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- PDB-5bj3: THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1 -

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Basic information

Entry
Database: PDB / ID: 5bj3
TitleTHERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1
ComponentsPROTEIN (ASPARTATE AMINOTRANSFERASE)
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL ENZYME
Function / homology
Function and homology information


aspartate-prephenate aminotransferase / aspartate-prephenate aminotransferase activity / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / 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 ...Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / 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
PYRIDOXAL-5'-PHOSPHATE / Aspartate/prephenate aminotransferase
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsUra, H. / Nakai, T. / Kawaguchi, S.I. / Miyahara, I. / Hirotsu, K. / Kuramitsu, S.
CitationJournal: J.BIOCHEM.(TOKYO) / Year: 2001
Title: Substrate recognition mechanism of thermophilic dual-substrate enzyme
Authors: Ura, H. / Nakai, T. / Kawaguchi, S.I. / Miyahara, I. / Hirotsu, K. / Kuramitsu, S.
History
DepositionJan 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ASPARTATE AMINOTRANSFERASE)
B: PROTEIN (ASPARTATE AMINOTRANSFERASE)
C: PROTEIN (ASPARTATE AMINOTRANSFERASE)
D: PROTEIN (ASPARTATE AMINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,6088
Polymers168,6204
Non-polymers9894
Water5,999333
1
A: PROTEIN (ASPARTATE AMINOTRANSFERASE)
B: PROTEIN (ASPARTATE AMINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8044
Polymers84,3102
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-22 kcal/mol
Surface area25170 Å2
MethodPISA
2
C: PROTEIN (ASPARTATE AMINOTRANSFERASE)
D: PROTEIN (ASPARTATE AMINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8044
Polymers84,3102
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-21 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.440, 62.250, 154.770
Angle α, β, γ (deg.)90.00, 109.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (ASPARTATE AMINOTRANSFERASE) / E.C.2.6.1.1 TRANSFERASE


Mass: 42154.969 Da / Num. of mol.: 4 / Mutation: S14D,T16P,K101S,S261R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / Strain (production host): AB1157 / References: UniProt: Q56232, aspartate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growpH: 4.3 / Details: CRYSTALLIZED FROM 30MM AMMONIUM PHOSPHATE, PH 4.3

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 77082 / % possible obs: 78.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.28 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3 / % possible all: 61.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJW

1bjw


Resolution: 2.2→8 Å / Rfactor Rfree error: 0.0028 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.243 7454 10 %RANDOM
Rwork0.215 ---
obs0.215 74025 77.4 %-
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11228 0 60 333 11621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.331.5
X-RAY DIFFRACTIONx_mcangle_it4.272
X-RAY DIFFRACTIONx_scbond_it5.942
X-RAY DIFFRACTIONx_scangle_it8.852.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 3.17 Å2 / Rms dev position: 0.076 Å / Weight Biso : 1 / Weight position: 500
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3112 710 10 %
Rwork0.2816 6487 -
obs--60.53 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.PLPTOPHCSDX.PRO

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