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- PDB-4ino: The crystal structure of Helicobacter pylori Ceue (HP1561) -

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Basic information

Entry
Database: PDB / ID: 4ino
TitleThe crystal structure of Helicobacter pylori Ceue (HP1561)
ComponentsNickel (II) ABC transporter, periplasmic nickel-binding protein
KeywordsTRANSPORT PROTEIN / heme-binding protein / Fe transport / ABC transporter substrate binding protein / periplasmic space
Function / homologyABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / cellular response to iron ion / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Iron (III) ABC transporter, periplasmic iron-bindin gprotein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nickel (II) ABC transporter, periplasmic nickel-binding protein
B: Nickel (II) ABC transporter, periplasmic nickel-binding protein


Theoretical massNumber of molelcules
Total (without water)75,0592
Polymers75,0592
Non-polymers00
Water8,881493
1
A: Nickel (II) ABC transporter, periplasmic nickel-binding protein


Theoretical massNumber of molelcules
Total (without water)37,5291
Polymers37,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nickel (II) ABC transporter, periplasmic nickel-binding protein


Theoretical massNumber of molelcules
Total (without water)37,5291
Polymers37,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.370, 87.020, 105.900
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: GLN / Beg label comp-ID: GLN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 5 / Auth seq-ID: 34 - 335 / Label seq-ID: 1 - 302

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

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Components

#1: Protein Nickel (II) ABC transporter, periplasmic nickel-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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / pH: 8
Details: 0.1 M SPG buffer, 25% w/v PEG1500, pH 8.0, VAPOR DIFFUSION, temperature 393K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM1410.97627
SYNCHROTRONESRF ID2920.9792
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDAug 31, 2011
PSI PILATUS 6M2PIXELMay 5, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.976271
20.97921
ReflectionResolution: 1.65→47.59 Å / Num. obs: 73090 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.3 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→45.234 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU ML: 0.18 / σ(F): 1.33 / Phase error: 22.46 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE BINDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2246 3661 5.01 %
Rwork0.1932 --
obs0.1948 73002 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 0 493 5289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074904
X-RAY DIFFRACTIONf_angle_d1.1496620
X-RAY DIFFRACTIONf_dihedral_angle_d13.7541840
X-RAY DIFFRACTIONf_chiral_restr0.082746
X-RAY DIFFRACTIONf_plane_restr0.005832
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
1208medium positional0.20.5
1190loose positional0.445
1208medium thermal2.352
1190loose thermal2.2710
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 263 -
Rwork0.289 5064 -
obs--96.4 %

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