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- PDB-2dkj: Crystal Structure of T.th.HB8 Serine Hydroxymethyltransferase -

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Basic information

Entry
Database: PDB / ID: 2dkj
TitleCrystal Structure of T.th.HB8 Serine Hydroxymethyltransferase
Componentsserine hydroxymethyltransferase
KeywordsTRANSFERASE / PLP dependent enzyme / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
PYRIDOXAL-5'-PHOSPHATE / : / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsKai, K. / Goto, M. / Miyahara, I. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of T.th.HB8 Serine Hydroxymethyltransferase
Authors: Goto, M. / Kai, K. / Miyahara, I. / Hirotsu, K.
History
DepositionApr 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0476
Polymers89,3602
Non-polymers6864
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-83 kcal/mol
Surface area25290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.988, 82.884, 94.074
Angle α, β, γ (deg.)90.00, 91.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein serine hydroxymethyltransferase /


Mass: 44680.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 55772906, UniProt: Q5SI56*PLUS, glycine hydroxymethyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.8M lithium sulfate, 0.4M ammonium sulfate, 0.1M sodium citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.75 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.15→53.5 Å / Num. all: 302432 / Num. obs: 302432 / % possible obs: 95.8 % / Biso Wilson estimate: 6.6 Å2
Reflection shellResolution: 1.15→1.19 Å / % possible all: 90.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KKJ

1kkj


Resolution: 1.15→42 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 1624501.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.19 29947 10 %RANDOM
Rwork0.18 ---
obs0.18 299961 95.2 %-
all-302432 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3395 Å2 / ksol: 0.398493 e/Å3
Displacement parametersBiso mean: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0.13 Å2
2---0.04 Å20 Å2
3---0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.15→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 40 896 7077
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it0.731.5
X-RAY DIFFRACTIONc_mcangle_it1.072
X-RAY DIFFRACTIONc_scbond_it14.032
X-RAY DIFFRACTIONc_scangle_it6.32.5
LS refinement shellResolution: 1.15→1.22 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.227 4712 10 %
Rwork0.216 42479 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramtop.wat
X-RAY DIFFRACTION3so4.parso4.top
X-RAY DIFFRACTION4param.plptop.plp
X-RAY DIFFRACTION5param.etcintshiff.top

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