[English] 日本語
Yorodumi
- PDB-1gve: Aflatoxin aldehyde reductase (AKR7A1) from Rat Liver -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gve
TitleAflatoxin aldehyde reductase (AKR7A1) from Rat Liver
ComponentsAFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
KeywordsOXIDOREDUCTASE / ALDO-KETO REDUCTASE / AFLATOXIN B1 / SUCCINIC SEMIALDEHYDE OXIDOREDUCTASE / AKR7 FAMILY
Function / homology
Function and homology information


Aflatoxin activation and detoxification / aflatoxin catabolic process / aflatoxin metabolic process / aldo-keto reductase (NADPH) activity / Oxidoreductases / identical protein binding / cytosol
Similarity search - Function
NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aflatoxin B1 aldehyde reductase member 3
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsKozma, E. / Brown, E. / Ellis, E.M. / Lapthorn, A.J.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The Crystal Structure of Rat Liver Akr7A1: A Dimeric Member of the Aldo-Keto Reductase Superfamily
Authors: Kozma, E. / Brown, E. / Ellis, E.M. / Lapthorn, A.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: An Ethoxyquin-Inducible Aldehyde Reductase from Rat Liver that Metabolizes Aflatoxin B1 Defines a Subfamily of Aldo-Keto Reductases
Authors: Ellis, E.M. / Judah, D.J. / Neal, G.E. / Hayes, J.D.
History
DepositionFeb 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
B: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,62116
Polymers73,5802
Non-polymers2,04114
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-16.5 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.540, 64.680, 112.840
Angle α, β, γ (deg.)90.00, 91.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97152, -0.04903, -0.23181), (-0.03974, -0.99822, 0.04455), (-0.23358, -0.03407, -0.97174)
Vector: 8.0454, 10.75928, 66.67067)

-
Components

#1: Protein AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3 / AFLATOXIN B1 ALDEHYDE REDUCTASE / AFLATOXIN ALDEHYDE REDUCTASE / AKR7A1 / AFB1-AR / B1 ALDEHYDE ...AFLATOXIN B1 ALDEHYDE REDUCTASE / AFLATOXIN ALDEHYDE REDUCTASE / AKR7A1 / AFB1-AR / B1 ALDEHYDE REDUCTASE MEMBER 1 / RAFAR1


Mass: 36789.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: LIVER / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P38918, Oxidoreductases
#2: 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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.7 Å3/Da / Density % sol: 55 %
Description: DATA EFFECTIVELY 100% COMPLETE TO 1.7A RESOLUTION. DATA WERE ANISOTROPIC RESULTING IN THE LOW COMPLETENESS AT HIGH RESOLUTION
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: SITTING DROP METHOD WITH 1MICROLITRE PROTEIN (6 MG/ML) AND 1MICROLITRE WELL 20% PEG8K, 0.2M LITHIUM SULPHATE, 0.1M SODIUM CITRATE PH 5.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG80001reservoir
20.2 Mlithium sulfate1reservoir
30.1 Msodium citrate1reservoirpH5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.83
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2000 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 1.38→30 Å / Num. obs: 134602 / % possible obs: 85.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 24
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.2 / % possible all: 43
Reflection
*PLUS
Num. obs: 158665
Reflection shell
*PLUS
% possible obs: 42.8 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EXB

1exb


Resolution: 1.38→28.75 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.993 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 7094 5 %RANDOM
Rwork0.158 ---
obs0.159 3768 73.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.38→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4895 0 133 504 5532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215173
X-RAY DIFFRACTIONr_bond_other_d0.0020.024610
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.7011.9716992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg2.207310745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025675
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021063
X-RAY DIFFRACTIONr_nbd_refined0.2430.31123
X-RAY DIFFRACTIONr_nbd_other0.2050.34636
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.2960.58
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.5495
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.04203
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.325
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5790.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5891.53102
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14324972
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.33832071
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5774.52020
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.38→1.42 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 198
Rwork0.295 3768
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6672-0.33740.68640.7703-0.25761.7787-0.00720.2314-0.0409-0.20430.07680.1059-0.12130.0019-0.06950.2371-0.04670.00380.01330.02350.144233.0999.29210.766
21.00610.32750.47540.22880.10270.52420.03-0.1489-0.01-0.00110.01320.0230.0417-0.1193-0.04320.1609-0.01510.03980.05050.02120.191438.5010.60447.945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 327
2X-RAY DIFFRACTION1A1328
3X-RAY DIFFRACTION2B4 - 327
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 134602 / Rfactor Rfree: 0.178 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.023
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

+
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