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- PDB-3ecd: Crystal structure of serine hydroxymethyltransferase from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 3ecd
TitleCrystal structure of serine hydroxymethyltransferase from Burkholderia pseudomallei
ComponentsSerine hydroxymethyltransferase 2
KeywordsTRANSFERASE / SSGCID / deCODE / BupsA00008a / One-carbon metabolism / Pyridoxal phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding / cytoplasm
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) / Pyridoxal phosphate-dependent transferase, small 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 2 / Serine hydroxymethyltransferase 2
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of serine hydroxymethyltransferase from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionAug 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Serine hydroxymethyltransferase 2
B: Serine hydroxymethyltransferase 2
C: Serine hydroxymethyltransferase 2
D: Serine hydroxymethyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,7158
Polymers182,3474
Non-polymers3684
Water28,9501607
1
A: Serine hydroxymethyltransferase 2
D: Serine hydroxymethyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3584
Polymers91,1732
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-23 kcal/mol
Surface area28470 Å2
MethodPISA
2
B: Serine hydroxymethyltransferase 2
C: Serine hydroxymethyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3584
Polymers91,1732
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-18 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.212, 61.865, 117.577
Angle α, β, γ (deg.)97.790, 89.970, 110.240
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Serine hydroxymethyltransferase 2 / Serine methylase 2 / SHMT 2


Mass: 45586.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: glyA2, BPSS0547 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63MV1, UniProt: Q3JGP5*PLUS, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1607 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TARGETDB ID BUPSA00008A DOES NOT EXIST IN TARGETDB AT THE TIME OF PROCESSING.

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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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PACT SCREEN CONDITION C6, 20% PEG 6000, 0.2 M NaCl, 0.1 M HEPES-KOH pH 7.0, 24.1 mg/mL protein, 0.4/0.4 uL drops, Crystal ID 109933C6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99994 Å
DetectorDate: Aug 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 1.4→58.222 Å / Num. all: 408650 / Num. obs: 190206 / % possible obs: 94.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 12.358
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.692.10.4081.854497253830.40886.4
1.69-1.792.20.2792.757302263350.27994.8
1.79-1.912.20.1664.453937248820.16695.4
1.91-2.072.20.0997.350523233450.09995.9
2.07-2.262.20.06310.146376215360.06396.2
2.26-2.532.10.04515.241861194990.04596.4
2.53-2.922.10.03419.136732172520.03496.8
2.92-3.582.10.02622.130534145010.02696.5
3.58-5.062.10.02225.522921111640.02296.2
5.06-58.222.20.02126.21396763090.02199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KKJ

1kkj


Resolution: 1.6→58.222 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.87 / SU B: 1.824 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1 / SU Rfree: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 9593 5 %RANDOM
Rwork0.187 ---
obs0.188 190195 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.39 Å2 / Biso mean: 20.891 Å2 / Biso min: 6.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20.52 Å2-0.09 Å2
2--1.13 Å20.24 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→58.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11605 0 24 1607 13236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211811
X-RAY DIFFRACTIONr_bond_other_d0.0010.027947
X-RAY DIFFRACTIONr_angle_refined_deg1.21.96215975
X-RAY DIFFRACTIONr_angle_other_deg1.33319325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45251528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73123.674528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.699151932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.93415100
X-RAY DIFFRACTIONr_chiral_restr0.0580.21839
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113368
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022380
X-RAY DIFFRACTIONr_mcbond_it0.4761.57630
X-RAY DIFFRACTIONr_mcbond_other0.0861.53162
X-RAY DIFFRACTIONr_mcangle_it0.911212141
X-RAY DIFFRACTIONr_scbond_it1.47234181
X-RAY DIFFRACTIONr_scangle_it2.5954.53834
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 554 -
Rwork0.276 11137 -
all-11691 -
obs--78.47 %

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