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- PDB-5vep: MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB S... -

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Basic information

Entry
Database: PDB / ID: 5vep
TitleMOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2F
ComponentsKynurenine--oxoglutarate transaminase 3
KeywordsTRANSFERASE / AMINOTRANSFERASE III / MOUSE / RE-REFINEMENT
Function / homology
Function and homology information


L-kynurenine catabolic process / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process ...L-kynurenine catabolic process / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process / biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / 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 ...: / 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
DI(HYDROXYETHYL)ETHER / Kynurenine--oxoglutarate transaminase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsWlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Porebski, P. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B.
CitationJournal: Mol. Cell. Biol. / Year: 2009
Title: Biochemical and structural properties of mouse kynurenine aminotransferase III.
Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J.
History
DepositionApr 5, 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 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Remark 0This entry reflects an alternative modeling of the original data in 3E2F, determined by Q.HAN,R. ...This entry reflects an alternative modeling of the original data in 3E2F, determined by Q.HAN,R.ROBINSON,T.CAI,D.A.TAGLE,J.LI
Remark 200SEE THE ORIGINAL DATA, ENTRY 3E2F
Remark 280SEE THE ORIGINAL DATA, ENTRY 3E2F

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kynurenine--oxoglutarate transaminase 3
B: Kynurenine--oxoglutarate transaminase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,30816
Polymers92,9062
Non-polymers1,40214
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-23 kcal/mol
Surface area29240 Å2
MethodPISA
2
A: Kynurenine--oxoglutarate transaminase 3
B: Kynurenine--oxoglutarate transaminase 3
hetero molecules

A: Kynurenine--oxoglutarate transaminase 3
B: Kynurenine--oxoglutarate transaminase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,61632
Polymers185,8124
Non-polymers2,80328
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area18530 Å2
ΔGint-83 kcal/mol
Surface area57860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.820, 91.820, 233.649
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-672-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Kynurenine--oxoglutarate transaminase 3 / Cysteine-S-conjugate beta-lyase 2 / Kynurenine aminotransferase 3 / Kynurenine aminotransferase III ...Cysteine-S-conjugate beta-lyase 2 / Kynurenine aminotransferase 3 / Kynurenine aminotransferase III / KATIII / Kynurenine--glyoxylate transaminase / Kynurenine--oxoglutarate transaminase III


Mass: 46453.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kyat3, Ccbl2, Kat3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q71RI9, kynurenine-oxoglutarate transaminase, cysteine-S-conjugate beta-lyase, kynurenine-glyoxylate transaminase

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 53.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% PEG 400, 150 MM CACL2, 10%, GLYCEROL, 100 MM HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.59→29.21 Å / Num. obs: 29301 / % possible obs: 91.1 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.4

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.22data extraction
DENZOdata collection
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→29.21 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.885 / SU B: 13.469 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.982 / ESU R Free: 0.356
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 1476 5.1 %RANDOM
Rwork0.1907 ---
obs0.1942 27593 90.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.57 Å2 / Biso mean: 36.919 Å2 / Biso min: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 2.59→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 84 162 6782
Biso mean--47.99 34.37 -
Num. residues----820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196786
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9619200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1245818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03424.225284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.196151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7441528
X-RAY DIFFRACTIONr_chiral_restr0.1320.21010
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215028
LS refinement shellResolution: 2.592→2.658 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 63 -
Rwork0.379 1184 -
all-1247 -
obs--54.45 %

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