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- PDB-9cg8: CRYSTAL STRUCTURE OF THE P285S VARIANT OF SERINE HYDROXYMETHYLTRA... -

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Basic information

Entry
Database: PDB / ID: 9cg8
TitleCRYSTAL STRUCTURE OF THE P285S VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / enzyme / missense variant
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / chloroplast / methyltransferase activity / pyridoxal phosphate binding / methylation
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBeamer, L.J. / Samarakoon, V. / Owuocha, L.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 2152548 United States
CitationJournal: Biochem.J. / Year: 2024
Title: Key structural role of a conserved cis-proline revealed by the P285S variant of soybean serine hydroxymethyltransferase 8.
Authors: Samarakoon, V. / Owuocha, L.F. / Hammond, J. / Mitchum, M.G. / Beamer, L.J.
History
DepositionJun 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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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
E: Serine hydroxymethyltransferase
F: Serine hydroxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)326,8126
Polymers326,8126
Non-polymers00
Water15,583865
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase

C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)217,8744
Polymers217,8744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,x+1,-z1
2
E: Serine hydroxymethyltransferase

F: Serine hydroxymethyltransferase

E: Serine hydroxymethyltransferase

F: Serine hydroxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)217,8744
Polymers217,8744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+y,-x,z-1/31
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)174.175, 174.175, 183.658
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein
Serine hydroxymethyltransferase


Mass: 54468.586 Da / Num. of mol.: 6 / Mutation: P285S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: SHMT / Production host: Escherichia coli (E. coli)
References: UniProt: K4FW35, glycine hydroxymethyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2 % v/v tacsimate 0.1 M Hepes, pH 7.5 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.5 Å / Num. obs: 251510 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 30.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.045 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.5 % / Rmerge(I) obs: 2.561 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 12415 / CC1/2: 0.568 / Rpim(I) all: 0.946 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.5 Å / SU ML: 0.3206 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 33.3289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 12634 5.04 %
Rwork0.2271 238184 -
obs0.2291 250818 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20464 0 0 865 21329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007621004
X-RAY DIFFRACTIONf_angle_d0.988828545
X-RAY DIFFRACTIONf_chiral_restr0.05443129
X-RAY DIFFRACTIONf_plane_restr0.00923740
X-RAY DIFFRACTIONf_dihedral_angle_d8.72183012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.59153860.56297837X-RAY DIFFRACTION98.89
1.92-1.940.41334400.39647864X-RAY DIFFRACTION99.98
1.94-1.970.38364570.36497834X-RAY DIFFRACTION100
1.97-1.990.37114600.35557937X-RAY DIFFRACTION100
1.99-2.020.38894400.33747861X-RAY DIFFRACTION100
2.02-2.050.37824070.35237894X-RAY DIFFRACTION99.93
2.05-2.080.43364220.38887929X-RAY DIFFRACTION99.81
2.08-2.110.35964100.30347887X-RAY DIFFRACTION99.96
2.11-2.140.34424200.28367925X-RAY DIFFRACTION99.94
2.14-2.170.32244100.28337922X-RAY DIFFRACTION99.98
2.17-2.210.35624360.2957888X-RAY DIFFRACTION99.98
2.21-2.250.47124070.43097540X-RAY DIFFRACTION95.3
2.25-2.30.3074270.2657955X-RAY DIFFRACTION100
2.3-2.340.28854310.24177890X-RAY DIFFRACTION99.98
2.34-2.390.27563710.22827962X-RAY DIFFRACTION99.99
2.39-2.450.2733950.22497982X-RAY DIFFRACTION99.89
2.45-2.510.29433770.22157944X-RAY DIFFRACTION99.86
2.51-2.580.2643810.22657981X-RAY DIFFRACTION99.89
2.58-2.650.28834130.22657957X-RAY DIFFRACTION99.9
2.65-2.740.27324260.22657977X-RAY DIFFRACTION99.94
2.74-2.840.28044340.22327869X-RAY DIFFRACTION99.92
2.84-2.950.26224450.21957964X-RAY DIFFRACTION99.95
2.95-3.090.26464640.22487933X-RAY DIFFRACTION99.95
3.09-3.250.24174350.22297949X-RAY DIFFRACTION99.89
3.25-3.450.27944050.2198012X-RAY DIFFRACTION99.77
3.45-3.720.23113930.19878050X-RAY DIFFRACTION99.8
3.72-4.090.20654470.18427962X-RAY DIFFRACTION99.56
4.09-4.680.19284390.16218039X-RAY DIFFRACTION99.98
4.68-5.90.23034350.1828128X-RAY DIFFRACTION99.96
5.9-48.50.20494210.17758312X-RAY DIFFRACTION99.35

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