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- PDB-2xrh: Crystal structure of the truncated form of HP0721 -

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Basic information

Entry
Database: PDB / ID: 2xrh
TitleCrystal structure of the truncated form of HP0721
ComponentsPROTEIN HP0721
KeywordsUNKNOWN FUNCTION
Function / homologyHP0721 helical bundle / Protein of unknown function DUF1104 / DUF1104 superfamily / Protein of unknown function (DUF1104) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / NICOTINIC ACID / Zinc ABC transporter substrate-binding protein
Function and homology information
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsCioci, G. / Terradot, L. / Dian, C. / Muller-Dieckmann, C. / Leonard, G.
CitationJournal: Proteins / Year: 2011
Title: Crystal Structure of Hp0721, a Novel Secreted Protein from Helicobacter Pylori.
Authors: Cioci, G. / Terradot, L. / Dian, C. / Mueller-Dieckmann, C. / Leonard, G.
History
DepositionSep 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_source
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PROTEIN HP0721
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6352
Polymers11,5121
Non-polymers1231
Water2,018112
1
A: PROTEIN HP0721
hetero molecules

A: PROTEIN HP0721
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2714
Polymers23,0242
Non-polymers2462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area1380 Å2
ΔGint-7.3 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.770, 47.770, 83.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

21A-2014-

HOH

31A-2022-

HOH

41A-2048-

HOH

51A-2107-

HOH

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Components

#1: Protein PROTEIN HP0721


Mass: 11512.160 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PET151/DTOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O25423
#2: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNICOTINIC ACID (NIO): ENDOGENOUS LIGAND. IDENTITY NOT CONFIRMED.

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7 / Details: 2.9M SODIUM MALONATE, PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.954, 1.907
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
21.9071
ReflectionResolution: 1.5→41.38 Å / Num. obs: 17909 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 5.11 % / Biso Wilson estimate: 17.636 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.58
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.06 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 93.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.5.0102refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.5→41.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.892 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 875 4.9 %RANDOM
Rwork0.17486 ---
obs0.17661 17033 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.761 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 9 112 923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022872
X-RAY DIFFRACTIONr_bond_other_d0.0120.02630
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.991166
X-RAY DIFFRACTIONr_angle_other_deg1.01231551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1375109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08825.85441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92615187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.453154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02163
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_it1.6021.5532
X-RAY DIFFRACTIONr_mcbond_other0.5231.5209
X-RAY DIFFRACTIONr_mcangle_it2.6052858
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2383340
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.7364.5308
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.74131502
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 53 -
Rwork0.239 1108 -
obs--87.42 %

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