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- PDB-2wuj: DivIVA N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2wuj
TitleDivIVA N-terminal domain
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 / SYNCHROTRON / SAD / Resolution: 1.4 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


Theoretical massNumber of molelcules
Total (without water)13,6772
Polymers13,6772
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-28.5 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.089, 32.753, 134.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

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


Mass: 6838.684 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-57
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.: 211 / 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: 2.3 Å3/Da / Density % sol: 45.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.4→33 Å / Num. obs: 22664 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.8 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0054refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.4→67.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 0.913 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22189 1233 4.9 %RANDOM
Rwork0.18635 ---
obs0.18815 23742 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.766 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.4→67.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms842 0 0 211 1053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.022871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5991.9591174
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3935104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48825.38552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58615172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.633156
X-RAY DIFFRACTIONr_chiral_restr0.1490.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02664
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4214507
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3724.5828
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3495.5364
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.66.5343
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 80 -
Rwork0.228 1654 -
obs--90.98 %

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