[English] 日本語
Yorodumi
- PDB-4kfu: Structure of the genome packaging NTPase B204 from Sulfolobus tur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kfu
TitleStructure of the genome packaging NTPase B204 from Sulfolobus turreted icosahedral virus 2 in complex with AMPPCP
ComponentsGenome packaging NTPase B204
KeywordsHYDROLASE / FtsK-HerA superfamily / P-loop ATPase / genome packaging NTPase
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / CITRATE ANION / Uncharacterized protein
Similarity search - Component
Biological speciesSulfolobus turreted icosahedral virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsHapponen, L.J. / Oksanen, E. / Kajander, T. / Goldman, A. / Butcher, S.
CitationJournal: J.Virol. / Year: 2013
Title: The Structure of the NTPase That Powers DNA Packaging into Sulfolobus Turreted Icosahedral Virus 2.
Authors: Happonen, L.J. / Oksanen, E. / Liljeroos, L. / Goldman, A. / Kajander, T. / Butcher, S.J.
History
DepositionApr 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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: Genome packaging NTPase B204
B: Genome packaging NTPase B204
C: Genome packaging NTPase B204
D: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,69522
Polymers99,6314
Non-polymers4,06418
Water7,710428
1
A: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4359
Polymers24,9081
Non-polymers1,5278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4359
Polymers24,9081
Non-polymers1,5278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4132
Polymers24,9081
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Genome packaging NTPase B204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4132
Polymers24,9081
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.558, 65.227, 72.118
Angle α, β, γ (deg.)90.85, 93.77, 91.56
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Genome packaging NTPase B204


Mass: 24907.756 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus turreted icosahedral virus 2
Gene: B204, STIV2_B204 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566/pTF16 / References: UniProt: D5IEZ9, Hydrolases

-
Non-polymers , 5 types, 446 molecules

#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1 M Tris-HCl, 0.2 M magnesium chloride, 30% PEG8000, 5 mM AMPPCP, protein in 50 mM sodium citrate, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.89→48.717 Å / Num. all: 65868 / Num. obs: 65868 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.94 % / Biso Wilson estimate: 32.05 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.78
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 1.94 / Num. unique all: 10093 / % possible all: 92.4

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KFR

4kfr


Resolution: 1.892→48.717 Å / SU ML: 0.5 / σ(F): 1.99 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 3296 5.01 %RANDOM
Rwork0.1883 ---
obs0.1906 65852 97.41 %-
all-65852 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.506 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6749 Å20.0473 Å22.8092 Å2
2--8.9918 Å2-1.2774 Å2
3----5.3169 Å2
Refinement stepCycle: LAST / Resolution: 1.892→48.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 0 214 428 6994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116766
X-RAY DIFFRACTIONf_angle_d1.149233
X-RAY DIFFRACTIONf_dihedral_angle_d16.5042415
X-RAY DIFFRACTIONf_chiral_restr0.0781031
X-RAY DIFFRACTIONf_plane_restr0.0051101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.91860.30371130.28132093X-RAY DIFFRACTION78
1.9186-1.94720.31111340.23892580X-RAY DIFFRACTION97
1.9472-1.97760.26281390.23282622X-RAY DIFFRACTION97
1.9776-2.010.2871370.22882613X-RAY DIFFRACTION98
2.01-2.04470.30271370.23262625X-RAY DIFFRACTION97
2.0447-2.08190.32131370.22832592X-RAY DIFFRACTION97
2.0819-2.12190.26841400.22122646X-RAY DIFFRACTION98
2.1219-2.16520.28231350.21032545X-RAY DIFFRACTION98
2.1652-2.21230.27511400.1982670X-RAY DIFFRACTION98
2.2123-2.26380.23821380.18882594X-RAY DIFFRACTION98
2.2638-2.32040.20361410.18782665X-RAY DIFFRACTION98
2.3204-2.38310.25041360.1882614X-RAY DIFFRACTION98
2.3831-2.45330.27161370.19342619X-RAY DIFFRACTION98
2.4533-2.53240.27761390.20472621X-RAY DIFFRACTION98
2.5324-2.62290.27221380.20332639X-RAY DIFFRACTION98
2.6229-2.7280.27471400.20642661X-RAY DIFFRACTION99
2.728-2.85210.24921380.19822595X-RAY DIFFRACTION98
2.8521-3.00240.2431410.19492649X-RAY DIFFRACTION99
3.0024-3.19050.23671370.1922627X-RAY DIFFRACTION99
3.1905-3.43680.21641410.17682690X-RAY DIFFRACTION99
3.4368-3.78250.20781390.16142637X-RAY DIFFRACTION99
3.7825-4.32960.1741410.15212649X-RAY DIFFRACTION99
4.3296-5.45370.16681390.14982672X-RAY DIFFRACTION99
5.4537-48.73340.22591390.19772638X-RAY DIFFRACTION99

+
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