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- PDB-5fo3: ZapC cell division regulator from E. coli -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5fo3
TitleZapC cell division regulator from E. coli
ComponentsCELL DIVISION PROTEIN ZAPC
KeywordsCELL CYCLE / FTSZ / BACTERIAL CELL DIVISION / Z-RING ASSOCIATED PROTEIN C
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / regulation of cell division / identical protein binding / cytoplasm
Similarity search - Function
Cell division protein ZapC / : / : / Cell-division protein ZapC, C-terminal / Cell-division protein ZapC, N-terminal
Similarity search - Domain/homology
Cell division protein ZapC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsOrtiz, C. / Kureisaite-Ciziene, D. / Schmitz, F. / Vicente, M. / Lowe, J.
CitationJournal: FEBS Lett. / Year: 2015
Title: Crystal Structure of the Z-Ring Associated Cell Division Protein Zapc from Escherichia Coli.
Authors: Ortiz, C. / Kureisaite-Ciziene, D. / Schmitz, F. / Mclaughlin, S.H. / Vicente, M. / Lowe, J.
History
DepositionNov 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN ZAPC
B: CELL DIVISION PROTEIN ZAPC


Theoretical massNumber of molelcules
Total (without water)42,1612
Polymers42,1612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-8.7 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.371, 87.371, 118.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.820479, -0.557033, 0.128562), (-0.571474, 0.805163, -0.158524), (-0.01521, -0.203535, -0.978949)-32.45643, -5.81621, 45.87761

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Components

#1: Protein CELL DIVISION PROTEIN ZAPC / FTSZ-ASSOCIATED PROTEIN C / Z-RING-ASSOCIATED PROTEIN C


Mass: 21080.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P75862
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 56.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97858
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10807 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 41.8 % / Rmerge(I) obs: 0.3 / Net I/σ(I): 17
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 40.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→50.01 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / SU B: 33.423 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24734 508 4.8 %RANDOM
Rwork0.21306 ---
obs0.21474 10114 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 0 0 2700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192768
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5551.9753744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7365334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17223.881134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.62715422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8071520
X-RAY DIFFRACTIONr_chiral_restr0.1890.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212120
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_it1.421.5661342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5782.3381674
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5761.8651424
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 36 -
Rwork0.291 723 -
obs--99.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.94230.1695-0.80072.14230.35434.0559-0.17750.4367-0.014-0.4190.091-0.2283-0.48530.26030.08660.1881-0.0767-0.03480.07050.00760.14461.4191-26.681410.5544
25.7203-0.14141.65653.9418-1.13455.2318-0.5094-1.338-0.10960.47190.5660.3129-0.3396-1.3534-0.05660.15040.25310.01830.60650.02470.0415-15.3266-28.43442.2591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 168
2X-RAY DIFFRACTION2B1 - 168

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