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- PDB-1y2g: Crystal STructure of ZipA in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 1y2g
TitleCrystal STructure of ZipA in complex with an inhibitor
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-CL3 / Cell division protein ZipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMosyak, L. / Rush, T.S.
CitationJournal: J.Med.Chem. / Year: 2005
Title: A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
Authors: Rush, T.S. / Grant, J.A. / Mosyak, L. / Nicholls, A.
History
DepositionNov 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)31,6693
Polymers31,3262
Non-polymers3431
Water4,017223
1
A: Cell division protein zipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0062
Polymers15,6631
Non-polymers3431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein zipA


Theoretical massNumber of molelcules
Total (without water)15,6631
Polymers15,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.695, 39.521, 70.271
Angle α, β, γ (deg.)90.00, 104.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division protein zipA /


Mass: 15662.851 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: zipa / References: UniProt: P77173
#2: Chemical ChemComp-CL3 / N-METHYL-N-[3-(6-PHENYL[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-3-YL)PHENYL]ACETAMIDE


Mass: 343.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, temperature 298.0K

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 22159 / Biso Wilson estimate: 28.2 Å2
Reflection shellResolution: 1.9→1.97 Å

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F46

1f46


Resolution: 1.9→23.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 606413.33 / 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
Rfree0.241 1044 4.9 %RANDOM
Rwork0.207 ---
obs0.207 21488 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2251 Å2 / ksol: 0.338309 e/Å3
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.6 Å20 Å25.62 Å2
2---2.51 Å20 Å2
3---8.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 26 223 2420
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.82
X-RAY DIFFRACTIONc_scangle_it4.242.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 155 4.9 %
Rwork0.328 2996 -
obs--85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CL3.PARAMCL3.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM

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