[English] 日本語
Yorodumi
- PDB-3ctd: Crystal structure of a putative AAA family ATPase from Prochloroc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ctd
TitleCrystal structure of a putative AAA family ATPase from Prochlorococcus marinus subsp. pastoris
ComponentsPutative ATPase, AAA family
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


four-way junction helicase activity / DNA recombination / DNA replication / nucleotide binding / DNA repair / DNA binding
Similarity search - Function
post-AAA+ oligomerization domain-like / DNA polymerase III clamp loader subunits, C-terminal domain / MgsA AAA+ ATPase C-terminal / AAA C-terminal domain / MgsA AAA+ ATPase C terminal / AAA C-terminal domain / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / RuvB-like P-loop domain / Holliday junction DNA helicase RuvB P-loop domain ...post-AAA+ oligomerization domain-like / DNA polymerase III clamp loader subunits, C-terminal domain / MgsA AAA+ ATPase C-terminal / AAA C-terminal domain / MgsA AAA+ ATPase C terminal / AAA C-terminal domain / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / RuvB-like P-loop domain / Holliday junction DNA helicase RuvB P-loop domain / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative ATPase, AAA family
Similarity search - Component
Biological speciesProchlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Lau, C. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative AAA family ATPase from Prochlorococcus marinus subsp. pastoris.
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Lau, C. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative ATPase, AAA family
B: Putative ATPase, AAA family


Theoretical massNumber of molelcules
Total (without water)48,3232
Polymers48,3232
Non-polymers00
Water1,04558
1
A: Putative ATPase, AAA family
B: Putative ATPase, AAA family

A: Putative ATPase, AAA family
B: Putative ATPase, AAA family


Theoretical massNumber of molelcules
Total (without water)96,6454
Polymers96,6454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area15470 Å2
ΔGint-150.6 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.184, 108.184, 68.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Putative ATPase, AAA family /


Mass: 24161.311 Da / Num. of mol.: 2 / Fragment: Residues 228-429 / Mutation: L360M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria)
Species: Prochlorococcus marinus / Strain: CCMP 1378 / MED4 / Gene: yrvN, PMM0077 / Plasmid: Modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7V3J8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 100mM Hepes pH 7.0, 2% PEG 3350, 240mM Tri-sodium citrate dihydrate pH 7.0, VAPOR DIFFUSION, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 21, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.5→39.559 Å / Num. all: 14631 / Num. obs: 14631 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 22.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 12.5 / Num. unique all: 2094 / Rsym value: 0.123 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.875 / SU B: 8.107 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 728 5 %RANDOM
Rwork0.211 ---
obs0.214 14550 99.8 %-
all-14579 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 0 58 2435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222438
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9433320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21125.044113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25215354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.26156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211889
X-RAY DIFFRACTIONr_mcbond_it2.91421536
X-RAY DIFFRACTIONr_mcangle_it4.59232443
X-RAY DIFFRACTIONr_scbond_it3.7532902
X-RAY DIFFRACTIONr_scangle_it5.1123877
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 51 -
Rwork0.206 986 -
all-1037 -
obs-986 100 %

+
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