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- PDB-5e1l: Structural and functional analysis of the E. coli FtsZ interactin... -

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Basic information

Entry
Database: PDB / ID: 5e1l
TitleStructural and functional analysis of the E. coli FtsZ interacting protein, ZapC, reveals insight into molecular properties of a novel Z ring stabilizing protein
ComponentsCell division protein ZapC
KeywordsCELL CYCLE / Z ring / cell division
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 / Cell division protein ZapC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.15 Å
AuthorsSchumacher, M.A. / Huang, K.-H. / Tchorzewski, L. / Zeng, W. / Janakiraman, A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Analyses Reveal Insights into the Molecular Properties of the Escherichia coli Z Ring Stabilizing Protein, ZapC.
Authors: Schumacher, M.A. / Zeng, W. / Huang, K.H. / Tchorzewski, L. / Janakiraman, A.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein ZapC


Theoretical massNumber of molelcules
Total (without water)22,7831
Polymers22,7831
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.976, 46.741, 62.910
Angle α, β, γ (deg.)90.000, 105.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein ZapC


Mass: 22783.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ycbW, zapC, AC789_1c09860, BN1008_2209, ECONIH1_05985, EL75_2796, EL79_2872, EL80_2810, HUS2011_1029, HW43_08455, IY32_15190, PD07_27680, PGD_02344, PU06_12140, PU21_19080, PU69_14370, RR31_ ...Gene: ycbW, zapC, AC789_1c09860, BN1008_2209, ECONIH1_05985, EL75_2796, EL79_2872, EL80_2810, HUS2011_1029, HW43_08455, IY32_15190, PD07_27680, PGD_02344, PU06_12140, PU21_19080, PU69_14370, RR31_05140, UN86_22105, UN92_26695, WQ64_03785, WQ65_11505, WQ66_20855, WQ69_14055, WQ70_10055, WQ71_17640, WQ72_12045, WQ73_04655, WQ74_18750, WQ77_23190, WQ79_17420, WQ84_15610, WQ86_15290, WQ88_01710, WQ92_17480, WQ95_04390, WQ99_00770, WR00_01300, WR01_18315, WR03_21275, WR05_24825, WR12_12790, WR13_00430, WR16_17045, WR17_22160, WR18_05905, WR19_22835, WR23_12280, WR24_08325, XB00_15425
Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: W8SPQ2, UniProt: P75862*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.5 M sodium citrate, 0.1 M cacodylate pH 6.5 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→60.5 Å / Num. obs: 9961 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.02 / Net I/σ(I): 11.5
Reflection shellRmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.15→37.643 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 989 9.98 %
Rwork0.197 8925 -
obs0.2003 9914 97.33 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.377 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 80.85 Å2 / Biso mean: 27.4791 Å2 / Biso min: 8.67 Å2
Baniso -1Baniso -2Baniso -3
1-8.7294 Å2-0 Å24.5827 Å2
2--2.1796 Å20 Å2
3----10.909 Å2
Refinement stepCycle: final / Resolution: 2.15→37.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 0 100 1479
Biso mean---32.25 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091414
X-RAY DIFFRACTIONf_angle_d1.4681914
X-RAY DIFFRACTIONf_chiral_restr0.091204
X-RAY DIFFRACTIONf_plane_restr0.007248
X-RAY DIFFRACTIONf_dihedral_angle_d14.228525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1502-2.26360.35171380.30661233137195
2.2636-2.40540.25961380.23121258139697
2.4054-2.5910.26421440.1931293143799
2.591-2.85170.24481450.1911300144599
2.8517-3.26420.23971430.18631286142999
3.2642-4.11170.19671380.17921243138194
4.1117-37.64880.19741430.1811312145597

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