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- PDB-1bjo: THE STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM E. COLI IN C... -

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Basic information

Entry
Database: PDB / ID: 1bjo
TitleTHE STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM E. COLI IN COMPLEX WITH ALPHA-METHYL-L-GLUTAMATE
Components(PHOSPHOSERINE AMINOTRANSFERASEPhosphoserine transaminase) x 2
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 / cytosol / cytoplasm
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
ALPHA-METHYL-L-GLUTAMIC ACID / PYRIDOXAL-5'-PHOSPHATE / : / Phosphoserine aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.8 Å
AuthorsHester, G. / Stark, W. / 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: Non-polymer description / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,0554
Polymers79,6462
Non-polymers4082
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-24 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.860, 94.450, 131.810
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: (0.45212, -0.73722, 0.50209), (-0.73241, -0.62812, -0.26276), (0.50908, -0.24894, -0.82393)
Vector: 27.27194, 123.37072, 100.81561)

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Components

#1: Protein PHOSPHOSERINE AMINOTRANSFERASE / Phosphoserine transaminase / PSAT


Mass: 39709.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IN CHAIN A AN EXTERNAL ALDIMINE INTERMEDIATE BETWEEN PYRIDOXAL-5'-PHOSPHATE AND ALPHA-METHYL-L-GLUTAMATE IS NON-COVALENTLY BOUND WHILE IN CHAIN B A PYRIDOXAL-5'-PHOSPHATE MOLECULE IS ...Details: IN CHAIN A AN EXTERNAL ALDIMINE INTERMEDIATE BETWEEN PYRIDOXAL-5'-PHOSPHATE AND ALPHA-METHYL-L-GLUTAMATE IS NON-COVALENTLY BOUND WHILE IN CHAIN B A PYRIDOXAL-5'-PHOSPHATE MOLECULE IS COVALENTLY BOUND IN AN ALDIMINE LINKAGE TO A LYSINE SIDE CHAIN
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SERC
References: PIR: S28806, UniProt: P23721*PLUS, phosphoserine transaminase
#2: Protein PHOSPHOSERINE AMINOTRANSFERASE / Phosphoserine transaminase / PSAT


Mass: 39937.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IN CHAIN A AN EXTERNAL ALDIMINE INTERMEDIATE BETWEEN PYRIDOXAL-5'-PHOSPHATE AND ALPHA-METHYL-L-GLUTAMATE IS NON-COVALENTLY BOUND WHILE IN CHAIN B A PYRIDOXAL-5'-PHOSPHATE MOLECULE IS ...Details: IN CHAIN A AN EXTERNAL ALDIMINE INTERMEDIATE BETWEEN PYRIDOXAL-5'-PHOSPHATE AND ALPHA-METHYL-L-GLUTAMATE IS NON-COVALENTLY BOUND WHILE IN CHAIN B A PYRIDOXAL-5'-PHOSPHATE MOLECULE IS COVALENTLY BOUND IN AN ALDIMINE LINKAGE TO A LYSINE SIDE CHAIN
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SERC
References: PIR: S28806, UniProt: P23721*PLUS, phosphoserine transaminase
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-GAM / ALPHA-METHYL-L-GLUTAMIC ACID


Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: PSAT HAS BEEN CRYSTALLIZED AT 4-7 DEGREES CELSIUS BY THE HANGING DROP METHOD, USING PEG4000 AS A PRECIPITANT, BUFFERED WITH SODIUM ACETATE TO PH 7.2 IN THE DROP AND PH 5.6 IN THE RESERVOIR. ...Details: PSAT HAS BEEN CRYSTALLIZED AT 4-7 DEGREES CELSIUS BY THE HANGING DROP METHOD, USING PEG4000 AS A PRECIPITANT, 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: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jul 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→39.8 Å / Num. obs: 19908 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 45.4 Å2 / Rsym value: 0.094 / Net I/σ(I): 9.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.402 / % possible all: 68.4
Reflection
*PLUS
Rmerge(I) obs: 0.094 / Biso Wilson estimate: 29.1 Å2
Reflection shell
*PLUS
% possible obs: 68.4 % / Rmerge(I) obs: 0.402

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
TRUNCATEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2.8→39.8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 965 4.8 %RANDOM
Rwork0.185 ---
obs0.185 19907 91.3 %-
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-39.8 Å
Luzzati sigma a0.56 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5603 0 26 50 5679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSRms dev Biso : 1.5 Å2 / Rms dev position: 0.48 Å / Weight position: 500
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.398 64 5 %
Rwork0.315 1223 -
obs--61.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PLP.PAR_OPLP.TOP_O
X-RAY DIFFRACTION4MGL.PAR_OMGL.TOP_O
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.86
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15
LS refinement shell
*PLUS
Rfactor obs: 0.315

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