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- PDB-4p3m: Crystal structure of serine hydroxymethyltransferase from Psychro... -

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Basic information

Entry
Database: PDB / ID: 4p3m
TitleCrystal structure of serine hydroxymethyltransferase from Psychromonas ingrahamii
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / SERINE HYDROXYMETHYLTRANSFERASE / PYRIDOXAL PHOSPHATE / PSYCHROPHILIC ENZYME
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding / cytosol
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / 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
Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesPsychromonas ingrahamii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDworkowski, F. / Angelaccio, S. / Pascarella, S. / Capitani, G.
CitationJournal: Proteins / Year: 2014
Title: Conformational transitions driven by pyridoxal-5'-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii.
Authors: Angelaccio, S. / Dworkowski, F. / Di Bello, A. / Milano, T. / Capitani, G. / Pascarella, S.
History
DepositionMar 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,83617
Polymers92,6052
Non-polymers1,23115
Water9,872548
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-181 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.820, 64.860, 116.940
Angle α, β, γ (deg.)90.00, 125.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine hydroxymethyltransferase / Serine methylase


Mass: 46302.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychromonas ingrahamii (bacteria) / Strain: 37 / Gene: glyA, Ping_1438 / Production host: Escherichia coli (E. coli)
References: UniProt: A1SUU0, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2 M AMMONIUM SULFATE, 150 mM SODIUM CHLORIDE, 100 mM SODIUM CACODYLATE pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→47.61 Å / Num. obs: 76583 / % possible obs: 99.7 % / Redundancy: 6.8 % / Net I/σ(I): 7.3
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.96 / % possible all: 99.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3gbx

3gbx


Resolution: 1.85→47.609 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 1531 2 %
Rwork0.1694 --
obs0.1703 76575 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→47.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5811 0 70 548 6429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156032
X-RAY DIFFRACTIONf_angle_d1.5148181
X-RAY DIFFRACTIONf_dihedral_angle_d12.8752184
X-RAY DIFFRACTIONf_chiral_restr0.046921
X-RAY DIFFRACTIONf_plane_restr0.0091058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90970.3091390.28736809X-RAY DIFFRACTION100
1.9097-1.9780.30841370.25736744X-RAY DIFFRACTION100
1.978-2.05720.31961390.22966813X-RAY DIFFRACTION100
2.0572-2.15080.27581380.21076757X-RAY DIFFRACTION100
2.1508-2.26420.22731390.17566792X-RAY DIFFRACTION100
2.2642-2.40610.19851390.1626804X-RAY DIFFRACTION100
2.4061-2.59180.22031390.15276837X-RAY DIFFRACTION100
2.5918-2.85260.20341390.14856805X-RAY DIFFRACTION100
2.8526-3.26530.1891400.14596823X-RAY DIFFRACTION100
3.2653-4.11360.18971390.13276858X-RAY DIFFRACTION100
4.1136-47.62480.15891430.15817002X-RAY DIFFRACTION100

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