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

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Basic information

Entry
Database: PDB / ID: 2big
TitleRadiation damage of the Schiff base in phosphoserine aminotransferase (structure I)
ComponentsPHOSPHOSERINE AMINOTRANSFERASEPhosphoserine transaminase
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 / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Phosphoserine aminotransferase
Similarity search - Component
Biological speciesBACILLUS ALCALOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.3 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 21, 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
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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)81,87016
Polymers80,7502
Non-polymers1,12014
Water15,781876
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)143.801, 84.297, 67.264
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 / Phosphoserine transaminase


Mass: 40374.754 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, 890 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal 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.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 876 / 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

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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: 2.18 Å3/Da / Density % sol: 43.6 %
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: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.921
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 1.3→12 Å / Num. obs: 187887 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 96
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.6 / % possible all: 94.7

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Processing

Software
NameClassification
SHELXL-97refinement
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.3→12 Å / Num. parameters: 59718 / Num. restraintsaints: 72392 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOUTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.035. RESIDUES A 215, A 216, A 218, AND B 218 WERE MODELLED AS ALANINES. RESIDUES A 1, A 2, B 1, B 2, B 214, B215 AND B 216 WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1559 9397 5 %RANDOM
all0.1166 187766 --
obs0.1154 -93.7 %-
Refine analyzeNum. disordered residues: 31 / Occupancy sum hydrogen: 4936 / Occupancy sum non hydrogen: 6524
Refinement stepCycle: LAST / Resolution: 1.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 63 876 6529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0.025
X-RAY DIFFRACTIONs_from_restr_planes0.0295
X-RAY DIFFRACTIONs_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0.094

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