[English] 日本語
Yorodumi
- PDB-1kq4: CRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kq4
TitleCRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTION
ComponentsHYPOTHETICAL PROTEIN TM0449
KeywordsTRANSFERASE / THY1-COMPLEMENTING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
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 / MAD / Resolution: 2.25 Å
AuthorsWilson, I.A. / Miller, M.D. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
Authors: Lesley, S.A. / Kuhn, P. / Godzik, A. / Deacon, A.M. / Mathews, I. / Kreusch, A. / Spraggon, G. / Klock, H.E. / McMullan, D. / Shin, T. / Vincent, J. / Robb, A. / Brinen, L.S. / Miller, M.D. ...Authors: Lesley, S.A. / Kuhn, P. / Godzik, A. / Deacon, A.M. / Mathews, I. / Kreusch, A. / Spraggon, G. / Klock, H.E. / McMullan, D. / Shin, T. / Vincent, J. / Robb, A. / Brinen, L.S. / Miller, M.D. / McPhillips, T.M. / Miller, M.A. / Scheibe, D. / Canaves, J.M. / Guda, C. / Jaroszewski, L. / Selby, T.L. / Elsliger, M.-A. / Wooley, J. / Taylor, S.S. / Hodgson, K.O. / Wilson, I.A. / Schultz, P.G. / Stevens, R.C.
History
DepositionJan 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN TM0449
B: HYPOTHETICAL PROTEIN TM0449
C: HYPOTHETICAL PROTEIN TM0449
D: HYPOTHETICAL PROTEIN TM0449
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2828
Polymers111,1404
Non-polymers3,1424
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20050 Å2
ΔGint-74 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.200, 116.610, 141.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homotetramer. The coordinates represent the asymmetric unit.

-
Components

#1: Protein
HYPOTHETICAL PROTEIN TM0449


Mass: 27785.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0449 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WYT0
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 50% (v/v)PEG-200, 0.1M HEPES pH7.5, final pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 30, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 43752 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.061 / Net I/σ(I): 10.6
Reflection shellResolution: 2.25→2.27 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 3.4 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→20 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4409 10 %RANDOM
Rwork0.192 ---
obs0.192 43369 99 %-
all-43450 --
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--9.296 Å20 Å20 Å2
2--3.164 Å20 Å2
3---6.132 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6981 0 212 274 7467
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3981.5
X-RAY DIFFRACTIONc_mcangle_it2.2282
X-RAY DIFFRACTIONc_scbond_it2.3792
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 2.25→2.27 Å /
RfactorNum. reflection
Rfree0.24 77
Rwork0.207 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2FAD.PAR
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2

+
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