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- PDB-1s1j: Crystal Structure of ZipA in complex with indoloquinolizin inhibitor 1 -

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Basic information

Entry
Database: PDB / ID: 1s1j
TitleCrystal Structure of ZipA in complex with indoloquinolizin inhibitor 1
ComponentsCell division protein zipA
KeywordsCELL CYCLE
Function / homology
Function and homology information


divisome complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / cell division / protein homodimerization activity / plasma membrane
Similarity search - Function
Cell Division Protein Zipa; Chain: A, / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal FtsZ-binding domain / Cell division protein ZipA / ZipA, C-terminal FtsZ-binding domain superfamily / ZipA, C-terminal FtsZ-binding domain / ZipA, C-terminal domain (FtsZ-binding) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IQZ / Cell division protein ZipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsJenning, L.D. / Foreman, K.W. / Rush III, T.S. / Tsao, D.H. / Mosyak, L. / Li, Y. / Sukhdeo, M.N. / Ding, W. / Dushin, E.G. / Kenney, C.H. ...Jenning, L.D. / Foreman, K.W. / Rush III, T.S. / Tsao, D.H. / Mosyak, L. / Li, Y. / Sukhdeo, M.N. / Ding, W. / Dushin, E.G. / Kenney, C.H. / Moghazeh, S.L. / Peterson, P.J. / Ruzin, A.V. / Tuckman, M. / Sutherland, A.G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2004
Title: Design and synthesis of indolo[2,3-a]quinolizin-7-one inhibitors of the ZipA-FtsZ interaction
Authors: Jennings, L.D. / Foreman, K.W. / Rush III, T.S. / Tsao, D.H. / Mosyak, L. / Li, Y. / Sukhdeo, M.N. / Ding, W. / Dushin, E.G. / Kenny, C.H. / Moghazeh, S.L. / Petersen, P.J. / Ruzin, A.V. / ...Authors: Jennings, L.D. / Foreman, K.W. / Rush III, T.S. / Tsao, D.H. / Mosyak, L. / Li, Y. / Sukhdeo, M.N. / Ding, W. / Dushin, E.G. / Kenny, C.H. / Moghazeh, S.L. / Petersen, P.J. / Ruzin, A.V. / Tuckman, M. / Sutherland, A.G.
History
DepositionJan 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 zipA
B: Cell division protein zipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5093
Polymers32,2692
Non-polymers2401
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.789, 39.461, 70.513
Angle α, β, γ (deg.)90.00, 105.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division protein zipA /


Mass: 16134.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ZIPA, B2412 / Production host: Escherichia coli (E. coli) / References: UniProt: P77173
#2: Chemical ChemComp-IQZ / (12bS)-1,2,3,4,12,12b-hexahydroindolo[2,3-a]quinolizin-7(6H)-one


Mass: 240.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N2O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.2 Å3/Da / Density % sol: 36 %
Crystal growpH: 6 / Details: 10-15% PEG 6K, 0.1M MES

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Data collection

Diffraction sourceSource: ROTATING ANODE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.17→99 Å / Num. obs: 14841 / % possible obs: 98.7 % / Redundancy: 4 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.04
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 3 % / Mean I/σ(I) obs: 10.6 / Rsym value: 0.122 / % possible all: 92.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→19.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 244860.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1023 7 %RANDOM
Rwork0.192 ---
obs0.192 14687 98.1 %-
all-14687 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.79 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.15 Å20 Å23.46 Å2
2---3.43 Å20 Å2
3---6.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2.18→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 18 226 2384
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.811.5
X-RAY DIFFRACTIONc_mcangle_it2.842
X-RAY DIFFRACTIONc_scbond_it2.972
X-RAY DIFFRACTIONc_scangle_it4.282.5
LS refinement shellResolution: 2.18→2.31 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 146 6.5 %
Rwork0.172 2096 -
obs--89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2W33.PARAMW33.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM

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