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- PDB-3pgy: Serine hydroxymethyltransferase from Staphylococcus aureus, S95P ... -

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Basic information

Entry
Database: PDB / ID: 3pgy
TitleSerine hydroxymethyltransferase from Staphylococcus aureus, S95P mutant.
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / structural genomics / IDP00749 / Center for Structural Genomics of Infectious Diseases / CSGID / serine hydroxymethyltransferase
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
CITRIC ACID / GLYCINE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsOsipiuk, J. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Serine hydroxymethyltransferase from Staphylococcus aureus, S95P mutant
Authors: Osipiuk, J. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,93617
Polymers182,0504
Non-polymers1,88613
Water19,0421057
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0199
Polymers91,0252
Non-polymers9947
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-44 kcal/mol
Surface area29090 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9188
Polymers91,0252
Non-polymers8936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-38 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.081, 86.531, 301.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 45512.461 Da / Num. of mol.: 4 / Mutation: S95P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: glyA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5HE87, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1057 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M tri-ammonium citrate, 20% PEG-3350, 10 mM glycine, 10 mM pyridoxal 5'-phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 136110 / Num. obs: 136110 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.266 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.92-1.956.10.8072.0264461.03795.4
1.95-1.996.30.65966711.03596.9
1.99-2.036.40.57867151.02297.4
2.03-2.076.40.47367251.0398.6
2.07-2.116.40.40367891.01798.3
2.11-2.166.40.32768221.03598.9
2.16-2.226.30.27168091.08199.3
2.22-2.286.30.23367851.10699
2.28-2.346.30.21368001.09498.7
2.34-2.426.20.18267801.13598.5
2.42-2.516.10.15967951.15198.3
2.51-2.616.10.1467671.1798.2
2.61-2.7260.11667831.23997.8
2.72-2.875.90.168021.31197.8
2.87-3.055.90.08367511.497.5
3.05-3.285.80.07268131.60397.3
3.28-3.615.70.06568122.03997.2
3.61-4.145.60.05768492.36697.4
4.14-5.215.70.04269671.60798.1
5.21-506.30.03274291.1499.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2W7E

2w7e


Resolution: 1.92→47.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.244 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 6799 5 %RANDOM
Rwork0.1655 ---
all0.1677 135637 --
obs0.1677 135637 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.86 Å2 / Biso mean: 30.106 Å2 / Biso min: 11.04 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20 Å2
2---0.65 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.92→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12410 0 127 1057 13594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02213142
X-RAY DIFFRACTIONr_bond_other_d0.0010.028930
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.97217809
X-RAY DIFFRACTIONr_angle_other_deg0.964321993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74351708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59625.337609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.377152377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.811558
X-RAY DIFFRACTIONr_chiral_restr0.1020.21983
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022513
X-RAY DIFFRACTIONr_mcbond_it0.8621.58138
X-RAY DIFFRACTIONr_mcbond_other0.251.53341
X-RAY DIFFRACTIONr_mcangle_it1.517213132
X-RAY DIFFRACTIONr_scbond_it2.55535004
X-RAY DIFFRACTIONr_scangle_it4.2924.54619
LS refinement shellResolution: 1.92→1.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 491 -
Rwork0.262 9128 -
all-9619 -
obs-9619 95.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.20710.01390.13770.26420.12441.1203-0.0064-0.0192-0.0389-0.02450.0541-0.0396-0.040.0628-0.04760.00570.00190.00340.0403-0.00140.0436-15.27253.580763.1278
20.19460.15460.190.58370.11470.6798-0.03860.0043-0.0161-0.05950.0463-0.0063-0.06980.0311-0.00770.0707-0.0330.03690.0244-0.0130.023-22.24822.924830.8629
30.30620.0860.09740.33260.18150.64850.0094-0.0128-0.01610.008-0.01310.02360.0521-0.06290.00380.0398-0.028-0.01230.0210.00690.03212.911846.341845.3245
40.2743-0.03280.15550.47220.31990.9207-0.01820.0074-0.015-0.05590.00590.054-0.0425-0.06830.01240.0561-0.0147-0.01780.0165-0.00160.02789.369542.369812.8042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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