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- PDB-2bp1: Structure of the aflatoxin aldehyde reductase in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 2bp1
TitleStructure of the aflatoxin aldehyde reductase in complex with NADPH
ComponentsAFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2
KeywordsOXIDOREDUCTASE / ALDO-KETO REDUCTASE FAMILY 7 / SSA REDUCTASE / TIM BARREL
Function / homology
Function and homology information


phenanthrene-9,10-epoxide hydrolase activity / : / cellular aldehyde metabolic process / Aflatoxin activation and detoxification / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / xenobiotic metabolic process / carbohydrate metabolic process / electron transfer activity ...phenanthrene-9,10-epoxide hydrolase activity / : / cellular aldehyde metabolic process / Aflatoxin activation and detoxification / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / xenobiotic metabolic process / carbohydrate metabolic process / electron transfer activity / Golgi apparatus / extracellular exosome / cytosol
Similarity search - Function
NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Chem-NDP / Aflatoxin B1 aldehyde reductase member 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDebreczeni, J.E. / Lukacik, P. / Kavanagh, K. / Dubinina, E. / Bray, J. / Colebrook, S. / Haroniti, A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. ...Debreczeni, J.E. / Lukacik, P. / Kavanagh, K. / Dubinina, E. / Bray, J. / Colebrook, S. / Haroniti, A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Gileadi, O. / Oppermann, U.
CitationJournal: To be Published
Title: Structure of the Aflatoxin Aldehyde Reductase in Complex with Nadph
Authors: Debreczeni, J.E. / Lukacik, P. / Kavanagh, K. / Dubinina, E. / Bray, J. / Colebrook, S. / Haroniti, A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Gileadi, O. / Oppermann, U.
History
DepositionApr 17, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA", "CA", "DA" IN EACH CHAIN ON ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA", "CA", "DA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE 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 2
B: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2
C: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2
D: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,63812
Polymers158,9004
Non-polymers3,7388
Water9,728540
1
A: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2
B: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3196
Polymers79,4502
Non-polymers1,8694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2
D: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3196
Polymers79,4502
Non-polymers1,8694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.989, 78.786, 86.019
Angle α, β, γ (deg.)88.72, 71.14, 75.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLYGLYAA38 - 9338 - 93
21ARGARGGLYGLYBB38 - 9338 - 93
31ARGARGGLYGLYCC38 - 9338 - 93
41ARGARGGLYGLYDD38 - 9338 - 93
12VALVALARGARGAA101 - 360101 - 360
22VALVALARGARGBB101 - 360101 - 360
32VALVALARGARGCC101 - 360101 - 360
42VALVALARGARGDD101 - 360101 - 360

NCS oper:
IDCodeMatrixVector
1given(0.84369, 0.52401, -0.11665), (0.52026, -0.85168, -0.06298), (-0.13235, -0.00755, -0.99117)-5.96727, 20.30972, -4.0198
2given(-0.74242, 0.04297, -0.66855), (0.04525, -0.99244, -0.11404), (-0.6684, -0.11492, 0.73487)-75.44745, 36.37584, -2.6085
3given(-0.52026, -0.47487, -0.70981), (-0.38244, 0.8727, -0.30354), (0.76359, 0.11354, -0.63564)-49.91826, -49.8671, 8.63759

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Components

#1: Protein
AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2 / AFLATOXIN ALDEHYDE REDUCTASE / AFB1-AR 1 / ALDOKETOREDUCTASE 7


Mass: 39725.000 Da / Num. of mol.: 4 / Fragment: RESIDUES 30-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: O43488
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, sitting drop
Details: SITTING DROP RESERVOIR: 0.2 M AMMONIUM CITRATE 20 % PEG3350 PROTEIN: 0.01 M HEPES PH 7.5 0.5 M NACL 5 % GLYCEROL 0.5 % TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.912
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2.4→39.98 Å / Num. obs: 49989 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 1.62 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 0.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.9 / % possible all: 60

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GVE

1gve


Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.093 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1828 3.7 %RANDOM
Rwork0.155 ---
obs0.157 48161 90.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20.7 Å20.22 Å2
2--0.43 Å20.91 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9951 0 244 540 10735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02110469
X-RAY DIFFRACTIONr_bond_other_d0.0020.029098
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.96714261
X-RAY DIFFRACTIONr_angle_other_deg1.025321087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96451280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90223.517472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.866151572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8231561
X-RAY DIFFRACTIONr_chiral_restr0.0730.21514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211749
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022180
X-RAY DIFFRACTIONr_nbd_refined0.2050.22206
X-RAY DIFFRACTIONr_nbd_other0.1810.29174
X-RAY DIFFRACTIONr_nbtor_refined0.1790.25010
X-RAY DIFFRACTIONr_nbtor_other0.0870.25487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2439
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.50536890
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.071510138
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.08984608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.576114123
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1855tight positional0.040.05
2B1855tight positional0.040.05
3C1855tight positional0.040.05
4D1855tight positional0.040.05
1A2740medium positional0.210.5
2B2740medium positional0.260.5
3C2740medium positional0.240.5
4D2740medium positional0.230.5
1A1855tight thermal0.120.5
2B1855tight thermal0.120.5
3C1855tight thermal0.110.5
4D1855tight thermal0.10.5
1A2740medium thermal0.772
2B2740medium thermal0.732
3C2740medium thermal0.712
4D2740medium thermal0.712
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 81
Rwork0.219 2280
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)
10.966-0.033-0.46570.5461-0.21950.51730.0233-0.0304-0.01390.12350.02280.0413-0.06640.0146-0.0462-0.0607-0.0011-0.0093-0.0832-0.006-0.0849-17.199625.8961-1.5812
20.8067-0.2395-0.25631.1863-0.01420.6908-0.0308-0.0299-0.03980.0692-0.00530.06920.06510.01310.0361-0.0736-0.0046-0.0113-0.0831-0.0027-0.0882-6.7825-10.7109-1.4874
30.166-0.00390.34840.2638-0.08631.53760.0026-0.046-0.0349-0.0466-0.0366-0.06620.13790.0510.034-0.06940.00680.0126-0.02470.0216-0.0209-44.520812.7872-37.0437
40.6428-0.01780.26811.12850.2371.40950.0302-0.025-0.0032-0.0838-0.05710.0373-0.2947-0.10860.02690.03190.01490.015-0.023-0.0111-0.0691-53.913749.5893-39.7371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 360
2X-RAY DIFFRACTION2B38 - 360
3X-RAY DIFFRACTION3C38 - 360
4X-RAY DIFFRACTION4D38 - 360

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