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- PDB-4ls3: THE crystal STRUCTURE OF HELICOBACTER PYLORI CEUE(HP1561)/NI-HIS COMPL -

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Basic information

Entry
Database: PDB / ID: 4ls3
TitleTHE crystal STRUCTURE OF HELICOBACTER PYLORI CEUE(HP1561)/NI-HIS COMPL
ComponentsNickel (III) ABC transporter, periplasmic iron-bindin gprotein
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER SUBSTRATE BINDING PROTEIN / ABC TRANSPORTER / PERIPLASMIC SPACE / Rossmann-like fold / Ni binding
Function / homology
Function and homology information


cellular response to iron ion
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / NICKEL (II) ION / Iron (III) ABC transporter, periplasmic iron-bindin gprotein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSalamina, M. / Shaik, M.M. / Cendron, L. / Zanotti, G.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Helicobacter pylori periplasmic receptor CeuE (HP1561) modulates its nickel affinity via organic metallophores.
Authors: Shaik, M.M. / Cendron, L. / Salamina, M. / Ruzzene, M. / Zanotti, G.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Nickel (III) ABC transporter, periplasmic iron-bindin gprotein
B: Nickel (III) ABC transporter, periplasmic iron-bindin gprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5818
Polymers74,8392
Non-polymers7426
Water17,907994
1
A: Nickel (III) ABC transporter, periplasmic iron-bindin gprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7904
Polymers37,4191
Non-polymers3713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nickel (III) ABC transporter, periplasmic iron-bindin gprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7904
Polymers37,4191
Non-polymers3713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.420, 60.650, 77.130
Angle α, β, γ (deg.)90.00, 91.02, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-1162-

HOH

21A-1181-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999441, 0.0022, 0.033349), (0.002144, -0.999996, 0.001697), (0.033353, -0.001624, -0.999442)-36.28893, 16.1183, 36.74372

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Components

#1: Protein Nickel (III) ABC transporter, periplasmic iron-bindin gprotein


Mass: 37419.387 Da / Num. of mol.: 2 / Fragment: UNP residues 32-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: HP1561, HPG27_1499 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: B5Z9J2
#2: Chemical
ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 994 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M LiCl, 0.1 M Tris-HCl, 30% PEG 4000., pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.952 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.952 Å / Relative weight: 1
ReflectionResolution: 1.7→30.33 Å / Num. all: 70159 / Num. obs: 70159 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.6 / % possible all: 94.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UI8

3ui8
PDB Unreleased entry


Resolution: 1.7→30.325 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.172 / SU ML: 0.072 / ESU R: 0.108 / ESU R Free: 0.112 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2041 3553 5.06 %
Rwork0.1676 --
obs0.1695 70151 96.5 %
all-70159 -
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: 18.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0.32 Å2
2---0.29 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 46 994 5838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194948
X-RAY DIFFRACTIONr_bond_other_d0.0020.024962
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9726674
X-RAY DIFFRACTIONr_angle_other_deg0.999311494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41925.347202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95315936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9931510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021028
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 225 -
Rwork0.265 4815 -
obs--94.24 %

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