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- PDB-5j1k: Crystal structure of Csd2-Csd2 dimer -

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Basic information

Entry
Database: PDB / ID: 5j1k
TitleCrystal structure of Csd2-Csd2 dimer
ComponentsToxR-activated gene (TagE)
KeywordsHYDROLASE / M23B family metallopeptidase / Homodimer
Function / homology: / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / metalloendopeptidase activity / membrane / ToxR-activated gene (TagE)
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsAn, D.R. / Suh, S.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation2013R1A2A1A05067303 Korea, Republic Of
CitationJournal: Plos One / Year: 2016
Title: Structural Basis of the Heterodimer Formation between Cell Shape-Determining Proteins Csd1 and Csd2 from Helicobacter pylori
Authors: An, D.R. / Im, H.N. / Jang, J.Y. / Kim, H.S. / Kim, J. / Yoon, H.J. / Hesek, D. / Lee, M. / Mobashery, S. / Kim, S.J. / Suh, S.W.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ToxR-activated gene (TagE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6433
Polymers24,4591
Non-polymers1842
Water1,74797
1
A: ToxR-activated gene (TagE)
hetero molecules

A: ToxR-activated gene (TagE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2866
Polymers48,9182
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
Buried area3900 Å2
ΔGint-33 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.772, 140.772, 40.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ToxR-activated gene (TagE)


Mass: 24458.762 Da / Num. of mol.: 1 / Fragment: UNP residues 125-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_1544 / Production host: Escherichia coli (E. coli) / References: UniProt: O26069
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: HEPES, Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→50.01 Å / Num. obs: 22028 / % possible obs: 99.8 % / Redundancy: 16.4 % / Net I/σ(I): 47.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 17 % / Mean I/σ(I) obs: 6.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→50.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.114 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21822 1130 5.1 %RANDOM
Rwork0.18057 ---
obs0.18249 20898 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.81→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 12 97 1566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191504
X-RAY DIFFRACTIONr_bond_other_d0.0020.021452
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9462031
X-RAY DIFFRACTIONr_angle_other_deg0.92833344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41725.21171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3215261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.463153
X-RAY DIFFRACTIONr_chiral_restr0.1020.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021691
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02354
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_it1.481.959727
X-RAY DIFFRACTIONr_mcbond_other1.4741.951726
X-RAY DIFFRACTIONr_mcangle_it2.3632.917907
X-RAY DIFFRACTIONr_mcangle_other2.3632.927908
X-RAY DIFFRACTIONr_scbond_it2.4722.475777
X-RAY DIFFRACTIONr_scbond_other2.4692.475777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0623.5641125
X-RAY DIFFRACTIONr_long_range_B_refined5.82516.9261690
X-RAY DIFFRACTIONr_long_range_B_other5.82516.9281690
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.807→1.853 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 77 -
Rwork0.2 1485 -
obs--98.12 %

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