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- PDB-2hrb: Crystal Structure of human Carbonyl Reductase 3, complexed with NADP+ -

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Basic information

Entry
Database: PDB / ID: 2hrb
TitleCrystal Structure of human Carbonyl Reductase 3, complexed with NADP+
ComponentsCarbonyl reductase [NADPH] 3
KeywordsOXIDOREDUCTASE / Retinol / dehydrogenase / peroxisome / structural genomics / short-chain dehydrogenase/reductase / structural genomics consortium / SGC
Function / homology
Function and homology information


phylloquinone catabolic process / 3-keto sterol reductase activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / Phase I - Functionalization of compounds / NADPH binding / xenobiotic metabolic process / cognition / extracellular space / nucleoplasm / cytosol
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / Carbonyl reductase [NADPH] 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPilka, E.S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of human Carbonyl Reductase 3, complexed with NADP+
Authors: Pilka, E.S. / Rojkova, A. / Kavanagh, K.L. / Niesen, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Oppermann, U.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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: Carbonyl reductase [NADPH] 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5595
Polymers30,5391
Non-polymers1,0204
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.356, 60.140, 88.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonyl reductase [NADPH] 3 / NADPH-dependent carbonyl reductase 3


Mass: 30538.818 Da / Num. of mol.: 1 / Fragment: residues 4-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-SGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-R3 / References: UniProt: O75828, carbonyl reductase (NADPH)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M tri-ammonium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 19, 2006 / 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: 1.9→49.673 Å / Num. all: 24260 / Num. obs: 24038 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3 / Num. unique all: 3417 / Rsym value: 0.391 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WMA
Resolution: 1.9→30.06 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.976 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.156
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1205 5.1 %RANDOM
Rwork0.212 ---
all0.213 24260 --
obs0.215 24038 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 66 253 2443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222255
X-RAY DIFFRACTIONr_angle_refined_deg1.6462.0043060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7435280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91623.846104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87815395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2051522
X-RAY DIFFRACTIONr_chiral_restr0.1090.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021685
X-RAY DIFFRACTIONr_nbd_refined0.2010.21070
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.220
X-RAY DIFFRACTIONr_mcbond_it0.9171.51420
X-RAY DIFFRACTIONr_mcangle_it1.41522222
X-RAY DIFFRACTIONr_scbond_it2.653930
X-RAY DIFFRACTIONr_scangle_it4.3444.5834
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 79 -
Rwork0.349 1639 -
obs-3417 96.9 %
Refinement TLS params.Method: refined / Origin x: 12.0805 Å / Origin y: 12.5816 Å / Origin z: 13.5933 Å
111213212223313233
T-0.0386 Å2-0.0044 Å20.0125 Å2--0.0471 Å20.0068 Å2---0.0631 Å2
L1.0999 °2-0.317 °20.054 °2-0.7522 °20.0564 °2--0.3845 °2
S-0.0109 Å °0.001 Å °-0.004 Å °-0.0178 Å °0.0065 Å °-0.052 Å °-0.0104 Å °0.0244 Å °0.0044 Å °

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