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- PDB-3bhi: Crystal structure of human Carbonyl Reductase 1 in complex with NADP -

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Basic information

Entry
Database: PDB / ID: 3bhi
TitleCrystal structure of human Carbonyl Reductase 1 in complex with NADP
ComponentsCarbonyl reductase [NADPH] 1
KeywordsOXIDOREDUCTASE / Acetylation / Cytoplasm / NADP / Polymorphism
Function / homology
Function and homology information


alcohol dehydrogenase [NAD(P)+] / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) activity / prostaglandin-E2 9-reductase / prostaglandin E2 9-reductase activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / vitamin K metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity ...alcohol dehydrogenase [NAD(P)+] / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) activity / prostaglandin-E2 9-reductase / prostaglandin E2 9-reductase activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / vitamin K metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / alcohol dehydrogenase (NADP+) activity / glucocorticoid metabolic process / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / epithelial cell differentiation / xenobiotic metabolic process / positive regulation of reactive oxygen species metabolic process / extracellular vesicle / extracellular exosome / cytosol
Similarity search - Function
Carbonyl reductase [NADPH] 1-like / 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] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsRauh, D. / Bateman, R.L. / Shokat, K.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Human carbonyl reductase 1 is an s-nitrosoglutathione reductase
Authors: Bateman, R.L. / Rauh, D. / Tavshanjian, B. / Shokat, K.M.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Carbonyl reductase [NADPH] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0643
Polymers30,2851
Non-polymers7792
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.662, 55.662, 169.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 30284.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBR1, CBR, CRN / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P16152, carbonyl reductase (NADPH)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: vapor diffusion, hanging drop, temperature 298K, pH7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 13104 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.178 / Χ2: 1.068 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.27-2.355.30.66512801.088100
2.35-2.455.40.59212841.093100
2.45-2.565.40.52712561.066100
2.56-2.695.50.4312891.094100
2.69-2.865.40.30112741.088100
2.86-3.085.40.22313161.1100
3.08-3.395.40.1512981.028100
3.39-3.8850.11613081.09399.2
3.88-4.895.30.0813510.989100
4.89-504.90.0814481.0597.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WMA

1wma


Resolution: 2.27→46.56 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.856 / SU B: 7.764 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 640 4.9 %RANDOM
Rwork0.202 ---
obs0.206 13056 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.561 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.27→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 49 165 2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222193
X-RAY DIFFRACTIONr_angle_refined_deg2.0762.0012984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2425280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62723.86488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47315368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2921516
X-RAY DIFFRACTIONr_chiral_restr0.1390.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021635
X-RAY DIFFRACTIONr_nbd_refined0.2140.21036
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.26
X-RAY DIFFRACTIONr_mcbond_it1.1061.51428
X-RAY DIFFRACTIONr_mcangle_it1.7622214
X-RAY DIFFRACTIONr_scbond_it3.0913877
X-RAY DIFFRACTIONr_scangle_it4.5894.5768
LS refinement shellResolution: 2.272→2.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 58 -
Rwork0.217 899 -
all-957 -
obs--100 %

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