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- PDB-3r9i: 2.6A resolution structure of MinD complexed with MinE (12-31) peptide -

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Basic information

Entry
Database: PDB / ID: 3r9i
Title2.6A resolution structure of MinD complexed with MinE (12-31) peptide
Components
  • Cell division topological specificity factor
  • Septum site-determining protein minD
KeywordsCELL CYCLE / HYDROLASE/CELL CYCLE / ATPase / 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 / intracellular mRNA localization / ATPase activator activity / 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 / intracellular mRNA localization / ATPase activator activity / 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 / Cell division topological specificity factor MinE superfamily / Septum formation 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 nucleotide triphosphate hydrolases ...ATP binding protein MinD / Cell division topological specificity factor MinE / Cell division topological specificity factor MinE superfamily / Septum formation 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
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: 2.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Septum site-determining protein minD
B: Septum site-determining protein minD
C: Septum site-determining protein minD
D: Septum site-determining protein minD
E: Cell division topological specificity factor
F: Cell division topological specificity factor
G: Cell division topological specificity factor
H: Cell division topological specificity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,25512
Polymers123,5468
Non-polymers1,7094
Water3,189177
1
A: Septum site-determining protein minD
B: Septum site-determining protein minD
E: Cell division topological specificity factor
F: Cell division topological specificity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6276
Polymers61,7734
Non-polymers8542
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-33 kcal/mol
Surface area18940 Å2
MethodPISA
2
C: Septum site-determining protein minD
D: Septum site-determining protein minD
G: Cell division topological specificity factor
H: Cell division topological specificity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6276
Polymers61,7734
Non-polymers8542
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-32 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.293, 71.796, 76.644
Angle α, β, γ (deg.)102.640, 95.870, 111.720
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 2:258 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)A0
211CHAIN B AND (RESSEQ 2:258 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)B0
311CHAIN C AND (RESSEQ 2:258 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)C0
411CHAIN D AND (RESSEQ 2:258 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)D0
112CHAIN E AND (RESSEQ 13:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)E0
212CHAIN F AND (RESSEQ 13:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)F0
312CHAIN G AND (RESSEQ 13:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)G0
412CHAIN H AND (RESSEQ 13:26 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)H0

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.816296, -0.576484, 0.036422), (-0.577459, 0.812876, -0.075984), (0.014197, -0.083057, -0.996444)-0.055686, 0.103241, 0.02754
2given(0.457269, 0.060284, -0.887283), (0.697792, -0.642862, 0.315935), (-0.551354, -0.763606, -0.336026)-16.221001, 63.756199, -2.59737
3given(-0.783577, 0.318854, 0.533234), (0.339721, -0.498707, 0.797422), (0.520189, 0.805992, 0.282454)-23.9396, 61.1619, -2.25755
4given(-0.829505, -0.558349, 0.012932), (-0.557704, 0.826868, -0.072486), (0.029779, -0.06734, -0.997286)-0.43301, -0.150494, -0.130804
5given(0.464161, 0.029462, -0.88526), (0.684016, -0.646897, 0.337115), (-0.56274, -0.762008, -0.320417)-15.0434, 63.797401, -2.65225
6given(-0.789982, 0.310548, 0.528667), (0.33423, -0.504751, 0.795937), (0.514022, 0.805473, 0.29495)-23.9715, 61.3634, -2.08804

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Components

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


Mass: 28500.656 Da / Num. of mol.: 4 / 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/peptide
Cell division topological specificity factor / minE


Mass: 2385.811 Da / Num. of mol.: 4 / Fragment: UNP residues 12-31 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P0A734
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: 20% w/v PEG3350, 100 mM citrate, 200 mM sodium citrate, pH 4.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→73.24 Å / Num. all: 36883 / Num. obs: 36883 / % possible obs: 98.47 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 7.149
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.6-2.743.470.572.3718794541398.22
2.74-2.913.450.413.1617505507298.07
2.91-3.113.510.34.1716718476898.39
3.11-3.363.660.225.6916339446598.5
3.36-3.683.560.157.8714579409898.68
3.68-4.113.340.1110.0612398371298.67
4.11-4.753.420.0812.3511238328798.89
4.75-5.813.620.0812.2110060277898.72
5.81-8.223.40.0811.927242213299.07
8.22-73.243.570.0517.294134115897.52

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.74 Å45.53 Å
Translation2.74 Å45.53 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
MOLREPphasing
PHENIXdev_661refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q9L

3q9l


Resolution: 2.6→43.417 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1852 5.02 %RANDOM
Rwork0.2012 ---
obs0.2033 36875 98.47 %-
all-36883 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.393 Å2 / ksol: 0.434 e/Å3
Displacement parametersBiso max: 101.78 Å2 / Biso mean: 30.5946 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1-5.3529 Å2-6.5611 Å2-0.8253 Å2
2--2.2676 Å2-0.8367 Å2
3----7.6206 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8182 0 108 177 8467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118372
X-RAY DIFFRACTIONf_angle_d1.35611333
X-RAY DIFFRACTIONf_chiral_restr0.0671368
X-RAY DIFFRACTIONf_plane_restr0.0041455
X-RAY DIFFRACTIONf_dihedral_angle_d16.9593161
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1913X-RAY DIFFRACTIONPOSITIONAL0.072
12B1913X-RAY DIFFRACTIONPOSITIONAL0.072
13C1914X-RAY DIFFRACTIONPOSITIONAL0.068
14D1948X-RAY DIFFRACTIONPOSITIONAL0.049
21E110X-RAY DIFFRACTIONPOSITIONAL0.073
22F110X-RAY DIFFRACTIONPOSITIONAL0.073
23G103X-RAY DIFFRACTIONPOSITIONAL0.071
24H110X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.67030.30111310.26772731286298
2.6703-2.74890.30441390.26072691283098
2.7489-2.83760.25691480.24242676282498
2.8376-2.9390.30731390.21962690282998
2.939-3.05670.26911360.22222713284998
3.0567-3.19570.29881380.21682688282698
3.1957-3.36420.2821420.22532653279599
3.3642-3.57490.28181270.21782730285799
3.5749-3.85070.2281710.19382666283799
3.8507-4.23790.20141210.1642731285299
4.2379-4.85050.16071380.14922693283199
4.8505-6.10840.23271480.19132708285699
6.1084-43.4230.21271740.18482653282798

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