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- PDB-1hyq: MIND BACTERIAL CELL DIVISION REGULATOR FROM A. FULGIDUS -

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Basic information

Entry
Database: PDB / ID: 1hyq
TitleMIND BACTERIAL CELL DIVISION REGULATOR FROM A. FULGIDUS
ComponentsCELL DIVISION INHIBITOR (MIND-1)
KeywordsCELL CYCLE / MinC / FtsZ / bacterial cell division
Function / homology
Function and homology information


negative regulation of cell division / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
ATP binding protein MinD, archaea / CobQ/CobB/MinD/ParA nucleotide binding domain / ATP binding protein MinD/FleN / CobQ/CobB/MinD/ParA nucleotide binding 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
Cell division inhibitor (MinD-1)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsCordell, S.C. / Lowe, J.
CitationJournal: FEBS Lett. / Year: 2001
Title: Crystal structure of the bacterial cell division regulator MinD.
Authors: Cordell, S.C. / Lowe, J.
History
DepositionJan 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION INHIBITOR (MIND-1)


Theoretical massNumber of molelcules
Total (without water)27,6901
Polymers27,6901
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.312, 90.312, 83.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CELL DIVISION INHIBITOR (MIND-1) / MIND


Mass: 27689.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0696 / Plasmid: PHIS17 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: O29562
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 2% PEG6000, 100mM TRIS buffer pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %PEG60001reservoir
20.1 MTris-HCl1reservoir
35 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97900, 0.97920, 0.93930
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.93931
ReflectionResolution: 2.6→35 Å / Num. all: 11094 / Num. obs: 10622 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 60.81 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.8 / % possible all: 98.6
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameVersionClassification
SOLVEphasing
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2252 543 random
Rwork0.2058 --
all0.2058 11094 -
obs0.2058 10622 -
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-3.368 Å20 Å20 Å2
2--3.368 Å20 Å2
3----6.735 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 0 27 1718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.332
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection
Rfree0.337 54
Rwork0.2689 -
obs-1007

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