[English] 日本語
Yorodumi
- PDB-1bko: THERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bko
TitleTHERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS
ComponentsTHYMIDYLATE SYNTHASE A
KeywordsMETHYLTRANSFERASE / DTMP SYNTHASE
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol / cytoplasm
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Thymidylate synthase 1 / Thymidylate synthase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR/molecular replacement / Resolution: 2.75 Å
AuthorsStout, T.J. / Schellenberger, U. / Santi, D.V. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structures of a unique thermal-stable thymidylate synthase from Bacillus subtilis.
Authors: Stout, T.J. / Schellenberger, U. / Santi, D.V. / Stroud, R.M.
#1: Journal: Protein Sci. / Year: 1994
Title: Expression, Purification, and Characterization of Thymidylate Synthase from Lactococcus Lactis
Authors: Greene, P.J. / Yu, P.L. / Zhao, J. / Schiffer, C.A. / Santi, D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Two Thymidylate Synthetases in Bacillus Subtilis
Authors: Neuhard, J. / Price, A.R. / Schack, L. / Thomassen, E.
History
DepositionJul 9, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: 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: THYMIDYLATE SYNTHASE A
B: THYMIDYLATE SYNTHASE A
C: THYMIDYLATE SYNTHASE A
D: THYMIDYLATE SYNTHASE A


Theoretical massNumber of molelcules
Total (without water)130,8684
Polymers130,8684
Non-polymers00
Water63135
1
A: THYMIDYLATE SYNTHASE A
B: THYMIDYLATE SYNTHASE A


Theoretical massNumber of molelcules
Total (without water)65,4342
Polymers65,4342
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-6 kcal/mol
Surface area23420 Å2
MethodPISA
2
C: THYMIDYLATE SYNTHASE A
D: THYMIDYLATE SYNTHASE A


Theoretical massNumber of molelcules
Total (without water)65,4342
Polymers65,4342
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-5 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.363, 52.828, 129.391
Angle α, β, γ (deg.)90.00, 101.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999732, -0.022933, -0.003207), (-0.021468, 0.969811, -0.242913), (0.008681, -0.242779, -0.970043)40.6928, 8.4761, 64.9447
2given(-0.920918, 0.038337, 0.387866), (-0.031905, -0.999226, 0.023011), (0.388448, 0.008817, 0.921429)9.09847, 45.70549, 57.77644
3given(0.925561, -0.045288, -0.375881), (0.051774, -0.968352, 0.24416), (-0.375043, -0.245446, -0.893924)-3.19579, 36.84923, 133.2341

-
Components

#1: Protein
THYMIDYLATE SYNTHASE A


Mass: 32716.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: X2913 / Gene: THYA / Plasmid: PTRC-THYA / Cell line (production host): X2913 / Gene (production host): THYA / Production host: Escherichia coli (E. coli)
References: UniProt: P42326, UniProt: P0CI79*PLUS, thymidylate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.75 Å3/Da / Density % sol: 51.3 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mM1reservoirKPO4

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 31528 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.086 / Net I/σ(I): 8.4
Reflection shellResolution: 2.75→2.83 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.315 / % possible all: 81.8
Reflection
*PLUS
Num. measured all: 80025
Reflection shell
*PLUS
% possible obs: 81.8 %

-
Processing

Software
NameVersionClassification
AMoREphasing
DMmodel building
MLPHAREphasing
X-PLORmodel building
X-PLOR3.854refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
X-PLORphasing
RefinementMethod to determine structure: MIR/molecular replacement
Starting model: HOMOLOGY MODEL BASED ON 1TJS

1tjs


Resolution: 2.75→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.32 2743 10.4 %SHELLS
Rwork0.213 ---
obs0.213 26480 76.1 %-
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-8 Å
Luzzati sigma a0.65 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9204 0 0 35 9239
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.241.5
X-RAY DIFFRACTIONx_mcangle_it4.882
X-RAY DIFFRACTIONx_scbond_it4.822
X-RAY DIFFRACTIONx_scangle_it6.632.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 197 6.5 %
Rwork0.271 2833 -
obs--52.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.854 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor obs: 0.271

+
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