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- PDB-3q9l: The structure of the dimeric E.coli MinD-ATP complex -

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Basic information

Entry
Database: PDB / ID: 3q9l
TitleThe structure of the dimeric E.coli MinD-ATP complex
ComponentsSeptum site-determining protein minD
KeywordsCELL CYCLE / HYDROLASE / ATPase / bacterial cell division inhibitor / MinC / MinE
Function / homology
Function and homology information


division septum site selection / cell pole / intracellular mRNA localization / 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 / 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'-TRIPHOSPHATE / Septum site-determining protein MinD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.343 Å
AuthorsWu, W. / Park, K.-T. / Lutkenhaus, J. / Holyoak, T.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Determination of the structure of the MinD-ATP complex reveals the orientation of MinD on the membrane and the relative location of the binding sites for MinE and MinC.
Authors: Wu, W. / Park, K.T. / Holyoak, T. / Lutkenhaus, J.
History
DepositionJan 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _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.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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: Septum site-determining protein minD
B: Septum site-determining protein minD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0646
Polymers57,0012
Non-polymers1,0634
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Septum site-determining protein minD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0323
Polymers28,5011
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Septum site-determining protein minD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0323
Polymers28,5011
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.664, 86.595, 110.714
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 2 - 257 / Label seq-ID: 2 - 257

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 2:257 )AA
2chain B and (resseq 2:257 )BB

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Components

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


Mass: 28500.656 Da / Num. of mol.: 2 / Fragment: UNP residues 1-260 / Mutation: D40A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: minD / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEZ3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.6 M ammonium sulfate, 0.1 M HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9184,0.9788,0.9794
DetectorType: MAR 325 / Detector: CCD / Date: Dec 4, 2007 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.97881
30.97941
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 10.39 / Number: 197429 / Rmerge(I) obs: 0.125 / Χ2: 1.07 / D res high: 2.5 Å / D res low: 100 Å / Num. obs: 28505 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.3910097.910.051.1056.9
4.275.3999.810.0620.9777.2
3.734.2799.710.0791.0967.3
3.393.7399.710.1161.0737.3
3.153.3999.410.1761.0937.3
2.963.1599.110.2641.0527.1
2.822.969910.3911.1037
2.692.8297.910.5491.0756.8
2.592.6997.510.7731.0276.5
2.52.5996.410.971.0415.8
ReflectionResolution: 2.343→29.032 Å / Num. all: 34462 / Num. obs: 33165 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.092 / Χ2: 1.047 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.433.60.56532001.08994.6
2.43-2.533.70.49932091.07994.8
2.53-2.653.80.39432231.0794.4
2.65-2.793.80.29531911.0794.3
2.79-2.963.90.20932571.05795.3
2.96-3.193.90.14332961.03796.9
3.19-3.513.90.08933981.04698.5
3.51-4.0240.06234641.00599.9
4.02-5.0640.04634891.005100
5.06-1003.80.0436391.03199.2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.49 Å / D res low: 1000 Å / FOM : 0.34 / Reflection: 23783
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97944.1-8.27
3 wavelength120.91843.92-2.38
3 wavelength130.97885.12-7.01
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se27.9790.6260.7520.1580.755
2Se46.7370.3720.3940.1620.877
3Se49.7130.5710.1470.230.755
4Se44.8710.4270.9980.2270.922
5Se600.1190.8680.0050.907
6Se40.0810.880.9890.0060.611
7Se46.9520.7220.8230.040.773
8Se51.7330.4290.7080.2250.615
9Se50.4790.2750.3290.0360.623
10Se27.7320.2770.9980.2390.592
Phasing MAD shell
Resolution (Å)FOM Reflection
9.09-10000.591250
5.7-9.090.572183
4.44-5.70.512888
3.76-4.440.443295
3.32-3.760.353536
3-3.320.253697
2.76-30.173697
2.57-2.760.093237
Phasing dmFOM : 0.59 / FOM acentric: 0.58 / FOM centric: 0.65 / Reflection: 23779 / Reflection acentric: 21607 / Reflection centric: 2172
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-31.6340.770.770.771204927277
4.5-7.10.750.750.7435813103478
3.6-4.50.720.720.6945044030474
3.1-3.60.620.620.6542273871356
2.7-3.10.490.490.5168226410412
2.5-2.70.340.340.4134413266175

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.343→29.032 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.6723 / SU ML: 0.4 / σ(F): 0.17 / Phase error: 36.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3068 1668 5.04 %Random
Rwork0.2662 ---
obs0.2683 33082 96 %-
all-33082 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.547 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 130.49 Å2 / Biso mean: 37.2925 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.2223 Å20 Å2-0 Å2
2--1.1402 Å20 Å2
3----0.9179 Å2
Refinement stepCycle: LAST / Resolution: 2.343→29.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 64 240 4238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014048
X-RAY DIFFRACTIONf_angle_d1.3545483
X-RAY DIFFRACTIONf_chiral_restr0.076650
X-RAY DIFFRACTIONf_plane_restr0.004705
X-RAY DIFFRACTIONf_dihedral_angle_d16.6321549
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1959X-RAY DIFFRACTIONPOSITIONAL0.063
12B1959X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3431-2.42680.43291680.35332943311192
2.4268-2.52390.40381780.32813047322595
2.5239-2.63870.32581570.30223046320394
2.6387-2.77770.35141590.2913013317293
2.7777-2.95160.35221750.28013060323595
2.9516-3.17920.27751700.25273114328496
3.1792-3.49870.28641820.25183206338898
3.4987-4.00380.26751660.22953268343499
4.0038-5.04010.28941640.227833213485100
5.0401-29.03390.28611490.29363396354597

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