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- PDB-1bjn: STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1bjn
TitleSTRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM ESCHERICHIA COLI
ComponentsPHOSPHOSERINE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / L-SERINE BIOSYNTHESIS
Function / homology
Function and homology information


lysine biosynthetic process via diaminopimelate and N-succinyl-2-amino-6-ketopimelate / phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / L-serine metabolic process / L-serine biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Phosphoserine aminotransferase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / 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 ...Phosphoserine aminotransferase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / 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
Phosphoserine aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å
AuthorsHester, G. / Moser, M. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of phosphoserine aminotransferase from Escherichia coli at 2.3 A resolution: comparison of the unligated enzyme and a complex with alpha-methyl-l-glutamate.
Authors: Hester, G. / Stark, W. / Moser, M. / Kallen, J. / Markovic-Housley, Z. / Jansonius, J.N.
History
DepositionJun 25, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOSERINE AMINOTRANSFERASE
B: PHOSPHOSERINE AMINOTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)79,8742
Polymers79,8742
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-23 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.740, 94.740, 133.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.45112, -0.73331, 0.50868), (-0.72837, -0.63188, -0.26495), (0.51572, -0.25098, -0.81917)
Vector: 26.32915, 123.96355, 102.31523)

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Components

#1: Protein PHOSPHOSERINE AMINOTRANSFERASE / PSAT


Mass: 39937.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ONE COFACTOR, PYRIDOXAL PHOSPHATE (VITAMIN B6), IS PRESENT PER CHAIN
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SERC / References: UniProt: P23721, phosphoserine transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.7 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PROTEIN WAS CRYSTALLIZED AT 4-7 DEGREES CELSIUS BY HANGING DROP METHOD, USING PEG4000 AS A PRECIPITATING AGENT, BUFFERED WITH SODIUM ACETATE TO PH 7.2 IN THE DROP AND PH 5.6 IN THE RESERVOIR. ...Details: PROTEIN WAS CRYSTALLIZED AT 4-7 DEGREES CELSIUS BY HANGING DROP METHOD, USING PEG4000 AS A PRECIPITATING AGENT, BUFFERED WITH SODIUM ACETATE TO PH 7.2 IN THE DROP AND PH 5.6 IN THE RESERVOIR. THE PH-GRADIENT WAS ESSENTIAL FOR THE CRYSTALLIZATION., vapor diffusion - hanging drop, temperature 277K
PH range: 5.6-7.2
Crystal grow
*PLUS
Temperature: 4-7 ℃ / Method: vapor diffusion, hanging drop / Details: pH7.2 in the drop and pH5.6 in the reservoir
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1PEG40001reservoir
2sodium acetate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→32.5 Å / Num. obs: 38831 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 29.8 Å2 / Rsym value: 0.083 / Net I/σ(I): 14.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.474 / % possible all: 99.9
Reflection
*PLUS
Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→32.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. ATOMIC OCCUPANCIES OF RESIDUES WITH ALTERNATIVE CONFORMATIONS WERE REFINED DURING EACH REFINEMENT ROUND. IN THE LAST REFINEMENT ROUND THE OCCUPANCIES WERE FIXED, ...Details: BULK SOLVENT MODEL USED. ATOMIC OCCUPANCIES OF RESIDUES WITH ALTERNATIVE CONFORMATIONS WERE REFINED DURING EACH REFINEMENT ROUND. IN THE LAST REFINEMENT ROUND THE OCCUPANCIES WERE FIXED, RESULTING IN A TOTAL SUMMED OCCUPANCY FOR EACH RESIDUE OF 1.0.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1945 5 %RANDOM
Rwork0.175 ---
obs0.175 38831 98.3 %-
Displacement parametersBiso mean: 33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-32.5 Å
Luzzati sigma a0.31 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5609 0 30 241 5880
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.851.5
X-RAY DIFFRACTIONx_mcangle_it2.912
X-RAY DIFFRACTIONx_scbond_it3.652
X-RAY DIFFRACTIONx_scangle_it5.632.5
Refine LS restraints NCSRms dev Biso : 2.65 Å2 / Rms dev position: 0.54 Å / Weight Biso : 2.5 / Weight position: 100
LS refinement shellResolution: 2.3→2.35 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.333 129 5 %
Rwork0.285 2444 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PLP.PAR_OPLP.TOP_O
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.175 / Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16

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