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- PDB-2zat: Crystal structure of a mammalian reductase -

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Basic information

Entry
Database: PDB / ID: 2zat
TitleCrystal structure of a mammalian reductase
ComponentsDehydrogenase/reductase SDR family member 4
KeywordsOXIDOREDUCTASE / ALPHA/BETA
Function / homology
Function and homology information


RA biosynthesis pathway / 3-keto sterol reductase activity / Peroxisomal protein import / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / ketone metabolic process / retinal metabolic process / NADP-retinol dehydrogenase / all-trans-retinol dehydrogenase (NADP+) activity / retinoid metabolic process ...RA biosynthesis pathway / 3-keto sterol reductase activity / Peroxisomal protein import / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / ketone metabolic process / retinal metabolic process / NADP-retinol dehydrogenase / all-trans-retinol dehydrogenase (NADP+) activity / retinoid metabolic process / steroid metabolic process / peroxisome / mitochondrion / identical protein binding
Similarity search - Function
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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTanaka, N. / Aoki, K. / Nakamura, K.T.
CitationJournal: Structure / Year: 2008
Title: Molecular basis for peroxisomal localization of tetrameric carbonyl reductase.
Authors: Tanaka, N. / Aoki, K. / Ishikura, S. / Nagano, M. / Imamura, Y. / Hara, A. / Nakamura, K.T.
History
DepositionOct 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)114,2108
Polymers111,2364
Non-polymers2,9744
Water13,908772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18170 Å2
ΔGint-64 kcal/mol
Surface area33340 Å2
MethodPISA
2
A: Dehydrogenase/reductase SDR family member 4
D: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1054
Polymers55,6182
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-13 kcal/mol
Surface area20150 Å2
MethodPISA
3
B: Dehydrogenase/reductase SDR family member 4
C: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1054
Polymers55,6182
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-12 kcal/mol
Surface area20360 Å2
MethodPISA
4
C: Dehydrogenase/reductase SDR family member 4
D: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1054
Polymers55,6182
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-21 kcal/mol
Surface area20350 Å2
MethodPISA
5
A: Dehydrogenase/reductase SDR family member 4
B: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1054
Polymers55,6182
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-21 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.612, 109.612, 94.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
Dehydrogenase/reductase SDR family member 4 / NADPH-dependent carbonyl reductase/NADP-retinol dehydrogenase / CR / PHCR / Peroxisomal short-chain ...NADPH-dependent carbonyl reductase/NADP-retinol dehydrogenase / CR / PHCR / Peroxisomal short-chain alcohol dehydrogenase / NADPH-dependent retinol dehydrogenase/reductase / NDRD


Mass: 27809.072 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: pCR T7/CT TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8WNV7, carbonyl reductase (NADPH)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2M sodium acetate, 20%(v/v) glycerol, 0.1M Hepes/NaOH buffer, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 176173 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.102 / Net I/σ(I): 5.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.297 / % possible all: 98.1

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CYD

1cyd


Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.987 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 8816 5 %RANDOM
Rwork0.161 ---
obs0.162 167340 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7516 0 192 772 8480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217828
X-RAY DIFFRACTIONr_bond_other_d0.0020.027336
X-RAY DIFFRACTIONr_angle_refined_deg1.541.99610652
X-RAY DIFFRACTIONr_angle_other_deg0.856317016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47351000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.21280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028572
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021432
X-RAY DIFFRACTIONr_nbd_refined0.2120.21628
X-RAY DIFFRACTIONr_nbd_other0.2430.28839
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.24885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2563
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9291.54964
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73327996
X-RAY DIFFRACTIONr_scbond_it2.51232864
X-RAY DIFFRACTIONr_scangle_it4.1744.52656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.219 614
Rwork0.199 12265

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