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- PDB-1iug: The crystal structure of aspartate aminotransferase which belongs... -

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Basic information

Entry
Database: PDB / ID: 1iug
TitleThe crystal structure of aspartate aminotransferase which belongs to subgroup IV from Thermus thermophilus
Componentsputative aspartate aminotransferase
KeywordsTRANSFERASE / Wild Type / Pyridoxal-5'-Phosphate Form / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class V domain / Aminotransferase class-V / 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 ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class V domain / Aminotransferase class-V / 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
PHOSPHATE ION / Aspartate aminotransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKatsura, Y. / Shirouzu, M. / Yamaguchi, H. / Ishitani, R. / Nureki, O. / Kuramitsu, S. / Hayashi, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV.
Authors: Katsura, Y. / Shirouzu, M. / Yamaguchi, H. / Ishitani, R. / Nureki, O. / Kuramitsu, S. / Hayashi, H. / Yokoyama, S.
History
DepositionMar 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative aspartate aminotransferase
B: putative aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7184
Polymers76,5282
Non-polymers1902
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-42 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.849, 135.330, 133.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein putative aspartate aminotransferase


Mass: 38264.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83786
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: ammonium phosphate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMammonium phosphate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSPring-8 BL41XU20.9851,0.9799,0.9797,0.9733
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJan 1, 2000
MARRESEARCH2CCDJan 1, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni MIRROR + Ni FILTERSINGLE WAVELENGTHMx-ray1
2the rotated-inclined double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.98511
30.97991
40.97971
50.97331
ReflectionResolution: 2.2→50 Å / Num. all: 42996 / Num. obs: 41915 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.084 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.24 Å / % possible all: 96

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 2072 RANDOM
Rwork0.199 --
all-41888 -
obs-41892 -
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5338 0 10 192 5540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_bond_d0.0084
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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