[English] 日本語
Yorodumi
- PDB-4gtl: T. Maritima FDTS (R174K mutant) with FAD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gtl
TitleT. Maritima FDTS (R174K mutant) with FAD
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / Flavin-dependent thymidylate synthase / TM0449 / R174K mutant / FAD
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Gyrase A; domain 2 - #170 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.17 Å
AuthorsMathews, I.I. / Lesley, S.A. / Kohen, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Folate binding site of flavin-dependent thymidylate synthase.
Authors: Koehn, E.M. / Perissinotti, L.L. / Moghram, S. / Prabhakar, A. / Lesley, S.A. / Mathews, I.I. / Kohen, A.
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymidylate synthase thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2597
Polymers109,9034
Non-polymers2,3573
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18650 Å2
ΔGint-74 kcal/mol
Surface area34750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.780, 116.460, 141.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.954869, 0.249323, -0.161442), (0.275402, 0.53956, -0.795631), (-0.111262, -0.804185, -0.583873)73.53217, 101.43067, 220.42747
3given(0.955421, -0.257005, 0.145325), (-0.254488, -0.966406, -0.035977), (0.149689, -0.002611, -0.98873)-4.36265, 98.12175, 223.04779
4given(-0.999957, -0.007056, -0.006025), (-0.000849, -0.577084, 0.816684), (-0.009239, 0.816654, 0.577053)68.72907, -25.09503, 13.48981

-
Components

#1: Protein
Thymidylate synthase thyX / TS / TSase


Mass: 27475.666 Da / Num. of mol.: 4 / Mutation: R174K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: thyX, thy1, TM_0449 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT0, thymidylate synthase (FAD)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50-60% PEG 200 and 100mM Tris HCL (pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.17→40 Å / Num. all: 47764 / Num. obs: 47764 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.1
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1O26

1o26


Resolution: 2.17→38.05 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 15.526 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24073 2415 5.1 %RANDOM
Rwork0.18939 ---
obs0.19198 45284 99.79 %-
all-45284 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.402 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å20 Å20 Å2
2---1.07 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.17→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7218 0 141 81 7440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197581
X-RAY DIFFRACTIONr_bond_other_d0.0010.025269
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.96910277
X-RAY DIFFRACTIONr_angle_other_deg0.966312691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4735854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58422.593378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.664151306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.841564
X-RAY DIFFRACTIONr_chiral_restr0.0990.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021722
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 165 -
Rwork0.296 3050 -
obs--99.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.18981.5231.06973.40192.66167.0034-0.21460.37480.0523-0.77760.2475-0.1024-1.28520.4773-0.03290.33630.004-0.00240.21630.01930.143530.005264.277108.9674
21.32990.002-0.31042.39591.19934.506-0.0480.0973-0.0429-0.279-0.02410.05450.0083-0.34230.07210.0937-0.00940.01730.09620.01150.165326.4555.7971112.5779
30.7050.07490.89581.26240.75385.1984-0.0022-0.10380.04720.0433-0.05210.0343-0.237-0.34590.05430.1363-0.00790.01820.09370.00460.15727.46362.2837129.6837
40.73190.3560.94763.65592.74856.6629-0.0531-0.06870.255-0.6577-0.0211-0.1704-1.027-0.01340.07420.2028-0.03940.05940.1657-0.01150.253843.460557.5197101.3652
51.55440.63330.65262.49761.5383.0272-0.00420.0505-0.0376-0.19110.1013-0.30610.07420.2281-0.09710.1335-0.01260.07210.11960.04260.176943.747343.222296.121
60.5085-0.5965-0.91763.84842.22276.0642-0.0784-0.1896-0.10560.6930.02320.10261.3273-0.14340.05520.3505-0.1025-0.0140.14450.0090.186224.433624.6824118.5575
72.1339-0.3619-1.52212.27261.4994.91450.0942-0.0647-0.0408-0.0014-0.0374-0.0041-0.1781-0.2027-0.05690.015-0.0093-0.02750.08720.0440.160723.426133.1413115.654
81.0455-0.0043-1.01591.44350.83614.52130.00970.1353-0.0868-0.2531-0.01750.04680.1574-0.38450.00770.0828-0.0159-0.02490.08420.00570.196224.43726.851998.2894
91.02030.0823-0.98925.05933.036.4335-0.1030.0444-0.32720.8328-0.11180.09381.3509-0.02440.21480.31150.0081-0.00060.12940.04180.217137.959427.4533128
100.8161-0.4428-0.44073.44752.16593.44180.0142-0.0892-0.08720.27920.1535-0.25430.09020.2734-0.16760.034-0.0215-0.04980.16590.06960.149940.475441.4739134.0475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 33
2X-RAY DIFFRACTION2A37 - 88
3X-RAY DIFFRACTION3A90 - 217
4X-RAY DIFFRACTION4B0 - 31
5X-RAY DIFFRACTION5B37 - 219
6X-RAY DIFFRACTION6C0 - 32
7X-RAY DIFFRACTION7C36 - 88
8X-RAY DIFFRACTION8C94 - 220
9X-RAY DIFFRACTION9D0 - 32
10X-RAY DIFFRACTION10D36 - 218

+
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://pdbjlvh1.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