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- PDB-5hxx: Crystal structure of AspAT from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5hxx
TitleCrystal structure of AspAT from Corynebacterium glutamicum
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE / Aminotransferase
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity
Similarity search - Function
Aspartate aminotransferase Ic / Aspartate amino-transferase / 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 ...Aspartate aminotransferase Ic / Aspartate amino-transferase / 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
2-OXOGLUTARIC ACID / GLUTAMIC ACID / PYRIDOXAL-5'-PHOSPHATE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / : / Aspartate aminotransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSon, H.-F. / Kim, K.-J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation of Korea2014R1A2A2A01005752 Korea, Republic Of
National Research Foundation of Korea2014M1M2M2033626 Korea, Republic Of
National Research Foundation of Korea2015H1A2A1034233 Korea, Republic Of
CitationJournal: To be published
Title: Structural insights into a novel class of aspartate aminotransferase from Corynebacterium glutamicum
Authors: Son, H.-F. / Kim, K.-J.
History
DepositionJan 31, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8539
Polymers94,7892
Non-polymers1,0657
Water14,070781
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-19 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.388, 53.521, 170.224
Angle α, β, γ (deg.)90.000, 104.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 47394.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: aspB, cg0294 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0J9X1V2, UniProt: Q8NTR2*PLUS, aspartate transaminase

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Non-polymers , 6 types, 788 molecules

#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 23, 2014
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→165 Å / Num. obs: 56893 / % possible obs: 97.7 % / Redundancy: 3.6 % / Net I/σ(I): 41.62
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D6K

3d6k


Resolution: 2→28.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.863 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 3050 5.1 %RANDOM
Rwork0.1549 ---
obs0.1574 56893 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.15 Å2 / Biso mean: 14.42 Å2 / Biso min: 3.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å2-0.88 Å2
2--1.26 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 2→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 69 781 7384
Biso mean--34.69 26.48 -
Num. residues----847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196756
X-RAY DIFFRACTIONr_bond_other_d0.0020.026341
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9589177
X-RAY DIFFRACTIONr_angle_other_deg1.058314594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09324.412306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.415151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3131538
X-RAY DIFFRACTIONr_chiral_restr0.1130.21005
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217689
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021522
X-RAY DIFFRACTIONr_mcbond_it1.2311.2413389
X-RAY DIFFRACTIONr_mcbond_other1.2031.2413388
X-RAY DIFFRACTIONr_mcangle_it1.8351.8494231
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 204 -
Rwork0.146 4074 -
all-4278 -
obs--95.07 %

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