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- PDB-4j5u: X-ray crystal structure of a serine hydroxymethyltransferase with... -

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Basic information

Entry
Database: PDB / ID: 4j5u
TitleX-ray crystal structure of a serine hydroxymethyltransferase with covalently bound PLP from Rickettsia rickettsii str. Sheila Smith
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
Similarity search - Component
Biological speciesRickettsia rickettsii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray crystal structure of a serine hydroxymethyltransferase with covalently bound PLP from Rickettsia rickettsii str. Sheila Smith
Authors: Fairman, J.W. / Abendroth, J.A. / Edwards, T.E. / Lorimer, D.
History
DepositionFeb 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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


Theoretical massNumber of molelcules
Total (without water)92,5942
Polymers92,5942
Non-polymers00
Water13,890771
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-50 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.270, 113.280, 65.910
Angle α, β, γ (deg.)90.000, 114.910, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

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


Mass: 46297.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia rickettsii (bacteria) / Strain: Sheila Smith / Gene: glyA, A1G_06305 / Production host: Escherichia coli (E. coli)
References: UniProt: A8GTI9, glycine hydroxymethyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 771 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium Chloride, 0.1 M MES:NaOH pH 6.5, 10% (w/v) PEG 4000, 22.4 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.28357 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28357 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 82323 / Num. obs: 81184 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.198 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 25.37
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.740.25.42186645893197.4
1.74-1.790.1846.8218915911199.7
1.79-1.840.1478.4213175748199.8
1.84-1.90.148.82203245464198.3
1.9-1.960.08516.2180395193195.9
1.96-2.030.07216.26194645205199.5
2.03-2.110.05919.44189475067199.7
2.11-2.190.05221.94181374835199.6
2.19-2.290.04528.38153494542196.5
2.29-2.40.0427.48166044414199.5
2.4-2.530.03630.66160484269199.5
2.53-2.690.03233.82150263996199.6
2.69-2.870.02938.09141333759199.3
2.87-3.10.02543.7131493507199.5
3.1-3.40.02348.31119473210199.3
3.4-3.80.02351.18105172917198.4
3.8-4.390.02154.4492002578198.9
4.39-5.380.01955.9682192171199.2
5.38-7.60.0254.365221720199.2
7.6-500.01857.552700785181.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1255refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ECD

3ecd


Resolution: 1.7→19.625 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8713 / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 4057 5 %
Rwork0.176 --
obs0.1779 81155 98.89 %
all-82323 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.53 Å2 / Biso mean: 19.8207 Å2 / Biso min: 7.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6448 0 0 771 7219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066701
X-RAY DIFFRACTIONf_angle_d1.1459134
X-RAY DIFFRACTIONf_chiral_restr0.0761030
X-RAY DIFFRACTIONf_plane_restr0.0061202
X-RAY DIFFRACTIONf_dihedral_angle_d14.0332458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.720.23831300.18782533266396
1.72-1.74090.19181200.17312706282699
1.7409-1.7630.24021480.17626332781100
1.763-1.78610.25481360.175426852821100
1.7861-1.81060.23771540.17226912845100
1.8106-1.83640.24341380.17426772815100
1.8364-1.86380.22131300.186626622792100
1.8638-1.89290.29611330.23192684281798
1.8929-1.92390.54731280.39512562269096
1.9239-1.95710.3231520.25352560271295
1.9571-1.99260.24481440.187626622806100
1.9926-2.03090.18351320.160926572789100
2.0309-2.07230.21611640.164126992863100
2.0723-2.11730.2251430.154426592802100
2.1173-2.16650.22211340.168826732807100
2.1665-2.22070.19261310.18052681281299
2.2207-2.28060.39851130.32772579269296
2.2806-2.34760.21611390.17792695283499
2.3476-2.42330.20631570.165226352792100
2.4233-2.50970.19451520.16126672819100
2.5097-2.610.18761500.16926492799100
2.61-2.72840.22151360.167427112847100
2.7284-2.87190.20791530.164126892842100
2.8719-3.05120.2021370.164126732810100
3.0512-3.28580.18981620.159826752837100
3.2858-3.61460.15631340.145226922826100
3.6146-4.13340.15561410.14142682282398
4.1334-5.19160.16141270.12522694282199
5.1916-19.6250.1561390.14222633277296
Refinement TLS params.Method: refined / Origin x: 1.1982 Å / Origin y: 13.8831 Å / Origin z: 15.3186 Å
111213212223313233
T0.0678 Å20.0012 Å2-0.0042 Å2-0.0942 Å20.033 Å2--0.099 Å2
L0.3688 °20.0993 °2-0.0308 °2-0.653 °2-0.0199 °2--0.4671 °2
S-0.0069 Å °0.0082 Å °-0.0082 Å °0.0033 Å °0.0357 Å °0.0507 Å °0.0089 Å °-0.0255 Å °-0.0228 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:420 ) OR ( CHAIN B AND RESID 1:420 )A1 - 420
2X-RAY DIFFRACTION1( CHAIN A AND RESID 1:420 ) OR ( CHAIN B AND RESID 1:420 )B1 - 420

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