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- PDB-2wuk: DivIVA N-terminal domain, F17A mutant -

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Basic information

Entry
Database: PDB / ID: 2wuk
TitleDivIVA N-terminal domain, F17A mutant
ComponentsSEPTUM SITE-DETERMINING PROTEIN DIVIVA
KeywordsCELL CYCLE / BACTERIAL CELL DIVISION / SEPTATION / SPORULATION
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / division septum assembly / sporulation resulting in formation of a cellular spore / identical protein binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #660 / DivIVA family / DivIVA domain / DivIVA protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Septum site-determining protein DivIVA
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOliva, M.A. / Leonard, T.A. / Lowe, J.
CitationJournal: Embo J. / Year: 2010
Title: Features Critical for Membrane Binding Revealed by Diviva Crystal Structure.
Authors: Oliva, M.A. / Halbedel, S. / Freund, S.M. / Dutow, P. / Leonard, T.A. / Veprintsev, D.B. / Hamoen, L.W. / Lowe, J.
History
DepositionOct 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,0504
Polymers27,0504
Non-polymers00
Water6,990388
1
A: SEPTUM SITE-DETERMINING PROTEIN DIVIVA
B: SEPTUM SITE-DETERMINING PROTEIN DIVIVA


Theoretical massNumber of molelcules
Total (without water)13,5252
Polymers13,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-30 kcal/mol
Surface area7650 Å2
MethodPISA
2
C: SEPTUM SITE-DETERMINING PROTEIN DIVIVA
D: SEPTUM SITE-DETERMINING PROTEIN DIVIVA


Theoretical massNumber of molelcules
Total (without water)13,5252
Polymers13,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-27.1 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.682, 28.566, 66.179
Angle α, β, γ (deg.)90.00, 105.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2given(1), (1), (1)
3given(1), (1), (1)

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Components

#1: Protein
SEPTUM SITE-DETERMINING PROTEIN DIVIVA / CELL DIVISION INITIATION PROTEIN DIVIVA / MINICELL-ASSOCIATED PROTEIN DIVIVA


Mass: 6762.587 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-57 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P71021
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 17 TO ALA ENGINEERED RESIDUE IN CHAIN B, PHE 17 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, PHE 17 TO ALA ENGINEERED RESIDUE IN CHAIN B, PHE 17 TO ALA ENGINEERED RESIDUE IN CHAIN C, PHE 17 TO ALA ENGINEERED RESIDUE IN CHAIN D, PHE 17 TO ALA

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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: 1.9 Å3/Da / Density % sol: 36.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→21.3 Å / Num. obs: 14059 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 16.85 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.2 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15.551 Å / SU ML: 0.8 / σ(F): 0.96 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 1553 5 %
Rwork0.1591 --
obs0.1631 30928 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.14 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0508 Å2-0 Å2-1.7703 Å2
2--0.3733 Å20 Å2
3---0.6774 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 0 388 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071882
X-RAY DIFFRACTIONf_angle_d0.9492535
X-RAY DIFFRACTIONf_dihedral_angle_d16.283745
X-RAY DIFFRACTIONf_chiral_restr0.06281
X-RAY DIFFRACTIONf_plane_restr0.004336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.96130.32721170.24332591X-RAY DIFFRACTION95
1.9613-2.03120.27211130.1992707X-RAY DIFFRACTION96
2.0312-2.11240.26821390.16572592X-RAY DIFFRACTION96
2.1124-2.20820.2211670.1562687X-RAY DIFFRACTION96
2.2082-2.32430.27511620.15072622X-RAY DIFFRACTION97
2.3243-2.46940.23661290.15172714X-RAY DIFFRACTION98
2.4694-2.65920.2441550.15382689X-RAY DIFFRACTION98
2.6592-2.92520.21191370.15082739X-RAY DIFFRACTION98
2.9252-3.34480.22641650.14422699X-RAY DIFFRACTION99
3.3448-4.20030.20711370.12812727X-RAY DIFFRACTION99
4.2003-15.55180.23411320.1692608X-RAY DIFFRACTION94

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