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- PDB-4inp: The crystal structure of Helicobacter pylori Ceue (HP1561) with N... -

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Basic information

Entry
Database: PDB / ID: 4inp
TitleThe crystal structure of Helicobacter pylori Ceue (HP1561) with Ni(II) bound
ComponentsIron (III) ABC transporter, periplasmic iron-binding protein
KeywordsTRANSPORT PROTEIN / heme-binding protein / Fe transport / ABC transporter substrate binding protein / periplasmic space
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
ACETATE ION / 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: 2.3 Å
AuthorsShaik, 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
DepositionJan 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Iron (III) ABC transporter, periplasmic iron-binding protein
B: Iron (III) ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,88316
Polymers75,0592
Non-polymers82514
Water3,603200
1
A: Iron (III) ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9428
Polymers37,5291
Non-polymers4127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron (III) ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9428
Polymers37,5291
Non-polymers4127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.180, 76.950, 72.780
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A34 - 335
2115B34 - 335

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Components

#1: Protein Iron (III) ABC transporter, periplasmic iron-binding protein / CEUE


Mass: 37529.477 Da / Num. of mol.: 2 / Fragment: UNP residues 32-333 / Mutation: V102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: HPG27_1499 / Plasmid: pET101-HP1561 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5Z9J2
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1 M SPG buffer, 25% w/v PEG1500, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.4852
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4852 Å / Relative weight: 1
ReflectionResolution: 2.3→52.79 Å / Num. obs: 27148 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 5.2 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UI8

3ui8
PDB Unreleased entry


Resolution: 2.3→52.79 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.873 / SU B: 7.029 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1370 5.1 %RANDOM
Rwork0.189 ---
obs0.193 25743 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20.2 Å2
2---0.08 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→52.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4758 0 38 200 4996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9776597
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88925.408196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86615918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.441510
X-RAY DIFFRACTIONr_chiral_restr0.1270.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213578
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_it0.9891.53027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82824887
X-RAY DIFFRACTIONr_scbond_it2.84631866
X-RAY DIFFRACTIONr_scangle_it4.7244.51710
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
1068medium positional0.130.5
1047loose positional0.445
1068medium thermal1.152
1047loose thermal1.2710
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 123 -
Rwork0.167 1966 -
obs--96.31 %

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