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- PDB-5veh: Re-refinement OF THE PDB STRUCTURE 1yiz of Aedes aegypti kynureni... -

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Basic information

Entry
Database: PDB / ID: 5veh
TitleRe-refinement OF THE PDB STRUCTURE 1yiz of Aedes aegypti kynurenine aminotransferase
ComponentsKynurenine aminotransferase
KeywordsTRANSFERASE / Re-refinement / kynurenine aminotransferase / mosquito
Function / homology
Function and homology information


L-kynurenine catabolic process / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / Transferases; Transferring nitrogenous groups; Transaminases / biosynthetic process / pyridoxal phosphate binding / mitochondrion
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Kynurenine aminotransferase / Kynurenine aminotransferase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Porebski, P. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B.
CitationJournal: FEBS J. / Year: 2005
Title: Crystal structures of Aedes aegypti kynurenine aminotransferase.
Authors: Han, Q. / Gao, Y.G. / Robinson, H. / Ding, H. / Wilson, S. / Li, J.
History
DepositionApr 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0This entry reflects an alternative modeling of the original data in 1yiz, determined byHan, Q., ...This entry reflects an alternative modeling of the original data in 1yiz, determined byHan, Q., Gao, Y.G., Robinson, H., Ding, H., Wilson, S., Li, J.
Remark 200SEE THE ORIGINAL DATA, ENTRY 1yiz
Remark 280SEE THE ORIGINAL DATA, ENTRY 1yiz

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kynurenine aminotransferase
B: Kynurenine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,83115
Polymers96,7802
Non-polymers1,05113
Water14,430801
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-36 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.288, 94.984, 167.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kynurenine aminotransferase


Mass: 48390.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: KAT / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q95VY4, UniProt: Q17CS8*PLUS
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 1000, Tris.HCl pH 8.5

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.55→39.3 Å / Num. obs: 128458 / % possible obs: 99.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→39.3 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1275 1 %RANDOM
Rwork0.1853 ---
obs0.1856 122713 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 51.73 Å2 / Biso mean: 20.548 Å2 / Biso min: 9.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.85 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.55→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 18 801 7301
Biso mean--22.25 28.11 -
Num. residues----810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196698
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.969087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39424.385301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.429151117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8631528
X-RAY DIFFRACTIONr_chiral_restr0.1290.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215058
LS refinement shellResolution: 1.546→1.586 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 91 -
Rwork0.188 8368 -
all-8459 -
obs--89.2 %

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