[English] 日本語
Yorodumi
- PDB-2zat: Crystal structure of a mammalian reductase -

+
Open data


ID or keywords:

Loading...

-
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 / retinal metabolic process / : / retinal dehydrogenase activity / peroxisome / mitochondrion / identical protein binding
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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more