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- PDB-1w3u: Crystal structure of phosphoserine aminotransferase from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 1w3u
TitleCrystal structure of phosphoserine aminotransferase from Bacillus circulans var. alkalophilus
ComponentsPHOSPHOSERINE AMINOTRANSFERASEPhosphoserine transaminase
KeywordsTRANSFERASE / PHOSPHOSERINE AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE TRANSFERASE / PYRIDINE 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: 1.5 Å
AuthorsKapetaniou, E.G. / Dubnovitsky, A.P. / Papageorgiou, A.C.
CitationJournal: Protein Sci. / Year: 2005
Title: Enzyme Adaptation to Alkaline Ph: Atomic Resolution (1.08 A) Structure of Phosphoserine Aminotransferase from Bacillus Alcalophilus
Authors: Dubnovitsky, A.P. / Kapetaniou, E.G. / Papageorgiou, A.C.
History
DepositionJul 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 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 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3053
Polymers39,9661
Non-polymers3392
Water6,125340
1
A: PHOSPHOSERINE AMINOTRANSFERASE
hetero molecules

A: PHOSPHOSERINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6116
Polymers79,9322
Non-polymers6784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6040 Å2
ΔGint-31.4 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.287, 91.109, 42.374
Angle α, β, γ (deg.)90.00, 111.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PHOSPHOSERINE AMINOTRANSFERASE / Phosphoserine transaminase / PHOSPHOHYDROXYTHREONINE AMINOTRANSFERASE / PSAT


Mass: 39966.090 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINK BETWEEN A 197 AND A 363 / 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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES CHAIN A LYS 3 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: 2.1 Å3/Da / Density % sol: 39.7 %
Crystal growpH: 4.6
Details: CRYSTALLIZED AT ROOM TEMPERATURE FROM 0.1 M SODIUM ACETATE BUFFER, PH 4.6, 5% GLYCEROL, 4% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8015
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. obs: 49679 / % possible obs: 96 % / Observed criterion σ(I): 5 / Redundancy: 7.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 20
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.8 / % possible all: 91

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BT4

1bt4


Resolution: 1.5→15 Å / Num. parameters: 19381 / Num. restraintsaints: 21136 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.005
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2461 5 %RANDOM
all0.1441 49625 --
obs0.1421 -96.3 %-
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3117
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 21 340 3125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0.008
X-RAY DIFFRACTIONs_from_restr_planes0.0279
X-RAY DIFFRACTIONs_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.121
X-RAY DIFFRACTIONs_approx_iso_adps0.069

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