[English] 日本語
Yorodumi
- PDB-3r9j: 4.3A resolution structure of a MinD-MinE(I24N) protein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r9j
Title4.3A resolution structure of a MinD-MinE(I24N) protein complex
Components
  • Cell division topological specificity factor
  • Septum site-determining protein minD
KeywordsCELL CYCLE / HYDROLASE/CELL CYCLE / ATPase / protein complex / bacterial cell division inhibitor / mine / HYDROLASE-CELL CYCLE complex
Function / homology
Function and homology information


division septum site selection / regulation of division septum assembly / cell pole / negative regulation of cell division / division septum assembly / regulation of cell division / chromosome segregation / cytoplasmic side of plasma membrane / cell division / ATP hydrolysis activity ...division septum site selection / regulation of division septum assembly / cell pole / negative regulation of cell division / division septum assembly / regulation of cell division / chromosome segregation / cytoplasmic side of plasma membrane / cell division / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
ATP binding protein MinD / Cell division topological specificity factor MinE superfamily / Septum formation topological specificity factor MinE / Cell division topological specificity factor MinE / CobQ/CobB/MinD/ParA nucleotide binding domain / ATP binding protein MinD/FleN / CobQ/CobB/MinD/ParA nucleotide binding domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell division topological specificity factor / Septum site-determining protein MinD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.3 Å
AuthorsLovell, S. / Battaile, K.P. / Park, K.-T. / Wu, W. / Holyoak, T. / Lutkenhaus, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The Min Oscillator Uses MinD-Dependent Conformational Changes in MinE to Spatially Regulate Cytokinesis.
Authors: Park, K.T. / Wu, W. / Battaile, K.P. / Lovell, S. / Holyoak, T. / Lutkenhaus, J.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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 / _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: Septum site-determining protein minD
B: Septum site-determining protein minD
C: Cell division topological specificity factor
D: Cell division topological specificity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7066
Polymers74,8524
Non-polymers8542
Water0
1
A: Septum site-determining protein minD
B: Septum site-determining protein minD
hetero molecules

A: Septum site-determining protein minD
B: Septum site-determining protein minD
C: Cell division topological specificity factor
D: Cell division topological specificity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,56210
Polymers131,8536
Non-polymers1,7094
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
identity operation1_555x,y,z1
2
D: Cell division topological specificity factor

A: Septum site-determining protein minD
B: Septum site-determining protein minD
C: Cell division topological specificity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7066
Polymers74,8524
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-26 kcal/mol
Surface area27780 Å2
MethodPISA
3
A: Septum site-determining protein minD
B: Septum site-determining protein minD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8564
Polymers57,0012
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-15 kcal/mol
Surface area19570 Å2
MethodPISA
4
C: Cell division topological specificity factor
D: Cell division topological specificity factor


Theoretical massNumber of molelcules
Total (without water)17,8502
Polymers17,8502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-18 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.393, 94.393, 284.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Septum site-determining protein minD / Cell division inhibitor minD


Mass: 28500.656 Da / Num. of mol.: 2 / Mutation: D40A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1175, JW1164, minD / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEZ3
#2: Protein Cell division topological specificity factor / minE


Mass: 8925.203 Da / Num. of mol.: 2 / Fragment: UNP residues 12-88 / Mutation: I24N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1174, JW1163, minE / Plasmid: pJB216 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A734
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5
Details: 30% w/v PEG3000, 100 mM CHES, 10 mM EDTA, pH 9.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. all: 9437 / Num. obs: 9437 / % possible obs: 99.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.84 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.3547
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
4.3-4.5312.40.525.49162721312100
4.53-4.8113.760.47.21174771270100
4.81-5.1413.680.338.34164891205100
5.14-5.5513.510.289.27151741123100
5.55-6.0813.10.269.68134491027100
6.08-6.812.580.1514.9812029956100
6.8-7.8511.740.0921.149977850100
7.85-9.6211.860.0533.858740737100
9.62-13.612.780.0444.557576593100
13.6-5010.880.0539.89396036498.22

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.56 Å48.79 Å
Translation4.56 Å48.79 Å

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XSCALEdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R9I

3r9i


Resolution: 4.3→48.71 Å / Cor.coef. Fo:Fc: 0.8622 / Cor.coef. Fo:Fc free: 0.8486 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3106 455 4.85 %RANDOM
Rwork0.2939 ---
obs0.2947 9380 --
all-9380 --
Displacement parametersBiso max: 135 Å2 / Biso mean: 134.736 Å2 / Biso min: 65.88 Å2
Baniso -1Baniso -2Baniso -3
1--26.9717 Å20 Å20 Å2
2---26.9717 Å20 Å2
3---53.9434 Å2
Refine analyzeLuzzati coordinate error obs: 1.63 Å
Refinement stepCycle: LAST / Resolution: 4.3→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 54 0 4973
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2431SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes712HARMONIC5
X-RAY DIFFRACTIONt_it5027HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion8HARMONIC0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion691SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5633SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5027HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg6812HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion3.37
LS refinement shellResolution: 4.3→4.81 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3031 125 4.85 %
Rwork0.3141 2450 -
all0.3136 2575 -
obs-2450 -

+
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