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- PDB-4oeu: Crystal structure of NikZ from Campylobacter jejuni in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4oeu
TitleCrystal structure of NikZ from Campylobacter jejuni in complex with Ni(L-His)
ComponentsPutative peptide ABC-transport system periplasmic peptide-binding protein
KeywordsTRANSPORT PROTEIN / Extracytoplasmic / Nickel import / Metal transport / ABC-type importer / extracytoplasmic nickel-binding protein
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Peptide ABC-transport system periplasmic peptide-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLebrette, H. / Cavazza, C.
CitationJournal: Structure / Year: 2014
Title: Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins.
Authors: Lebrette, H. / Brochier-Armanet, C. / Zambelli, B. / de Reuse, H. / Borezee-Durant, E. / Ciurli, S. / Cavazza, C.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Sep 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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: Putative peptide ABC-transport system periplasmic peptide-binding protein
B: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,76215
Polymers113,6312
Non-polymers1,13213
Water5,531307
1
A: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3597
Polymers56,8151
Non-polymers5436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4048
Polymers56,8151
Non-polymers5887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.480, 72.770, 86.090
Angle α, β, γ (deg.)90.00, 111.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-503-

NI

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative peptide ABC-transport system periplasmic peptide-binding protein / NikZ


Mass: 56815.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: subsp. jejuni NCTC 11168 = ATCC 700819 / Gene: Cj1584c / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P844

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Non-polymers , 6 types, 320 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % PEG 3350, 100 mM HEPES pH 7.0, 0.2 M MgCl2. Crystal soaking in a solution containing 1 mM NiCl2 and 2 mM L-His., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97901 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.2→46.63 Å / Num. all: 45179 / Num. obs: 44298 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.057 / Net I/σ(I): 23.62
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 3.09 / Rsym value: 0.648 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OET

4oet


Resolution: 2.2→46.626 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 2215 5 %Random
Rwork0.1923 ---
obs0.1947 44286 98.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8032 0 66 307 8405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078309
X-RAY DIFFRACTIONf_angle_d0.88411224
X-RAY DIFFRACTIONf_dihedral_angle_d12.753054
X-RAY DIFFRACTIONf_chiral_restr0.0391188
X-RAY DIFFRACTIONf_plane_restr0.0041436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2480.40891300.33682476X-RAY DIFFRACTION94
2.248-2.30030.30491380.27282618X-RAY DIFFRACTION98
2.3003-2.35780.29751370.25182598X-RAY DIFFRACTION98
2.3578-2.42150.30481370.24892611X-RAY DIFFRACTION98
2.4215-2.49280.36031370.25072599X-RAY DIFFRACTION98
2.4928-2.57320.32671380.23342617X-RAY DIFFRACTION98
2.5732-2.66520.27881390.23382641X-RAY DIFFRACTION98
2.6652-2.77190.30991360.22152588X-RAY DIFFRACTION98
2.7719-2.8980.26311390.21262639X-RAY DIFFRACTION99
2.898-3.05080.28211390.2232637X-RAY DIFFRACTION98
3.0508-3.24190.22251370.21252615X-RAY DIFFRACTION99
3.2419-3.49210.23061400.19662648X-RAY DIFFRACTION99
3.4921-3.84340.2271400.16462668X-RAY DIFFRACTION99
3.8434-4.39920.18991400.15052663X-RAY DIFFRACTION99
4.3992-5.54110.18211420.15912690X-RAY DIFFRACTION99
5.5411-46.63640.23311460.17012763X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1194-0.1624-0.36234.6067-0.96943.02550.10010.04230.1814-0.0482-0.07180.3607-0.20270.1352-0.04040.2518-0.0254-0.07060.2376-0.02120.3181-57.687528.0337-6.8166
24.126-3.2169-1.67969.18072.96562.75740.13620.64130.1354-0.8769-0.1513-0.5575-0.0930.2475-0.03290.3752-0.07960.05340.5919-0.00830.324-40.935823.212-16.8149
31.41990.63510.16893.49240.63221.685-0.05860.019-0.0380.09090.088-0.05250.270.29120.00050.27150.0907-0.03770.32610.01910.2105-54.61160.1032-6.6435
41.5963-0.1559-0.63282.05860.92272.0322-0.3178-0.1491-0.44130.11120.21340.03320.49240.31490.09370.43950.1360.07950.3087-0.01130.4513-72.9418-29.750133.1529
51.45160.1512-0.24281.44180.36822.4696-0.1714-0.6876-0.26210.54630.1498-0.11820.50110.6018-0.00070.56130.24860.05240.6940.02930.4817-71.523-20.195653.3032
60.9708-0.4954-1.2983.43391.2112.31440.5786-0.38350.8624-0.38830.2143-0.0678-1.06180.7001-0.55290.73-0.16890.29750.4764-0.18090.8093-73.65289.168637.2178
72.3516-0.2525-0.79232.44040.59212.49740.0542-0.20540.2106-0.11020.1754-0.1083-0.1510.5793-0.14810.2511-0.01230.04640.3345-0.08240.289-71.8507-8.920435.3472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 178 )
2X-RAY DIFFRACTION2chain 'B' and (resid 179 through 208 )
3X-RAY DIFFRACTION3chain 'B' and (resid 209 through 494 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 151 )
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 246 )
6X-RAY DIFFRACTION6chain 'A' and (resid 247 through 357 )
7X-RAY DIFFRACTION7chain 'A' and (resid 358 through 494 )

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