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- PDB-1gde: CRYSTAL STRUCTURE OF PYROCOCCUS PROTEIN A-1 E-FORM -

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Basic information

Entry
Database: PDB / ID: 1gde
TitleCRYSTAL STRUCTURE OF PYROCOCCUS PROTEIN A-1 E-FORM
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE / aminotransferase / pyridoxal enzyme / temperature dependence of substrate recognition
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
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 ...: / 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
GLUTAMIC ACID / PYRIDOXAL-5'-PHOSPHATE / : / Aminotransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsUra, H. / Harata, K. / Matsui, I. / Kuramitsu, S.
Citation
Journal: J.Biochem. / Year: 2001
Title: Temperature dependence of the enzyme-substrate recognition mechanism.
Authors: Ura, H. / Harata, K. / Matsui, I. / Kuramitsu, S.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The Molecular Structure of Hyperthermostable Aromatic Aminotransferase with Novel Substrate Specificity from Pyrococcus horikoshii
Authors: Matsui, I. / Matsui, E. / Sakai, Y. / Kikuchi, H. / Kawarabayashi, Y. / Ura, H. / Kawaguchi, S. / Kuramitsu, S. / Harata, K.
History
DepositionSep 23, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Derived calculations
Category: citation / 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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.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.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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,7106
Polymers87,9222
Non-polymers7894
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-18 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.330, 121.900, 127.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 43960.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PET11A / Production host: Escherichia coli (E. coli)
References: GenBank: 3257794, UniProt: O59096*PLUS, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1,6-hexane diol, Tris, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMHEPES1drop
210 mM1dropKCl
30.2 mMprotein1drop
43 M1,6-hexanediol1reservoir
5100 mMHEPES1reservoir
610 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Jun 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 309808 / Num. obs: 84494 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.185 / Num. unique all: 12138 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 309808

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
X-PLORmodel building
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementResolution: 1.8→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 8485 11.166 %RANDOM
Rwork0.198 ---
all0.207 84471 --
obs0.206 75986 88.7 %-
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6164 0 50 330 6544
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.64
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_torsion_deg23.18
X-RAY DIFFRACTIONx_torsion_impr_deg1.39
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.198 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.18
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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