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- PDB-4kzs: Crystal structure of the secreted protein HP1454 from the human p... -

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Basic information

Entry
Database: PDB / ID: 4kzs
TitleCrystal structure of the secreted protein HP1454 from the human pathogen Helicobacter pylori
ComponentsLPP20 lipofamily protein
KeywordsUNKNOWN FUNCTION / Helicobacter pylori / secreted proteins / outer membrane / Tol-Pal system / Three-helix bundle
Function / homology
Function and homology information


Double Stranded RNA Binding Domain - #710 / Helix Hairpins - #1870 / : / : / LPP20 lipofamily protein, C-terminal domain / LPP20 lipofamily protein, middle domain / Acetamidase/Formamidase-like domains / Lipoprotein LPP20-like / LPP20 lipoprotein / Endonuclease I-creI ...Double Stranded RNA Binding Domain - #710 / Helix Hairpins - #1870 / : / : / LPP20 lipofamily protein, C-terminal domain / LPP20 lipofamily protein, middle domain / Acetamidase/Formamidase-like domains / Lipoprotein LPP20-like / LPP20 lipoprotein / Endonuclease I-creI / Helix Hairpins / Double Stranded RNA Binding Domain / Helix non-globular / Special / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LPP20 lipofamily protein
Similarity search - Component
Biological speciesHelicobacter pylori R046Wa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsQuarantini, S. / Cendron, L. / Fischer, W. / Zanotti, G.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of the secreted protein HP1454 from the human pathogen Helicobacter pylori.
Authors: Quarantini, S. / Cendron, L. / Zanotti, G.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: LPP20 lipofamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2582
Polymers32,0191
Non-polymers2381
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.640, 101.350, 121.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-523-

HOH

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Components

#1: Protein LPP20 lipofamily protein


Mass: 32019.309 Da / Num. of mol.: 1 / Mutation: V10M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori R046Wa (bacteria) / Strain: CCUG 17874 / Gene: hp1454, OUO_1490 / Plasmid: HP1454-pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K2KM35
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M Sodium Acetate, and 2.0 M Ammonium Sulfate, pH 4.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97887, 0.97826
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978871
20.978261
ReflectionResolution: 2.7→60.54 Å / Num. all: 12784 / Num. obs: 12784 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1854 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
SHARPphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→33.44 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.859 / SU B: 13.2 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.464 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30433 623 4.9 %RANDOM
Rwork0.24786 ---
obs0.25043 12075 99.26 %-
all-12784 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 85.21 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å20 Å20 Å2
2---6.96 Å20 Å2
3---2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 14 35 1961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021949
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9782623
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.0525.28787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18915368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5481510
X-RAY DIFFRACTIONr_chiral_restr0.1250.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211421
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 45 -
Rwork0.337 888 -
obs--100 %

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