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- PDB-4aub: the complex Structure of the bacterial aldo-keto reductase AKR14A... -

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Basic information

Entry
Database: PDB / ID: 4aub
Titlethe complex Structure of the bacterial aldo-keto reductase AKR14A1 with NADP and citrate
ComponentsALDO-KETO REDUCTASE AKR14A1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


methylglyoxal catabolic process / alcohol dehydrogenase (NADP+) / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / DNA damage response
Similarity search - Function
: / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-glyceraldehyde 3-phosphate reductase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhu, X. / Ellis, E.M. / Lapthorn, A.
CitationJournal: Chem.Biol.Interact / Year: 2013
Title: The Diversity of Microbial Aldo/Keto Reductases from Escherichia Coli K12.
Authors: Lapthorn, A.J. / Zhu, X. / Ellis, E.M.
History
DepositionMay 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references / Source and taxonomy
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site
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_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 "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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: ALDO-KETO REDUCTASE AKR14A1
B: ALDO-KETO REDUCTASE AKR14A1
C: ALDO-KETO REDUCTASE AKR14A1
D: ALDO-KETO REDUCTASE AKR14A1
E: ALDO-KETO REDUCTASE AKR14A1
F: ALDO-KETO REDUCTASE AKR14A1
G: ALDO-KETO REDUCTASE AKR14A1
H: ALDO-KETO REDUCTASE AKR14A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,09623
Polymers328,3808
Non-polymers6,71715
Water20,9151161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31020 Å2
ΔGint-105.8 kcal/mol
Surface area88050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.813, 191.092, 97.303
Angle α, β, γ (deg.)90.00, 105.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ALDO-KETO REDUCTASE AKR14A1


Mass: 41047.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q46851
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1161 / 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: 2.68 Å3/Da / Density % sol: 54.2 %
Description: STATISTICS ARE GOOD TO 2.21 ANGSTROM RESOLUTION, RMERGE 0.48 IN FINAL SHELL. HOWEVER THE WEAK REFLECTION EXTENDS TO 2.05 ANGSTROM RESOLUTION AND WAS INCLUDED IN REFINEMENT
Crystal growpH: 5.4
Details: 0.1M CITRATE BUFFER (PH 5.4), 18% W/V PEG 2000 MME AND 0.2 M AMMONIUM SULPHATE SUPPLEMENTED WITH 1 MM NADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→48.8 Å / Num. obs: 194971 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.8 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKLdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EXB

1exb


Resolution: 2.05→95.35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.57 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23819 9319 5 %RANDOM
Rwork0.20161 ---
obs0.20344 175739 92.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.481 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0.46 Å2
2--1.38 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.05→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19845 0 440 1161 21446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01920760
X-RAY DIFFRACTIONr_bond_other_d0.010.0214049
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.98928170
X-RAY DIFFRACTIONr_angle_other_deg1.656334123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91552500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59724.112980
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.483153502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.80915149
X-RAY DIFFRACTIONr_chiral_restr0.1040.23026
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02122994
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024266
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 596 -
Rwork0.317 11118 -
obs--79.61 %

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