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- PDB-1hf2: Crystal structure of the bacterial cell-division inhibitor MinC f... -

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Basic information

Entry
Database: PDB / ID: 1hf2
TitleCrystal structure of the bacterial cell-division inhibitor MinC from T. maritima
ComponentsSEPTUM SITE-DETERMINING PROTEIN MINC
KeywordsCELL DIVISION PROTEIN / FTSZ / SEPTUM / BACTERIAL CELL DIVISION / BETA HELIX
Function / homology
Function and homology information


regulation of cell septum assembly / division septum assembly / cell morphogenesis
Similarity search - Function
Cell-division inhibitor MinC, N-terminal domain / Septum formation inhibitor MinC, C-terminal / Septum formation inhibitor MinC / Septum formation inhibitor MinC, C-terminal domain superfamily / Septum formation inhibitor MinC, C-terminal domain / Pectate Lyase C-like - #70 / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Transcription Regulator spoIIAA / Pectate Lyase C-like / 3 Solenoid ...Cell-division inhibitor MinC, N-terminal domain / Septum formation inhibitor MinC, C-terminal / Septum formation inhibitor MinC / Septum formation inhibitor MinC, C-terminal domain superfamily / Septum formation inhibitor MinC, C-terminal domain / Pectate Lyase C-like - #70 / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Transcription Regulator spoIIAA / Pectate Lyase C-like / 3 Solenoid / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Probable septum site-determining protein MinC
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsCordell, S.C. / Anderson, R.E. / Lowe, J.
CitationJournal: Embo J. / Year: 2001
Title: Crystal Structure of the Bacterial Cell-Division Inhibitor Minc
Authors: Cordell, S.C. / Anderson, R.E. / Lowe, J.
History
DepositionNov 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 24, 2018Group: Atomic model / Source and taxonomy / Category: atom_site / entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEPTUM SITE-DETERMINING PROTEIN MINC
B: SEPTUM SITE-DETERMINING PROTEIN MINC
C: SEPTUM SITE-DETERMINING PROTEIN MINC
D: SEPTUM SITE-DETERMINING PROTEIN MINC


Theoretical massNumber of molelcules
Total (without water)91,0284
Polymers91,0284
Non-polymers00
Water11,890660
1
A: SEPTUM SITE-DETERMINING PROTEIN MINC
B: SEPTUM SITE-DETERMINING PROTEIN MINC


Theoretical massNumber of molelcules
Total (without water)45,5142
Polymers45,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SEPTUM SITE-DETERMINING PROTEIN MINC
D: SEPTUM SITE-DETERMINING PROTEIN MINC


Theoretical massNumber of molelcules
Total (without water)45,5142
Polymers45,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.580, 106.090, 162.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SEPTUM SITE-DETERMINING PROTEIN MINC / MINC


Mass: 22757.021 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Cellular location: CYTOPLASM / Gene: MINC / Plasmid: PHIS17 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9X0D7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.33 Å3/Da / Density % sol: 48 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
121 %PEG20001reservoir
20.1 Msodium citrate1reservoir
35.8 %ethanol1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40403 / % possible obs: 95 % / Redundancy: 3.2 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.7 / % possible all: 87.3

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→100 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.3001 2177 5 %RANDOM
Rwork0.237 ---
obs0.237 43859 94.8 %-
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1--19.862 Å20 Å20 Å2
2--12.796 Å20 Å2
3---7.067 Å2
Refinement stepCycle: LAST / Resolution: 2.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6029 0 0 660 6689
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.279
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it22
X-RAY DIFFRACTIONc_mcangle_it44
X-RAY DIFFRACTIONc_scbond_it44
X-RAY DIFFRACTIONc_scangle_it66
Refine LS restraints NCSRms dev position: 0.5024 Å / Weight position: 0.5024
LS refinement shellResolution: 2.2→2.22 Å / Total num. of bins used: 43
RfactorNum. reflection% reflection
Rfree0.3516 51 5 %
Rwork0.3109 873 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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