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- PDB-5gnp: Crystal structure of a Z-ring associated protein from Salmonella ... -

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Basic information

Entry
Database: PDB / ID: 5gnp
TitleCrystal structure of a Z-ring associated protein from Salmonella typhimurium
ComponentsCell division protein ZapD
KeywordsSTRUCTURAL PROTEIN / ZapD / cytokinesis / cell division / FtsZ
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / cytoplasm
Similarity search - Function
YacF-like / YacF-like / YacF-like / YacF-like domains / Cell division protein ZapD / Z ring-associated protein D, C-terminal / ZapD domain superfamily / Cell division protein / Sandwich / Orthogonal Bundle ...YacF-like / YacF-like / YacF-like / YacF-like domains / Cell division protein ZapD / Z ring-associated protein D, C-terminal / ZapD domain superfamily / Cell division protein / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
MALONATE ION / Cell division protein ZapD
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChoi, H. / Yoon, H.J. / Lee, H.H.
CitationJournal: To Be Published
Title: Crystal structure of a Z-ring associated protein from Salmonella typhimurium
Authors: Choi, H. / Yoon, H.J. / Lee, H.H.
History
DepositionJul 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein ZapD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2922
Polymers28,1901
Non-polymers1021
Water64936
1
A: Cell division protein ZapD
hetero molecules

A: Cell division protein ZapD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5854
Polymers56,3812
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4100 Å2
ΔGint-22 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.239, 84.239, 149.865
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

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Components

#1: Protein Cell division protein ZapD / Z ring-associated protein D


Mass: 28190.363 Da / Num. of mol.: 1 / Fragment: UNP residues 3-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: zapD, STM0139 / Production host: Escherichia coli (E. coli) / References: UniProt: P67693
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: Sodium malonate, HEPES, Jeffamin ED-2001(pH7.0).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 8289 / % possible obs: 99.7 % / Redundancy: 13 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 48.6
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.802 / SU B: 14.796 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2829 383 4.6 %RANDOM
Rwork0.25134 ---
obs0.25283 7871 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 7 36 2026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192026
X-RAY DIFFRACTIONr_bond_other_d0.0050.021986
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.9742742
X-RAY DIFFRACTIONr_angle_other_deg0.70734543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.155244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2323.75104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11915366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7041521
X-RAY DIFFRACTIONr_chiral_restr0.050.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
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_it2.858.116979
X-RAY DIFFRACTIONr_mcbond_other2.8498.117978
X-RAY DIFFRACTIONr_mcangle_it4.86412.1681222
X-RAY DIFFRACTIONr_mcangle_other4.86212.1671223
X-RAY DIFFRACTIONr_scbond_it2.7238.4371047
X-RAY DIFFRACTIONr_scbond_other2.7228.4351045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6512.5411520
X-RAY DIFFRACTIONr_long_range_B_refined7.77462.5892204
X-RAY DIFFRACTIONr_long_range_B_other7.76962.6032203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 27 -
Rwork0.304 548 -
obs--99.83 %

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