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- PDB-1kkj: Crystal Structure of Serine Hydroxymethyltransferase from B.stear... -

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Basic information

Entry
Database: PDB / ID: 1kkj
TitleCrystal Structure of Serine Hydroxymethyltransferase from B.stearothermophilus
ComponentsSerine Hydroxymethyltransferase
KeywordsTRANSFERASE / SHMT PLP tetrahydrofolate
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion 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) / 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
PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsTrivedi, V. / Gupta, A. / Jala, V.R. / Saravanan, P. / Rao, G.S.J. / Rao, N.A. / Savithri, H.S. / Subramanya, H.S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism.
Authors: Trivedi, V. / Gupta, A. / Jala, V.R. / Saravanan, P. / Rao, G.S. / Rao, N.A. / Savithri, H.S. / Subramanya, H.S.
History
DepositionDec 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING. ...SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING. ALSO, RESIDUES 403-419 ARE CLONING ARTIFACTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine Hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9592
Polymers45,7121
Non-polymers2471
Water4,071226
1
A: Serine Hydroxymethyltransferase
hetero molecules

A: Serine Hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9184
Polymers91,4232
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8560 Å2
ΔGint-45 kcal/mol
Surface area27020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.154, 106.637, 56.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Serine Hydroxymethyltransferase / SERINE METHYLASE / SHMT


Mass: 45711.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pRSETC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7SIB6, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMHEPES1droppH7.5
20.2 mMEDTA1drop
35 mM2-mercaptoethanol1drop
4100 mM1dropNaCl
515 mg/mlprotein1drop
6100 mMHEPES1reservoirpH7.5
70.2 mMEDTA1reservoir
85 mM2-mercaptoethanol1reservoir
950 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 4, 2001 / Details: mirrors
RadiationMonochromator: mar mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→15 Å / Num. all: 27767 / Num. obs: 27746 / % possible obs: 97 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 2.47 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 21.8
Reflection shellResolution: 1.93→2 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.031 / Mean I/σ(I) obs: 21.8 / Num. unique all: 2530 / % possible all: 90.3
Reflection
*PLUS
% possible obs: 97 % / Num. measured all: 68643 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
Rmerge(I) obs: 0.031

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DFO

1dfo


Resolution: 1.93→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1397 -RANDOM
Rwork0.178 ---
all-27609 --
obs-27609 97 %-
Refinement stepCycle: LAST / Resolution: 1.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 15 226 3357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.026
X-RAY DIFFRACTIONp_planar_d0.057
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.2034 / Rfactor Rwork: 0.1786
Solvent computation
*PLUS
Displacement parameters
*PLUS

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