[English] 日本語
Yorodumi
- PDB-4xds: Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xds
TitleDeoxyguanosinetriphosphate Triphosphohydrolase from Escherichia coli with Nickel
ComponentsDeoxyguanosinetriphosphate triphosphohydrolase
KeywordsHYDROLASE/DNA / TRIPHOSPHOHYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


dGTPase / dGTPase activity / dGTP catabolic process / nucleobase-containing small molecule interconversion / cobalt ion binding / single-stranded DNA binding / manganese ion binding / GTPase activity / magnesium ion binding / identical protein binding
Similarity search - Function
Phosphohydrolase-associated domain / dNTP triphosphohydrolase, type 1 / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. ...Phosphohydrolase-associated domain / dNTP triphosphohydrolase, type 1 / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Deoxyguanosinetriphosphate triphosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.354 Å
AuthorsSingh, D. / Gawel, D. / Itsko, M. / Krahn, J.M. / London, R.E. / Schaaper, R.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure of Escherichia coli dGTP Triphosphohydrolase: A HEXAMERIC ENZYME WITH DNA EFFECTOR MOLECULES.
Authors: Singh, D. / Gawel, D. / Itsko, M. / Hochkoeppler, A. / Krahn, J.M. / London, R.E. / Schaaper, R.M.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyguanosinetriphosphate triphosphohydrolase
B: Deoxyguanosinetriphosphate triphosphohydrolase
C: Deoxyguanosinetriphosphate triphosphohydrolase
D: Deoxyguanosinetriphosphate triphosphohydrolase
E: Deoxyguanosinetriphosphate triphosphohydrolase
F: Deoxyguanosinetriphosphate triphosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,76691
Polymers356,8256
Non-polymers7,94185
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20700 Å2
ΔGint-32 kcal/mol
Surface area107850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.800, 189.800, 296.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62
13
23
33
43
53
63
14
24
34
44
54
64
15
25
35
45
55
65
16
26
36
46
56
66

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain C and (resid 1000:1004 or resid 1007 or resid...
211(chain A and (resid 1000:1004 or resid 1007 or resid...
311(chain B and (resid 1000:1004 or resid 1007 or resid...
411(chain D and (resid 1000:1004 or resid 1007 or resid...
511(chain E and (resid 1000:1004 or resid 1007 or resid...
611(chain F and (resid 1000:1004 or resid 1007 or resid...
112(chain C and (resid 4:11 or resid 80:110 or resid...
212(chain A and (resid 4:11 or resid 80:110 or resid...
312(chain B and (resid 4:11 or resid 80:110 or resid...
412(chain D and (resid 4:11 or resid 80:110 or resid...
512(chain E and (resid 4:11 or resid 80:110 or resid...
612(chain F and (resid 4:11 or resid 80:110 or resid...
113(chain D and (resid 122:257 or resid 1008))
213(chain A and (resid 122:257 or resid 1008))
313(chain B and (resid 122:257 or resid 1008))
413(chain C and (resid 122:257 or resid 1008))
513(chain E and (resid 122:257 or resid 1008))
613(chain F and (resid 122:257 or resid 1008))
114(chain C and (resid 258:270 or resid 341:393) and not...
214(chain A and (resid 258:270 or resid 341:393) and not...
314(chain B and (resid 258:270 or resid 341:393) and not...
414(chain D and (resid 258:270 or resid 341:393) and not...
514(chain E and (resid 258:270 or resid 341:393) and not...
614(chain F and (resid 258:270 or resid 341:393) and not...
115(chain C and (resid 274:340) and not ((resid 317:318 or...
215(chain A and (resid 274:340) and not ((resid 317:318 or...
315(chain B and (resid 274:340) and not ((resid 317:318 or...
415(chain D and (resid 274:340) and not ((resid 317:318 or...
515(chain E and (resid 274:340) and not ((resid 317:318 or...
615(chain F and (resid 274:340) and not ((resid 317:318 or...
116(chain C and (resid 394:505 or resid 1005:1006 or resid...
216(chain A and (resid 394:505 or resid 1005:1006 or resid...
316(chain B and (resid 394:505 or resid 1005:1006 or resid...
416(chain D and (resid 394:505 or resid 1005:1006 or resid...
516(chain E and (resid 394:505 or resid 1005:1006 or resid...
616(chain F and (resid 394:505 or resid 1005:1006 or resid...

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Deoxyguanosinetriphosphate triphosphohydrolase / dGTPase


Mass: 59470.863 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dgt, b0160, JW0156 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15723, dGTPase
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.64 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein solution (10 mg/mL dGTPase, 20mM Tris-HCl, pH 7.0, 1mM deoxy-CCC) mixed 1:1 with well solution (0.5mM NH4SO4, 0.1M NaCitrate, 1M LiSO4, pH 5.6). Cryo conditions are well solution ...Details: Protein solution (10 mg/mL dGTPase, 20mM Tris-HCl, pH 7.0, 1mM deoxy-CCC) mixed 1:1 with well solution (0.5mM NH4SO4, 0.1M NaCitrate, 1M LiSO4, pH 5.6). Cryo conditions are well solution mixed with 25% ethylene glycol.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→20 Å / Num. obs: 76628 / % possible obs: 98.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 8.1
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 5 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.354→19.99 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 3404 5.14 %
Rwork0.172 --
obs0.1739 66200 85.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.354→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24119 0 401 18 24538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01425067
X-RAY DIFFRACTIONf_angle_d1.24234056
X-RAY DIFFRACTIONf_dihedral_angle_d15.7179072
X-RAY DIFFRACTIONf_chiral_restr0.0443638
X-RAY DIFFRACTIONf_plane_restr0.0054304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C624X-RAY DIFFRACTIONPOSITIONAL
12A624X-RAY DIFFRACTIONPOSITIONAL0.049
13B618X-RAY DIFFRACTIONPOSITIONAL0.046
14D634X-RAY DIFFRACTIONPOSITIONAL0.056
15E640X-RAY DIFFRACTIONPOSITIONAL0.056
16F631X-RAY DIFFRACTIONPOSITIONAL0.054
21C286X-RAY DIFFRACTIONPOSITIONAL
22A286X-RAY DIFFRACTIONPOSITIONAL0.046
23B285X-RAY DIFFRACTIONPOSITIONAL0.044
24D300X-RAY DIFFRACTIONPOSITIONAL0.06
25E310X-RAY DIFFRACTIONPOSITIONAL0.052
26F307X-RAY DIFFRACTIONPOSITIONAL0.058
31D1093X-RAY DIFFRACTIONPOSITIONAL
32A1093X-RAY DIFFRACTIONPOSITIONAL0.045
33B1106X-RAY DIFFRACTIONPOSITIONAL0.043
34C1099X-RAY DIFFRACTIONPOSITIONAL0.045
35E1115X-RAY DIFFRACTIONPOSITIONAL0.045
36F1101X-RAY DIFFRACTIONPOSITIONAL0.052
41C516X-RAY DIFFRACTIONPOSITIONAL
42A516X-RAY DIFFRACTIONPOSITIONAL0.046
43B521X-RAY DIFFRACTIONPOSITIONAL0.041
44D517X-RAY DIFFRACTIONPOSITIONAL0.05
45E517X-RAY DIFFRACTIONPOSITIONAL0.046
46F518X-RAY DIFFRACTIONPOSITIONAL0.047
51C439X-RAY DIFFRACTIONPOSITIONAL
52A439X-RAY DIFFRACTIONPOSITIONAL0.039
53B442X-RAY DIFFRACTIONPOSITIONAL0.036
54D446X-RAY DIFFRACTIONPOSITIONAL0.04
55E485X-RAY DIFFRACTIONPOSITIONAL0.043
56F456X-RAY DIFFRACTIONPOSITIONAL0.042
61C933X-RAY DIFFRACTIONPOSITIONAL
62A933X-RAY DIFFRACTIONPOSITIONAL0.045
63B929X-RAY DIFFRACTIONPOSITIONAL0.045
64D930X-RAY DIFFRACTIONPOSITIONAL0.05
65E927X-RAY DIFFRACTIONPOSITIONAL0.045
66F929X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3535-3.47280.30152960.26675547X-RAY DIFFRACTION76
3.4728-3.6110.27613230.23265678X-RAY DIFFRACTION79
3.611-3.77440.25093310.2055822X-RAY DIFFRACTION80
3.7744-3.97190.22852870.19055907X-RAY DIFFRACTION80
3.9719-4.21850.22153210.17016038X-RAY DIFFRACTION82
4.2185-4.54070.19063020.14566211X-RAY DIFFRACTION84
4.5407-4.99120.17833600.13616460X-RAY DIFFRACTION88
4.9912-5.69880.19983660.15386682X-RAY DIFFRACTION90
5.6988-7.12540.214040.17637015X-RAY DIFFRACTION94
7.1254-19.990.18014140.1627436X-RAY DIFFRACTION96
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)
12.82991.0487-0.10812.55530.34121.61090.06450.4689-0.2191-0.85930.1862-0.7569-0.08390.6081-0.20821.12180.22120.37191.28110.02260.838371.7315-36.1126-13.1933
21.31260.2635-0.11582.6859-0.04513.5652-0.04230.2970.2861-0.7922-0.0275-0.3852-0.75110.51850.04450.8749-0.07780.15450.91090.14880.777667.8905-4.88623.7473
32.6843-0.67410.56331.648-0.59781.51150.15030.4329-0.1571-0.3585-0.1192-0.01560.2630.2959-0.01910.57110.0926-0.07380.6137-0.02460.522618.6974-43.9682-4.0231
43.56310.6190.3881.4953-0.15631.24430.0884-0.04640.30650.1813-0.08050.0588-0.02960.15970.00750.49010.0102-0.03210.48060.08610.534917.3574-16.224217.9481
51.2471-0.186-0.53321.393-0.57653.43440.11220.3581-0.1441-0.2384-0.1220.18220.3628-0.15230.01020.49170.0755-0.05080.58190.0160.583155.9179-64.75929.8479
61.9703-0.76870.33762.0391-0.82521.738-0.0478-0.09690.3047-0.01150.0384-0.1208-0.15540.2104-0.00190.4096-0.05930.00880.46560.00250.498958.0956-34.848448.3606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

+
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