[English] 日本語
Yorodumi
- PDB-4oyt: Crystal structure of ternary complex of Plasmodium vivax SHMT wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oyt
TitleCrystal structure of ternary complex of Plasmodium vivax SHMT with D-serine and folinic acid
ComponentsSerine hydroxymethyltransferase, putative
KeywordsTRANSFERASE / alpha and beta protein / methyltransferase activity
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding / mitochondrion
Similarity search - Function
: / 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 ...: / 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-1W9 / TRIFLUOROETHANOL / Chem-FON / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U.
Funding support Thailand, 5items
OrganizationGrant numberCountry
Cluster Program and Management Office, National Science and Technology development AgencyCPMO-P-00-20029 Thailand
the Cluster Program and Management Office for Discovery based Development GrantCPMO-DD/P-10-11274 Thailand
Synchron Light Research Institute-Public Organization2-2549/LS01 Thailand
Synchron Light Research Institute-Public Organization2551/08 Thailand
The Thailand Research FundRTA5680001 Thailand
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control.
Authors: Chitnumsub, P. / Jaruwat, A. / Riangrungroj, P. / Ittarat, W. / Noytanom, K. / Oonanant, W. / Vanichthanankul, J. / Chuankhayan, P. / Maenpuen, S. / Chen, C.J. / Chaiyen, P. / Yuthavong, Y. ...Authors: Chitnumsub, P. / Jaruwat, A. / Riangrungroj, P. / Ittarat, W. / Noytanom, K. / Oonanant, W. / Vanichthanankul, J. / Chuankhayan, P. / Maenpuen, S. / Chen, C.J. / Chaiyen, P. / Yuthavong, Y. / Leartsakulpanich, U.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly_auth_evidence ...entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine hydroxymethyltransferase, putative
B: Serine hydroxymethyltransferase, putative
C: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,66914
Polymers147,7473
Non-polymers2,92111
Water4,828268
1
A: Serine hydroxymethyltransferase, putative
B: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3909
Polymers98,4982
Non-polymers1,8927
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-46 kcal/mol
Surface area29480 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase, putative
hetero molecules

C: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,55810
Polymers98,4982
Non-polymers2,0608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12150 Å2
ΔGint-29 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.619, 58.115, 236.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121
Detailsgel filtration

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Serine hydroxymethyltransferase, putative


Mass: 49249.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: D-serine and folinic acid at the pockets
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: Salvador I / Gene: PVX_100730 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K8L9

-
Non-polymers , 6 types, 279 molecules

#2: Chemical ChemComp-1W9 / (2R)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-oxidanyl-propanoic acid


Mass: 334.219 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N2O8P
#3: Chemical ChemComp-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H23N7O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-ETF / TRIFLUOROETHANOL


Mass: 100.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3F3O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 8.5
Details: PEG4000, 0.06-0.12 M sodium chloride, 0.1 M Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 51056 / % possible obs: 94.6 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.047 / Χ2: 1.426 / Net I/av σ(I): 20.384 / Net I/σ(I): 30.3 / Num. measured all: 126391
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.491.80.17245061.02584.9
2.49-2.592.10.15847981.07689.4
2.59-2.72.20.13649621.30693
2.7-2.852.40.09952101.38997.1
2.85-3.022.50.08252891.47298.1
3.02-3.262.70.0652881.53997.7
3.26-3.582.80.0552451.73197.6
3.58-4.12.70.04252441.57697
4.1-5.162.70.03951691.48594.9
5.16-302.80.03453451.24995.8

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data collection
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O6Z

4o6z


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.919 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.045 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 2518 10.1 %RANDOM
Rwork0.1996 45907 --
obs0.2049 51056 93.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 103.69 Å2 / Biso mean: 43.375 Å2 / Biso min: 21.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20.18 Å2
2--2.54 Å20 Å2
3----4.79 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 178 268 10820
Biso mean--51.38 38.54 -
Num. residues----1327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0210764
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.97914542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79951323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14825.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.772151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0981548
X-RAY DIFFRACTIONr_chiral_restr0.090.21616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218076
LS refinement shellResolution: 2.395→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 293 -
Rwork0.267 2644 -
all-2937 -
obs--75.27 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more