[English] 日本語
Yorodumi
- PDB-4r7z: PfMCM-AAA double-octamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r7z
TitlePfMCM-AAA double-octamer
ComponentsCell division control protein 21
KeywordsHYDROLASE / AAA+ / MCM / helicase / ATPase / DNA replication
Function / homology
Function and homology information


intein-mediated protein splicing / DNA duplex unwinding / endonuclease activity / DNA helicase / cell division / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / MCM N-terminal domain / MCM N-terminal domain ...Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Intein N-terminal splicing region / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / Intein N-terminal splicing motif profile. / minichromosome maintenance proteins / MCM domain / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA helicase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsMiller, J.M. / Arachea, B.T. / Epling, L.B. / Enemark, E.J.
CitationJournal: Elife / Year: 2014
Title: Analysis of the crystal structure of an active MCM hexamer.
Authors: Miller, J.M. / Arachea, B.T. / Epling, L.B. / Enemark, E.J.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Nov 19, 2014Group: Database references
Revision 1.4Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Sep 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
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_label_asym_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_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division control protein 21
B: Cell division control protein 21
C: Cell division control protein 21
D: Cell division control protein 21
E: Cell division control protein 21
F: Cell division control protein 21
G: Cell division control protein 21
H: Cell division control protein 21
I: Cell division control protein 21
J: Cell division control protein 21
K: Cell division control protein 21
L: Cell division control protein 21
M: Cell division control protein 21
N: Cell division control protein 21
O: Cell division control protein 21
P: Cell division control protein 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)602,19048
Polymers594,96616
Non-polymers7,22432
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.956, 127.082, 128.025
Angle α, β, γ (deg.)71.85, 72.82, 80.39
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.8904, -0.1012, 0.4438), (0.3355, 0.8047, -0.4897), (-0.3076, 0.5849, 0.7505)-2.6787, -1.4274, -0.3107
3given(0.5642, 0.0966, 0.82), (0.7617, 0.3223, -0.5621), (-0.3185, 0.9417, 0.1082)-1.2184, -2.6937, -1.4272
4given(0.1983, 0.5139, 0.8347), (0.9801, -0.1112, -0.1643), (0.0084, 0.8506, -0.5257)-0.6017, -1.175, -3.0426
5given(0.0594, 0.8491, 0.5249), (0.8646, -0.3066, 0.398), (0.4988, 0.4302, -0.7524)0.036, -2.105, -0.3409
6given(0.172, 0.985, -0.0125), (0.5203, -0.0801, 0.8502), (0.8365, -0.1527, -0.5263)-1.9193, -1.6436, -1.6245
7given(0.4854, 0.7946, -0.3648), (0.0643, 0.3837, 0.9212), (0.872, -0.4706, 0.1352)-1.1845, -0.2126, 1.3924
8given(0.8474, 0.3571, -0.3929), (-0.085, 0.8217, 0.5635), (0.5241, -0.4441, 0.7267)-2.6752, -0.164, -1.075
9given(-0.3154, -0.3482, -0.8828), (-0.2879, -0.8513, 0.4386), (-0.9042, 0.3925, 0.1683)-0.1324, 3.9814, -0.6047
10given(-0.0949, -0.7072, -0.7006), (-0.6785, -0.4691, 0.5654), (-0.7285, 0.529, -0.4353)-0.2673, 1.9515, 3.7513
11given(-0.0732, -0.9779, -0.196), (-0.9527, 0.0105, 0.3036), (-0.2948, 0.2089, -0.9324)1.2934, 3.0541, 1.1895
12given(-0.3599, -0.9038, 0.2315), (-0.9095, 0.2846, -0.3031), (0.2081, -0.3197, -0.9244)0.1219, 0.0744, 0.7814
13given(-0.7202, -0.5498, 0.4232), (-0.577, 0.1359, -0.8053), (0.3852, -0.8242, -0.4151)1.9536, -0.4716, 0.9467
14given(-0.9738, -0.1136, 0.1971), (-0.1569, -0.2916, -0.9436), (0.1646, -0.9498, 0.2662)2.1176, -0.4055, 2.3189
15given(-0.9708, 0.1186, -0.2086), (0.0442, -0.7661, -0.6412), (-0.2359, -0.6317, 0.7384)5.1907, 1.5451, 2.5933
16given(-0.7066, 0.0207, -0.7073), (0.0483, -0.9958, -0.0774), (-0.7059, -0.0888, 0.7027)1.3612, 2.0459, 1.1107

-
Components

#1: Protein
Cell division control protein 21


Mass: 37185.352 Da / Num. of mol.: 16 / Fragment: AAA+ domain of PfMCM (UNP 263-361/729-966)
Source method: isolated from a genetically manipulated source
Details: Constructed as Sumo fusion (Mossessova and Lima, 2000)
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: MCM, PF0482 / Plasmid: pRSF-duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q8U3I4
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
Sequence detailsThe UNK region in the sequence is due to unknown registration. The missing sequence is ...The UNK region in the sequence is due to unknown registration. The missing sequence is GKSSSAAGLTAAAVRDEFTGGWVLEAGALVLAD

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6 mg/mL PfMCM-AAA; 5 mM ADP; 50 mM MgCl2; 18 mM Hepes, pH 7.6; 180 mM NaCl; 4.5 mM 2-mercaptoethanol mixed 1:1 with 50 mM sodium cacodylate, pH 6.0; 50 mM magnesium acetate; 30% MPD; 5% ...Details: 6 mg/mL PfMCM-AAA; 5 mM ADP; 50 mM MgCl2; 18 mM Hepes, pH 7.6; 180 mM NaCl; 4.5 mM 2-mercaptoethanol mixed 1:1 with 50 mM sodium cacodylate, pH 6.0; 50 mM magnesium acetate; 30% MPD; 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. all: 70730 / Num. obs: 69970 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 0.169 / Net I/σ(I): 8.3
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.41 / Num. unique all: 7090 / Rsym value: 0.429 / % possible all: 97

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: placement of 16 copies of the ATPase domain of 4FDG (Slaymaker et al., 2013)

4fdg


Resolution: 3.8→48.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4895965.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED. Strict NCS was used using the matrices provided and only chain A coordinates
RfactorNum. reflection% reflectionSelection details
Rfree0.314 3486 5 %RANDOM
Rwork0.301 ---
obs0.301 69126 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0837 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 91.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.03 Å2-1.51 Å21.66 Å2
2--0.42 Å24.45 Å2
3----5.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.62 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.78 Å
Refinement stepCycle: LAST / Resolution: 3.8→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38848 0 448 0 39296
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it15.811.5
X-RAY DIFFRACTIONc_mcangle_it24.542
X-RAY DIFFRACTIONc_scbond_it24.762
X-RAY DIFFRACTIONc_scangle_it32.82.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.8→3.94 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.368 357 5.4 %
Rwork0.367 6206 -
obs-6206 93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6adp.paramadp.top

+
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