydrogenase/reductase SDR family member 1


Theoretical massNumber of molelcules
Total (without water)112,1774
Polymers112,1774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.225, 87.854, 100.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Dehydrogenase/reductase SDR family member 1 / DHRS1


Mass: 28044.129 Da / Num. of mol.: 1 / Fragment: Residues 3-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHRS1 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q96LJ7, Oxidoreductases; Acting on the CH-OH group of donors
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.4M Na Malonate pH 7.0, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 5, 2007 / Details: OSMIC
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→22.21 Å / Num. all: 91682 / Num. obs: 91499 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.056 / Rsym value: 0.065 / Net I/σ(I): 17.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2 / Num. unique all: 12938 / Rsym value: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8

2ae1

1ae1

2ew8

1zem

1ahh

1vl8


Resolution: 1.8→22.21 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.406 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used for phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19719 1203 5.1 %RANDOM
Rwork0.15681 ---
obs0.15881 22214 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---1.29 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 0 201 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221777
X-RAY DIFFRACTIONr_bond_other_d0.0020.021156
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.9562416
X-RAY DIFFRACTIONr_angle_other_deg0.91832825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66223.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48815277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3061512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_nbd_refined0.2350.2364
X-RAY DIFFRACTIONr_nbd_other0.1890.21180
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2915
X-RAY DIFFRACTIONr_nbtor_other0.0860.2855
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.31831204
X-RAY DIFFRACTIONr_mcbond_other0.713489
X-RAY DIFFRACTIONr_mcangle_it3.30651876
X-RAY DIFFRACTIONr_scbond_it4.7127650
X-RAY DIFFRACTIONr_scangle_it6.62111540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 77 -
Rwork0.218 1614 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 20.6303 Å / Origin y: 29.9874 Å / Origin z: 34.7302 Å
111213212223313233
T-0.0302 Å2-0.0097 Å20.0081 Å2--0.0431 Å2-0.0139 Å2---0.0434 Å2
L1.1019 °20.1959 °20.2673 °2-0.6329 °20.1904 °2--0.317 °2
S0.0221 Å °0.0353 Å °-0.1292 Å °0.0481 Å °-0.0277 Å °-0.0079 Å °0.0445 Å °-0.044 Å °0.0056 Å °

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