[English] 日本語
Yorodumi
- PDB-4a5b: Crystal structure of the C258S/C268S variant of Toxoplasma gondii... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a5b
TitleCrystal structure of the C258S/C268S variant of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 1 (NTPDase1)
ComponentsNUCLEOSIDE-TRIPHOSPHATASE 2
KeywordsHYDROLASE / NTPDASE
Function / homology
Function and homology information


symbiont-containing vacuole / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase
Similarity search - Function
Nucleotidyltransferase; domain 5 - #530 / Nucleotidyltransferase; domain 5 - #540 / Nucleoside-triphosphatase, alveolata / GDA1/CD39 family of nucleoside phosphatases signature. / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside-triphosphatase 2
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsKrug, U. / Zebisch, M. / Strater, N.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Insight Into Activation Mechanism of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolases by Disulfide Reduction.
Authors: Krug, U. / Zebisch, M. / Krauss, M. / Strater, N.
History
DepositionOct 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Dec 25, 2013Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NUCLEOSIDE-TRIPHOSPHATASE 2
B: NUCLEOSIDE-TRIPHOSPHATASE 2


Theoretical massNumber of molelcules
Total (without water)136,0882
Polymers136,0882
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-14 kcal/mol
Surface area51340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.730, 150.400, 242.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein NUCLEOSIDE-TRIPHOSPHATASE 2 / / NTPASE-II / NUCLEOSIDE TRIPHOSPHATE HYDROLASE 2 / NUCLEOSIDE-TRIPHOSPHATASE II


Mass: 68044.078 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q27895, apyrase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 268 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 268 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 268 TO SER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.23 % / Description: NONE
Crystal growpH: 8.2
Details: 100 MM TRIS PH 8.2, 50 MM MGCL2, 25% PENTAERYTHRITOL ETHOXYLATE (17/8 PO/OH), 2 MM AMPPNP AND 10 MM MAGNESIUM ACETATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→39.34 Å / Num. obs: 47598 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Biso Wilson estimate: 46.45 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 3 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→39.22 Å / Cor.coef. Fo:Fc: 0.9346 / Cor.coef. Fo:Fc free: 0.8918 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 972 2.04 %RANDOM
Rwork0.1757 ---
obs0.1767 47551 --
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.2942 Å20 Å20 Å2
2---0.3569 Å20 Å2
3---0.0628 Å2
Refine analyzeLuzzati coordinate error obs: 0.287 Å
Refinement stepCycle: LAST / Resolution: 2.48→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9249 0 0 247 9496
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019444HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1912793HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3333SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes252HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1369HARMONIC5
X-RAY DIFFRACTIONt_it9444HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion18.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1219SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10568SEMIHARMONIC4
LS refinement shellResolution: 2.48→2.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3306 64 2.19 %
Rwork0.2092 2859 -
all0.212 2923 -
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)
10.00991.2241.57015.9697-2.91041.2144-0.00460.1117-0.1220.0269-0.03490.0281-0.0282-0.03440.0395-0.3040.02270.06940.304-0.0862-0.0773-7.2407-27.4487-92.5775
20.93670.11-0.28450.4929-0.2652.3169-0.0332-0.0353-0.1232-0.0228-0.0111-0.01660.19710.07410.0443-0.085-0.01770.0281-0.06030.0039-0.0372-12.4154-27.7191-45.3689
30.4612-0.26852.44980.013-0.044500.0121-0.0855-0.00110.02110.02760.077-0.13740.0694-0.0397-0.0202-0.00010.06890.02990.0040.0116-23.27180.5817-61.8492
41.16680.318-0.23120.8401-0.1460.85620.056-0.08340.02930.08840.01140.1447-0.0299-0.1286-0.0674-0.0954-0.00020.0314-0.037-0.0139-0.0521-36.0775-19.5865-32.1648
51.956-1.4824-1.41571.0168-1.55840.63730.0346-0.1957-0.05170.2073-0.16740.1048-0.0653-0.21260.13280.0157-0.03840.02310.0134-0.0211-0.0572-19.2774-17.9645-14.3493
61.507-2.7051.13780.00021.47420.0989-0.0302-0.0140.00950.0579-0.03630.0583-0.14150.16290.0666-0.1172-0.0611-0.04650.26620.0211-0.161328.728814.0215-73.4326
71.161-0.2356-0.26370.6747-0.05330.89080.04330.05370.1108-0.0245-0.0269-0.0143-0.18280.0118-0.0165-0.0118-0.01810.023-0.07-0.0117-0.0462-4.843414.494-41.5741
80.06740.76330.05810.01280.57351.4732-0.0243-0.0482-0.11320.03090.0173-0.0402-0.0806-0.01220.0071-0.12450.03940.00190.03980.03610.089614.7844-13.5441-43.0478
90.5103-0.2288-0.02670.80040.15381.7935-0.0606-0.19940.09370.21790.0987-0.1475-0.2590.3121-0.0381-0.0379-0.05270.0067-0.04-0.0276-0.1357-0.71376.8083-14.5725
100.5508-1.8535-2.66671.614-0.42062.26790.0387-0.0539-0.04420.2122-0.04960.0779-0.0823-0.19120.01090.0685-0.03670.0818-0.035-0.044-0.0713-25.39614.8526-17.3686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 35 :58
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 59:256, 586:629
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 257 :268
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 269:394, 425:585
5X-RAY DIFFRACTION5CHAIN A AND RESSEQ 395 :424
6X-RAY DIFFRACTION6CHAIN B AND RESSEQ 37 :58
7X-RAY DIFFRACTION7CHAIN B AND RESSEQ 59:256, 586:629
8X-RAY DIFFRACTION8CHAIN B AND RESSEQ 257 :268
9X-RAY DIFFRACTION9CHAIN B AND RESSEQ 269:394, 425:585
10X-RAY DIFFRACTION10CHAIN B AND RESSEQ 395 :424

+
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