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- PDB-1gve: Aflatoxin aldehyde reductase (AKR7A1) from Rat Liver -

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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 / alcohol dehydrogenase (NADP+) / aflatoxin metabolic process / : / NADP+ binding / identical protein binding / cytoplasm
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 / Aldo-keto reductase family 7 member A3
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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

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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: 2.7 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

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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 %

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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

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