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- PDB-1rvy: E75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, ... -

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Basic information

Entry
Database: PDB / ID: 1rvy
TitleE75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE
ComponentsSerine hydroxymethyltransferase, cytosolic
KeywordsHYDROLASE / ONE CARBON METABOLISM
Function / homology
Function and homology information


cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process ...cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleoplasm / 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
Chem-PLG / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Rigid body refinement of unliganded E75Q rcSHMT structure / Resolution: 2.9 Å
AuthorsSzebenyi, D.M. / Musayev, F.N. / Di Salvo, M.L. / Safo, M.K. / Schirch, V.
CitationJournal: Biochemistry / Year: 2004
Title: Serine Hydroxymethyltransferase: Role of Glu75 and Evidence that Serine Is Cleaved by a Retroaldol Mechanism.
Authors: Szebenyi, D.M. / Musayev, F.N. / Di Salvo, M.L. / Safo, M.K. / Schirch, V.
History
DepositionDec 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Sep 21, 2016Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,4795
Polymers105,8302
Non-polymers6483
Water1,838102
1
A: Serine hydroxymethyltransferase, cytosolic
B: Serine hydroxymethyltransferase, cytosolic
hetero molecules

A: Serine hydroxymethyltransferase, cytosolic
B: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,95710
Polymers211,6614
Non-polymers1,2976
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)114.700, 114.700, 156.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe asymmetric unit contains a homodimer. The biological assembly is a tetramer consisting of a pair of dimers. The second dimer in the tetramer is generated by the operation: y,x,1-z.

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Components

#1: Protein Serine hydroxymethyltransferase, cytosolic / Serine methylase / Glycine hydroxymethyltransferase / SHMT


Mass: 52915.129 Da / Num. of mol.: 2 / Mutation: E75Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SHMT1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli)
References: UniProt: P07511, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O7P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 4000, KCl, KMES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 3, 2003 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→27.2 Å / Num. all: 22342 / Num. obs: 22342 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.188 / Net I/σ(I): 3.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 3388 / Rsym value: 0.626 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DPSdata reduction
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNS1.1phasing
RefinementMethod to determine structure: Rigid body refinement of unliganded E75Q rcSHMT structure
Starting model: PDB entry 1RVU

1rvu


Resolution: 2.9→27.16 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 4024355.57 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Solvent molecules carried over from (higher resolution) unliganded structure
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1242 5.6 %RANDOM
Rwork0.22 ---
all0.224 22026 --
obs0.224 22026 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.6844 Å2 / ksol: 0.26216 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.51 Å20 Å20 Å2
2---5.51 Å20 Å2
3---11.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.9→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7186 0 40 102 7328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 199 5.1 %
Rwork0.288 3679 -
obs-3679 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLS2.PARAMPLS.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP

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