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- PDB-4ast: The apo structure of a bacterial aldo-keto reductase AKR14A1 -

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Basic information

Entry
Database: PDB / ID: 4ast
TitleThe apo structure of a bacterial aldo-keto reductase AKR14A1
ComponentsALDO-KETO REDUCTASE AKR14A1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


methylglyoxal catabolic process / 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
L-glyceraldehyde 3-phosphate reductase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 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 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references / Other / Source and taxonomy
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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


Theoretical massNumber of molelcules
Total (without water)311,0098
Polymers311,0098
Non-polymers00
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-77.9 kcal/mol
Surface area88090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.808, 144.317, 113.896
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ALDO-KETO REDUCTASE AKR14A1


Mass: 38876.094 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.65 Å3/Da / Density % sol: 53.7 % / Description: NONE
Crystal growpH: 4.6
Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Jun 10, 2009 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 121898 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.8
Reflection shellResolution: 2.39→2.43 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QRQ

1qrq


Resolution: 2.38→113.16 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.844 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27889 5959 5 %RANDOM
Rwork0.2392 ---
obs0.24119 112710 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.313 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-1 Å2
2--1.57 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.38→113.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19297 0 0 681 19978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01919777
X-RAY DIFFRACTIONr_bond_other_d0.010.0213417
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.96226795
X-RAY DIFFRACTIONr_angle_other_deg1.594332600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54452446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7824.162961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.609153376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2515144
X-RAY DIFFRACTIONr_chiral_restr0.0940.22903
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02122220
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024068
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: 2.383→2.445 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 409 -
Rwork0.345 7423 -
obs--84.51 %

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