[English] 日本語
Yorodumi
- PDB-4a59: Crystal structure of Toxoplasma gondii nucleoside triphosphate di... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a59
TitleCrystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) in complex with AMP
ComponentsNUCLEOSIDE-TRIPHOSPHATASE 1
KeywordsHYDROLASE / NTPDASE
Function / homology
Function and homology information


symbiont-containing vacuole / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / membrane
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
ADENOSINE MONOPHOSPHATE / Nucleoside-triphosphatase 1
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKrug, U. / Zebisch, M. / Straeter, N.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Insight Into the Activation Mechanism of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolases by Disulfide Reduction.
Authors: Krug, U. / Zebisch, M. / Krauss, M. / Straeter, N.
History
DepositionOct 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 1.3Dec 25, 2013Group: Structure summary
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NUCLEOSIDE-TRIPHOSPHATASE 1
B: NUCLEOSIDE-TRIPHOSPHATASE 1
C: NUCLEOSIDE-TRIPHOSPHATASE 1
D: NUCLEOSIDE-TRIPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,3689
Polymers270,6324
Non-polymers1,7365
Water15,925884
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17480 Å2
ΔGint-69.1 kcal/mol
Surface area97410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.170, 166.030, 97.940
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.148347, -0.182129, 0.97202), (-0.171908, -0.963182, -0.206709), (0.973879, -0.197763, 0.111575)-25.7277, 12.32325, 22.635
2given(0.058623, 0.569961, -0.819578), (0.539846, -0.708689, -0.454231), (-0.83972, -0.415817, -0.349237)51.73873, 12.45954, 73.40094
3given(-0.934217, -0.338744, -0.11176), (-0.334881, 0.724997, 0.601858), (-0.12285, 0.599693, -0.790744)33.89645, -21.48132, 80.75194

-
Components

#1: Protein
NUCLEOSIDE-TRIPHOSPHATASE 1 / NTPDASE3 / NTPASE-I / NUCLEOSIDE TRIPHOSPHATE HYDROLASE 1 / NUCLEOSIDE-TRIPHOSPHATASE I


Mass: 67657.922 Da / Num. of mol.: 4
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: Q27893, apyrase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.52 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→43.4 Å / Num. obs: 142618 / % possible obs: 96.9 % / Observed criterion σ(I): 2.9 / Redundancy: 3 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 2 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A57

4a57


Resolution: 2.2→42.3 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9244 / 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
Rfree0.2277 1399 0.98 %RANDOM
Rwork0.1797 ---
obs0.1802 142579 --
Displacement parametersBiso mean: 41.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.617 Å20 Å22.5628 Å2
2---2.4929 Å20 Å2
3---0.8758 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18381 0 115 884 19380
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0118997HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1425764HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6732SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes520HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2768HARMONIC5
X-RAY DIFFRACTIONt_it18997HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion17.53
X-RAY DIFFRACTIONt_improper_torsion20HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion2427SEMIHARMONIC5
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_contact21623SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2965 100 0.96 %
Rwork0.2121 10366 -
all0.2129 10466 -
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)
10.2879-1.9014-1.12932.0589-3.1717-0.2879-0.0379-0.28430.1835-0.12120.06310.09680.0015-0.0845-0.0253-0.1668-0.0511-0.02830.22170.05-0.08799.173414.957982.2599
21.559-0.0170.45860.9854-0.27551.1646-0.0506-0.06440.1397-0.0315-0.0120.0501-0.1578-0.09210.0626-0.07110.0339-0.0423-0.09190.0004-0.0757-4.736226.608939.8057
30.2380.1453-0.93370.24530.2022-0.238-0.0080.0030.00290.02230.00840.0033-0.023-0.0013-0.0004-0.00640.09960.06830.00310.05560.2169-4.4828-12.372641.7553
40.7608-0.03430.11160.6941-0.0320.57510.04780.0528-0.1284-0.0359-0.0472-0.0068-0.0173-0.0302-0.0007-0.03030.015-0.0174-0.0524-0.0217-0.0614-28.485815.013326.8398
52.8149-1.4027-0.1593.6760.11371.87090.00980.0704-0.0896-0.12040.0067-0.1471-0.05960.2193-0.01650.02880.03990.00850.06050.0075-0.1018-14.306917.99979.0499
61.27782.9321-1.53150.97020.0089-0.3291-0.01250.08070.0556-0.2310.0664-0.08720.00420.2175-0.0538-0.1129-0.01230.05260.1360.0813-0.116353.18-19.796839.9815
71.4882-0.44210.80031.4796-1.43662.16950.23960.1311-0.3379-0.35770.02930.29250.54660.1591-0.2689-0.02840.0792-0.1442-0.1765-0.0201-0.111.2459-21.080119.3666
80.24760.1236-0.991100.17260.0694-0.0038-0.01040.0076-0.00970.0098-0.01560.01420.0075-0.0060.0792-0.05190.07790.0562-0.0167-0.040719.398916.484827.1843
91.35120.39990.19091.0240.15121.7208-0.10460.1161-0.1214-0.0620.1086-0.01810.07440.0481-0.004-0.10680.02580.0104-0.14180.0038-0.04624.2139-3.6908-2.4612
102.3366-0.0878-1.82702.8744-0.49510.0044-0.070.12990.0434-0.01790.00660.0595-0.05840.01350.08040.13650.1602-0.05490.13290.0542-17.4673-5.25427.3708
112.0972-2.584-1.05470.8114-2.7841-0.2947-0.0307-0.08620.0640.05180.0417-0.05010.1249-0.0034-0.0109-0.1427-0.0934-0.18950.01970.14150.1175-6.7694-28.953631.5894
121.3234-0.25350.01260.7315-0.0641.14840.06530.0783-0.0688-0.0221-0.02260.03580.03780.0124-0.0427-0.03470.0063-0.0277-0.11230.0177-0.042532.4243-28.324351.7532
130.19011.0346-0.74570.57050.5283-0.19010.0139-0.0034-0.023-0.0138-0.00120.0079-0.04810.0329-0.01260.0164-0.00920.091-0.06180.10830.19099.9485-0.468868.1333
140.94170.0740.30370.8301-0.08280.97220.0373-0.04960.00270.2433-0.0223-0.0793-0.1032-0.0184-0.0150.0252-0.0593-0.0285-0.1185-0.0111-0.102635.8562-28.251380.2791
152.9449-1.4546-2.41951.39121.85370.1440.05620.19860.2517-0.05090.0795-0.0893-0.0961-0.0459-0.1357-0.0976-0.0783-0.07860.02010.09020.081453.2213-14.230874.1768
16-0.0773-0.53040.12260-0.3832.95780.02310.11090.3141-0.0278-0.0034-0.06060.0237-0.001-0.0197-0.1590.00130.01180.0820.15320.057310.89437.29722.9342
171.2083-0.15180.21150.3613-0.35591.2425-0.0344-0.1060.17110.05760.0005-0.0212-0.1750.09580.0338-0.0437-0.0262-0.0226-0.0566-0.0236-0.063824.958923.473565.633
18-0.1054-0.2020.40490.24510.34230.24240.0037-0.0444-0.0034-0.0033-0.00710.0002-0.0581-0.01630.00340.1123-0.0184-0.0294-0.0268-0.08840.081139.2005-3.247840.5541
191.00690.01380.52520.72110.31943.8557-0.0417-0.16720.00150.0385-0.12750.0082-0.36820.52750.1691-0.1861-0.07-0.00830.05670.0978-0.214551.706515.948571.6358
20-0.56620.25082.18394.487-1.37671.1628-0.0061-0.0537-0.03550.0666-0.0432-0.20070.1481-0.02280.0493-0.047-0.0464-0.0568-0.11250.02390.115541.23831.390487.3499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 37:58)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 59:256, 586:628)
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 36:58)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 59:256, 586:628)
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)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 40:58)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 59:256, 586:628)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 257:268)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 269:394, 425:585)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 395:424)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 35:58)
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 59:256, 586:628)
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 257:268)
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 269:394, 425:585)
20X-RAY DIFFRACTION20CHAIN D 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