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- PDB-2bi3: Radiation damage of the Schiff base in phosphoserine aminotransfe... -

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Basic information

Entry
Database: PDB / ID: 2bi3
TitleRadiation damage of the Schiff base in phosphoserine aminotransferase (structure D)
ComponentsPHOSPHOSERINE AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / RADIATION DAMAGE
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
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Phosphoserine aminotransferase
Similarity search - Component
Biological speciesBACILLUS ALCALOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.69 Å
AuthorsDubnovitsky, A.P. / Ravelli, R.B.G. / Popov, A.N. / Papageorgiou, A.C.
CitationJournal: Protein Sci. / Year: 2005
Title: Strain Relief at the Active Site of Phosphoserine Aminotransferase Induced by Radiation Damage.
Authors: Dubnovitsky, A.P. / Ravelli, R.B.G. / Popov, A.N. / Papageorgiou, A.C.
History
DepositionJan 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2005Provider: 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

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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)81,77716
Polymers80,4872
Non-polymers1,29014
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)143.061, 83.772, 66.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHOSPHOSERINE AMINOTRANSFERASE


Mass: 40243.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL-5'-PHOSPHATE LINKED TO 196 / Source: (gene. exp.) BACILLUS ALCALOPHILUS (bacteria) / Plasmid: PBALC-PSAT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RME2, phosphoserine transaminase

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Non-polymers , 6 types, 618 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHIS ENTRY CONTAINS ONE OF NINE STRUCTURES THAT ARE DESCRIBED IN THE ACCOMPANYING JOURNAL ARTICLE. ...THIS ENTRY CONTAINS ONE OF NINE STRUCTURES THAT ARE DESCRIBED IN THE ACCOMPANYING JOURNAL ARTICLE. IN THE ARTICLE THE STRUCTURES ARE REFERRED TO BY LETTER, RATHER THAN BY PDB ACCESSION CODE. THE MAPPING BETWEEN LABEL AND ACCESSION CODE IS AS FOLLOWS: A - 2BHX F - 2BI9 B - 2BI1 G - 2BIA C - 2BI2 H - 2BIE D - 2BI3 I - 2BIG E - 2BI5
Sequence detailsTHE N-TERMINAL METHIONINE IS CLEAVED OFF IN THE MATURE PROTEIN

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growpH: 8.2
Details: 30% PEG 400, 200 MM MGCL2, 5% GLYCEROL, 100 MM TRIS PH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: May 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.69→15 Å / Num. obs: 90981 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 1.69→1.73 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameClassification
SHELXL-97refinement
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.69→15 Å / Num. parameters: 25439 / Num. restraintsaints: 23526 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: RESIDUES A 1, A 215, A 216, A 218, B 2 AND B 218 WERE MODELLED AS ALANINES. RESIDUES B 1, B 214, B 215, B216 WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 4472 5 %RANDOM
all0.1808 89142 --
obs0.1793 -98.7 %-
Refine analyzeNum. disordered residues: 22 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6278
Refinement stepCycle: LAST / Resolution: 1.69→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5601 0 75 604 6280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.01
X-RAY DIFFRACTIONs_from_restr_planes0.0279
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.078
X-RAY DIFFRACTIONs_approx_iso_adps0

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