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- PDB-2jee: Xray structure of E. coli YiiU -

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Basic information

Entry
Database: PDB / ID: 2jee
TitleXray structure of E. coli YiiU
ComponentsCELL DIVISION PROTEIN ZAPB
KeywordsCELL CYCLE / FTSZ / SEPTUM / COILED-COIL / CELL DIVISION / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / identical protein binding / cytosol
Similarity search - Function
Cell division protein ZapB / Cell division protein ZapB / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cell division protein ZapB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsMoller-Jensen, J. / Gerdes, K. / Lowe, J.
CitationJournal: Mol.Microbiol. / Year: 2008
Title: Novel Coiled-Coil Cell Division Factor Zapb Stimulates Z Ring Assembly and Cell Division.
Authors: Ebersbach, G. / Galli, E. / Moller-Jensen, J. / Lowe, J. / Gerdes, K.
History
DepositionJan 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN ZAPB
B: CELL DIVISION PROTEIN ZAPB
C: CELL DIVISION PROTEIN ZAPB
D: CELL DIVISION PROTEIN ZAPB


Theoretical massNumber of molelcules
Total (without water)38,5834
Polymers38,5834
Non-polymers00
Water43224
1
A: CELL DIVISION PROTEIN ZAPB
B: CELL DIVISION PROTEIN ZAPB


Theoretical massNumber of molelcules
Total (without water)19,2922
Polymers19,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-45.9 kcal/mol
Surface area13780 Å2
MethodPQS
2
C: CELL DIVISION PROTEIN ZAPB
D: CELL DIVISION PROTEIN ZAPB


Theoretical massNumber of molelcules
Total (without water)19,2922
Polymers19,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-39.9 kcal/mol
Surface area13830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)40.386, 40.777, 80.134
Angle α, β, γ (deg.)104.73, 97.03, 93.56
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 3 - 80 / Label seq-ID: 3 - 80

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2given(1), (1), (1)
3given(1), (1), (1)

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Components

#1: Protein
CELL DIVISION PROTEIN ZAPB / YIIU


Mass: 9645.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AF36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 11163 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / % possible all: 95.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.8→76.7 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.909 / SU B: 32.654 / SU ML: 0.478 / Cross valid method: THROUGHOUT / ESU R: 2.282 / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.321 577 5 %RANDOM
Rwork0.31 ---
obs0.31 10917 95.5 %-
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: 108.45 Å2
Baniso -1Baniso -2Baniso -3
1--4.11 Å2-0.92 Å2-0.01 Å2
2--15.15 Å2-3.61 Å2
3----12.99 Å2
Refinement stepCycle: LAST / Resolution: 2.8→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 0 24 2628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9613504
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5595308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.89527.143168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.28115568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7441516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021988
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2660.21106
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21735
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.50.294
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1093.51610
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86442484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14651119
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8156.51020
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 651 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.060.05
2Btight positional0.10.05
3Ctight positional0.060.05
4Dtight positional0.070.05
1Atight thermal0.110.5
2Btight thermal0.080.5
3Ctight thermal0.090.5
4Dtight thermal0.170.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.515 32
Rwork0.472 625

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