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- PDB-1gc3: THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 CO... -

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Basic information

Entry
Database: PDB / ID: 1gc3
TitleTHERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 2 COMPLEXED WITH TRYPTOPHAN
ComponentsASPARTATE AMINOTRANSFERASEAspartate transaminase
KeywordsTRANSFERASE / Aminotransferase / Dual-substrate enzyme / 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 / TRYPTOPHAN / Aspartate/prephenate aminotransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.3 Å
AuthorsUra, H. / Nakai, T. / Hirotsu, K. / Kuramitsu, S.
Citation
Journal: J.Biochem. / 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.
#1: Journal: Biochemistry / Year: 1999
Title: Structure of Thermus thermuophilus HB8 Aspartate Aminotransferase and its Complex with Maleate
Authors: Nakai, T. / Okada, K. / Akutsu, S. / Miyahara, I. / Kawaguchi, S. / Kato, R. / Kuramitsu, S. / Hirotsu, K.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: The Novel Substrate Recognition Mechanism Utilized by Aspartate Aminotransferse of the Extreme Thermophile Thermus thermophilus HB8
Authors: NOBE, Y. / Kawaguchi, S. / Ura, H. / Nakai, T. / Hirotsu, K. / Kato, R. / Kuramitsu, S.
#3: Journal: J.BIOCHEM.(TOKYO) / Year: 1996
Title: An Aspartate Aminotransferase from an Extremely Thermophilic Bacterium, Thermus thermophilus HB8
Authors: Okamoto, A. / Kato, R. / Masui, R. / Yamagishi, A. / Oshima, T. / Kuramitsu, S.
History
DepositionJul 18, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 10, 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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
C: ASPARTATE AMINOTRANSFERASE
D: ASPARTATE AMINOTRANSFERASE
E: ASPARTATE AMINOTRANSFERASE
F: ASPARTATE AMINOTRANSFERASE
G: ASPARTATE AMINOTRANSFERASE
H: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,86724
Polymers337,2568
Non-polymers3,61116
Water0
1
A: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2176
Polymers84,3142
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-12 kcal/mol
Surface area27660 Å2
MethodPISA
2
C: ASPARTATE AMINOTRANSFERASE
D: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2176
Polymers84,3142
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-11 kcal/mol
Surface area27590 Å2
MethodPISA
3
E: ASPARTATE AMINOTRANSFERASE
F: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2176
Polymers84,3142
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-12 kcal/mol
Surface area27400 Å2
MethodPISA
4
G: ASPARTATE AMINOTRANSFERASE
H: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2176
Polymers84,3142
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-11 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.5, 98.4, 187.0
Angle α, β, γ (deg.)90, 91.53, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ASPARTATE AMINOTRANSFERASE / Aspartate transaminase


Mass: 42156.984 Da / Num. of mol.: 8 / Mutation: S14D, T16V, K101S, S261R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q56232, aspartate transaminase
#2: Chemical
ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 6000, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMprotein1drop
25 mMHEPES1drop
310 mM1dropKCl
424 %(w/w)PEG60001reservoir
5100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 24, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 107884 / Num. obs: 42535 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 52.43 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 4.9
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.204 / Num. unique all: 4124 / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 107884

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.3→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 4290 10.667 %Random
Rwork0.203 ---
all0.223 42535 --
obs0.22 40218 96 %-
Refinement stepCycle: LAST / Resolution: 3.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23584 0 240 0 23824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg2.471
X-RAY DIFFRACTIONx_torsion_deg24.94
X-RAY DIFFRACTIONx_torsion_impr_deg1.871
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS

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