[English] 日本語
Yorodumi
- PDB-3f9v: Crystal Structure Of A Near Full-Length Archaeal MCM: Functional ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f9v
TitleCrystal Structure Of A Near Full-Length Archaeal MCM: Functional Insights For An AAA+ Hexameric Helicase
ComponentsMinichromosome maintenance protein MCM
KeywordsHYDROLASE / Replicative Helicase / DNA Replication / MCM Complex / AAA+ Protein / ATP-binding / DNA-binding / Helicase / Nucleotide-binding
Function / homology
Function and homology information


single-stranded 3'-5' DNA helicase activity / MCM complex / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / single-stranded DNA binding / DNA helicase / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
: / MCM protein C-terminal winged helix-turn-helix domain / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain ...: / MCM protein C-terminal winged helix-turn-helix domain / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Minichromosome maintenance protein MCM
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.35 Å
AuthorsChen, X.J. / Brewster, A.S. / Wang, G.G. / Yu, X. / Greenleaf, W. / Tjajadi, M. / Klein, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal structure of a near-full-length archaeal MCM: Functional insights for an AAA+ hexameric helicase.
Authors: Brewster, A.S. / Wang, G. / Yu, X. / Greenleaf, W.B. / Carazo, J.M. / Tjajadia, M. / Klein, M.G. / Chen, X.S.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Minichromosome maintenance protein MCM


Theoretical massNumber of molelcules
Total (without water)67,3191
Polymers67,3191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)202.526, 202.526, 128.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
DetailsA hexamer model can be created that aligns well with the N-terminal Methanobacterium thermoautotrophicum MCM hexamer (PDB ID 1LTL) using the following non-crystallographic matrices. Apply matrix 1 for monomer 1, and then apply the summation of matrix 1 and matrix N to create monomer N, where N is 2-6. 1) LSQ_RT_NTTONTAIMP R 12 (3f14.8) 0.43327817 0.61568034 0.65818518 -0.90081984 0.31867027 0.29491171 -0.02817271 -0.72068506 0.69268990 239.07376099 11.87045383 -79.62718964 2) LSQ_RT_ATOB2IMP R 12 (3f14.8) 0.50902790 -0.86062968 -0.01439116 0.86053950 0.50920200 -0.01360237 0.01903461 -0.00546018 0.99980390 -0.94980073 110.48052979 1.74927461 3) LSQ_RT_ATOCIMP R 12 (3f14.8) -0.49999857 0.86602622 -0.00000035 -0.86602622 -0.49999857 0.00000028 0.00000007 0.00000044 1.00000000 192.32089233 -0.00009566 0.00002129 4) LSQ_RT_ATODIMP R 12 (3f14.8) 0.49081263 0.87114632 -0.01439028 -0.87125200 0.49064746 -0.01360218 -0.00478894 0.01921368 0.99980396 97.11698151 -56.06281281 1.74919856 5) LSQ_RT_ATOEIMP R 12 (3f14.8) -0.49999991 -0.86602545 -0.00000097 0.86602545 -0.49999991 0.00000114 -0.00000147 -0.00000028 1.00000000 96.16052246 166.55490112 0.00005019 6) LSQ_RT_ATOFIMP R 12 (3f14.8) -0.99984115 -0.01051573 -0.01439001 0.01071160 -0.99985009 -0.01360323 -0.01424481 -0.01375521 0.99980390 192.31431580 112.13711548 1.74920392

-
Components

#1: Protein Minichromosome maintenance protein MCM


Mass: 67318.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: MCM, SSO0774 / Plasmid: pGEX-Kg / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UXG1, Hydrolases

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.88 Å3/Da / Density % sol: 74.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50mM NaCl, 65mM CalCl2, 20% MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794 Å
DetectorType: ADSC / Detector: CCD / Date: Oct 29, 2007
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 4.35→30 Å / Num. obs: 7760

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 4.35→30 Å / Cor.coef. Fo:Fc: 0.832 / Cor.coef. Fo:Fc free: 0.803 / Occupancy max: 1 / Occupancy min: 1 / SU B: 349.255 / SU ML: 2.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.467
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: Proline residues identified in remark 500 as having deviant covalent bond angles were modeled as alanines in the structure. As such the standard values used as a reference against these ...Details: Proline residues identified in remark 500 as having deviant covalent bond angles were modeled as alanines in the structure. As such the standard values used as a reference against these residues are not relevant to a poly-alanine structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.481 343 4.6 %RANDOM
Rwork0.412 ---
obs0.415 7390 82.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.98 Å2 / Biso mean: 185.302 Å2 / Biso min: 181.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å20 Å20 Å2
2--3.86 Å20 Å2
3----7.73 Å2
Refinement stepCycle: LAST / Resolution: 4.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 0 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222943
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.8494100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1595594
X-RAY DIFFRACTIONr_chiral_restr0.0670.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022376
X-RAY DIFFRACTIONr_nbd_refined0.2880.21314
X-RAY DIFFRACTIONr_nbtor_refined0.2920.22077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.222
X-RAY DIFFRACTIONr_mcbond_it0.1391.52943
X-RAY DIFFRACTIONr_mcangle_it0.25224100
LS refinement shellResolution: 4.35→4.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.559 17 -
Rwork0.55 460 -
all-477 -
obs--75.83 %
Refinement TLS params.Method: refined / Origin x: -10.973 Å / Origin y: 168.9816 Å / Origin z: 52.6142 Å
111213212223313233
T-0.9178 Å20.0393 Å2-0.114 Å2--0.7669 Å2-0.3005 Å2---0.6781 Å2
L3.7553 °21.7535 °23.0788 °2-2.2413 °21.0675 °2--5.2606 °2
S0.0647 Å °-0.2036 Å °-0.1283 Å °0.3326 Å °0.1617 Å °-0.6413 Å °-0.3058 Å °0.73 Å °-0.2264 Å °

+
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://pdbjlvh1.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