[English] 日本語
Yorodumi
- PDB-2xit: Crystal structure of monomeric MipZ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xit
TitleCrystal structure of monomeric MipZ
ComponentsMIPZ
KeywordsREPLICATION / ATPASE / CELL DIVISION / PROTEIN LOCALIZATION
Function / homology
Function and homology information


ATPase MipZ / ATPase MipZ / : / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Division plane positioning ATPase MipZ / Division plane positioning ATPase MipZ
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKiekebusch, D. / Michie, K.A. / Essen, L.O. / Lowe, J. / Thanbichler, M.
CitationJournal: Mol.Cell / Year: 2012
Title: Localized Dimerization and Nucleoid Binding Drive Gradient Formation by the Bacterial Cell Division Inhibitor Mipz.
Authors: Kiekebusch, D. / Michie, K.A. / Essen, L.O. / Lowe, J. / Thanbichler, M.
History
DepositionJun 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references / Other / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MIPZ
B: MIPZ


Theoretical massNumber of molelcules
Total (without water)65,2052
Polymers65,2052
Non-polymers00
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-7.4 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.670, 124.670, 239.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-2063-

HOH

21B-2167-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA4 - 594 - 59
21THRTHRLEULEUBB4 - 594 - 59
12PROPROILEILEAA67 - 10967 - 109
22PROPROILEILEBB67 - 10967 - 109
13ALAALAGLYGLYAA117 - 144117 - 144
23ALAALAGLYGLYBB117 - 144117 - 144
14LYSLYSTYRTYRAA155 - 269155 - 269
24LYSLYSTYRTYRBB155 - 269155 - 269

-
Components

#1: Protein MIPZ / DIVISION PLANE POSITIONING ATPASE MIPZ


Mass: 32602.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER CRESCENTUS (bacteria) / Strain: CB15N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3) / Variant (production host): PLYSS / References: UniProt: B8GY04, UniProt: A0A0H3CA70*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL HEXAHISTIDINE TAG CONNECTED VIA LINKER SEQUENCE AVDKLAAAL TO MIPZ

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.13 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: May 8, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→49.2 Å / Num. obs: 66140 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.27 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.244 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PARTS OF THE LINKER REGION BETWEEN MIPZ AND HEXAHISTIDINE TAG (A279-L287) ARE DEFINED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1215 1.8 %SHELLED FLAGS
Rwork0.18445 ---
obs0.18524 65042 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.153 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.36 Å20 Å2
2--0.71 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 0 0 420 4686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224351
X-RAY DIFFRACTIONr_bond_other_d0.0010.023007
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9745897
X-RAY DIFFRACTIONr_angle_other_deg0.90837270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32122.474194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29715745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8411552
X-RAY DIFFRACTIONr_chiral_restr0.0810.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02916
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6881.52764
X-RAY DIFFRACTIONr_mcbond_other0.1881.51125
X-RAY DIFFRACTIONr_mcangle_it1.26824417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0431587
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2674.51476
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1417medium positional0.240.5
2B1417medium positional0.240.5
1A1777loose positional0.645
2B1777loose positional0.645
1A1417medium thermal0.932
2B1417medium thermal0.932
1A1777loose thermal0.8810
2B1777loose thermal0.8810
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 81 -
Rwork0.254 4781 -
obs--99.92 %
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)
10.97670.2020.88451.02680.13912.07080.07370.0175-0.03960.04160.0124-0.07660.24750.0241-0.08620.10710.0019-0.01140.0733-0.00310.077224.202218.355778.1079
20.85850.1543-0.29841.77640.34281.03620.0064-0.04150.00290.07960.00470.034-0.05820.0146-0.0110.0135-0.0074-0.00760.06010.00610.041437.696441.335341.5063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 287
2X-RAY DIFFRACTION2B4 - 287

+
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