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- PDB-4inn: Protein HP1028 from the human pathogen Helicobacter pylori belong... -

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Basic information

Entry
Database: PDB / ID: 4inn
TitleProtein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family
ComponentsHP1028
KeywordsTRANSPORT PROTEIN / beta-barrel / lipocalins fold / binding protein
Function / homologyLipocalin - #520 / Domain of unknown function DUF2147 / Uncharacterized protein conserved in bacteria (DUF2147) / Lipocalin / Beta Barrel / Mainly Beta / DUF2147 domain-containing protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBarison, N. / Cendron, L. / Loconte, V. / Zanotti, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family.
Authors: Barison, N. / Cendron, L. / Loconte, V. / Proctor, E.A. / Dokholyan, N.V. / Zanotti, G.
History
DepositionJan 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: HP1028
B: HP1028
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0873
Polymers41,7602
Non-polymers3261
Water1,15364
1
A: HP1028
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2072
Polymers20,8801
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HP1028


Theoretical massNumber of molelcules
Total (without water)20,8801
Polymers20,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.240, 79.150, 131.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 16 - 161 / Label seq-ID: 33 - 178

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999918, -0.009497, 0.008557), (-0.010517, -0.991672, 0.128357), (0.007266, -0.128436, -0.991691)-2.13325, -9.68252, 222.30487

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Components

#1: Protein HP1028


Mass: 20880.230 Da / Num. of mol.: 2 / Fragment: UNP residues 17-161 / Mutation: L129M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: CCUG17874 / Gene: hp1028, HP17_02362 / Plasmid: pET151-hp1028 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I0ZEL6
#2: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2008
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50.71 Å / Num. all: 11665 / Num. obs: 11665 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 19
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1656 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→50.67 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.303 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.784 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24773 552 4.8 %RANDOM
Rwork0.19109 ---
obs0.19384 11069 99.91 %-
all-11665 --
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: 26.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--1.73 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 22 64 2507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022499
X-RAY DIFFRACTIONr_bond_other_d0.0020.022386
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9683338
X-RAY DIFFRACTIONr_angle_other_deg0.8893.0045513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05323.967121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.82215457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7591512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
860MEDIUM POSITIONAL0.30.5
1516LOOSE POSITIONAL0.675
860MEDIUM THERMAL4.012
1516LOOSE THERMAL5.2410
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 39 -
Rwork0.242 803 -
obs--100 %

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