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- PDB-2cst: CRYSTAL STRUCTURE OF THE CLOSED FORM OF CHICKEN CYTOSOLIC ASPARTA... -

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Basic information

Entry
Database: PDB / ID: 2cst
TitleCRYSTAL STRUCTURE OF THE CLOSED FORM OF CHICKEN CYTOSOLIC ASPARTATE AMINOTRANSFERASE AT 1.9 ANGSTROMS RESOLUTION
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE(AMINOTRANSFERASE)
Function / homology
Function and homology information


Amino acid metabolism / phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Gluconeogenesis / glycerol biosynthetic process / aspartate biosynthetic process / aspartate metabolic process ...Amino acid metabolism / phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Gluconeogenesis / glycerol biosynthetic process / aspartate biosynthetic process / aspartate metabolic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate catabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / cytosol
Similarity search - Function
Aspartate/other aminotransferase / 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 ...Aspartate/other aminotransferase / 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
MALEIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Strokopytov, B.V. / Borisov, V.V.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of the closed form of chicken cytosolic aspartate aminotransferase at 1.9 A resolution.
Authors: Malashkevich, V.N. / Strokopytov, B.V. / Borisov, V.V. / Dauter, Z. / Wilson, K.S. / Torchinsky, Y.M.
#1: Journal: Transaminases / Year: 1985
Title: Three-Dimensional Structure of the Complex of Chicken Cytosolic Aspartate Aminotransferase with 2-Oxoglutarate
Authors: Harutyunyan, E.G. / Malashkevich, V.N. / Kochkina, V.M. / Torchinsky, Y.M.
History
DepositionSep 6, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,4426
Polymers91,7162
Non-polymers7264
Water13,836768
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-16 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.400, 126.000, 124.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 138 / 2: CIS PROLINE - PRO A 195 / 3: CIS PROLINE - PRO B 138 / 4: CIS PROLINE - PRO B 195
5: RESIDUE PLP 258 IS A COVALENT ADDUCT (ALDIMINE) BETWEEN LYS 258 AND PLP.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.937, -0.349, -0.03), (-0.349, -0.937), (-0.028, 0.011, -1)
Vector: 6.907, 29.368, 103.47)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 45857.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Organ: HEART / Production host: unidentified (others) / References: UniProt: P00504, aspartate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 %(w/v)PEG40001reservoir
240 mMsodium maleate1reservoir
35 mM1reservoirMg(Ac)2
410 mg/mlprotein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. obs: 69643 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Num. measured all: 310873 / Rmerge(I) obs: 0.095

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.9→6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.175 67544
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6460 0 46 768 7274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d1.9
X-RAY DIFFRACTIONt_dihedral_angle_d23.3
X-RAY DIFFRACTIONt_dihedral_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.011

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