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- PDB-2c0r: CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS... -

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Basic information

Entry
Database: PDB / ID: 2c0r
TitleCRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS CIRCULANS VAR. ALKALOPHILUS AT pH 8.5
ComponentsPHOSPHOSERINE AMINOTRANSFERASE
KeywordsTRANSFERASE / PHOSPHOSERINE AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / PYRIDINE SERINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE / PYRIDOXINE BIOSYNTHESIS / SERINE BIOSYNTHESIS
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / pyridoxal phosphate binding / 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
PYRIDOXAL-5'-PHOSPHATE / Phosphoserine aminotransferase
Similarity search - Component
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKapetaniou, E.G. / Papageorgiou, A.C.
CitationJournal: Proteins: Struct., Funct., Bioinf. / Year: 2006
Title: Effect of Ph on the Structure and Stability of Bacillus Circulans Ssp. Alkalophilus Phosphoserine Aminotransferase: Thermodynamic and Crystallographic Studies.
Authors: Kapetaniou, E.G. / Thanassoulas, A. / Dubnovitsky, A.P. / Nounesis, G. / Papageorgiou, A.C.
History
DepositionSep 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PHOSPHOSERINE AMINOTRANSFERASE
B: PHOSPHOSERINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4264
Polymers79,9322
Non-polymers4942
Water14,574809
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.783, 90.544, 157.820
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: (-0.99995, 0.0063, 0.0079), (0.00501, 0.98815, -0.1534), (-0.00877, -0.15335, -0.98813)
Vector: 27.23261, 3.4414, 45.27913)

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Components

#1: Protein PHOSPHOSERINE AMINOTRANSFERASE / PSAT


Mass: 39966.090 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CIRCULANS (bacteria) / Variant: ALKALOPHILUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q59196, phosphoserine 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 2 TO GLU ENGINEERED RESIDUE IN CHAIN B, LYS 2 TO GLU

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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 Å3/Da / Density % sol: 38 %
Crystal growpH: 8.5
Details: 30% PEG 4000, 0.1 M TRIS-HCL BUFFER, PH 8.5, 5% GLYCEROL, 0.2 M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.2→15 Å / Num. obs: 171731 / % possible obs: 85.7 % / Observed criterion σ(I): 3 / Redundancy: 24.86 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.83
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 74.4

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Processing

Software
NameClassification
SHELXL-97refinement
HKLdata reduction
HKLdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJN

1bjn


Resolution: 1.2→12 Å / Num. parameters: 57709 / Num. restraintsaints: 69730 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 8576 5 %RANDOM
all0.1539 171522 --
obs0.152 -85.6 %-
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6397
Refinement stepCycle: LAST / Resolution: 1.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5561 0 30 809 6400
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0.015
X-RAY DIFFRACTIONs_from_restr_planes0.0286
X-RAY DIFFRACTIONs_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.076

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