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- PDB-4oet: Crystal structure of NikZ from Campylobacter jejuni, unliganded form -

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Basic information

Entry
Database: PDB / ID: 4oet
TitleCrystal structure of NikZ from Campylobacter jejuni, unliganded form
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


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / periplasmic space / metal ion binding
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
Peptide ABC-transport system periplasmic peptide-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.4 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 1.2Apr 18, 2018Group: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.detector
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 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)114,36810
Polymers113,6312
Non-polymers7378
Water7,782432
1
A: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3687
Polymers56,8151
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0003
Polymers56,8151
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.060, 85.210, 148.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 % PEG 5000, 100 mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.00446 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00446 Å / Relative weight: 1
ReflectionResolution: 2.4→46.06 Å / Num. all: 40944 / Num. obs: 40880 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rsym value: 0.113 / Net I/σ(I): 14.29
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 4.15 / Rsym value: 0.505 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: PDB ENTRY 1DPE

1dpe


Resolution: 2.4→46.058 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 2044 5 %
Rwork0.1793 --
obs0.1814 40880 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8050 0 48 432 8530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058300
X-RAY DIFFRACTIONf_angle_d0.90211208
X-RAY DIFFRACTIONf_dihedral_angle_d14.4013056
X-RAY DIFFRACTIONf_chiral_restr0.0391188
X-RAY DIFFRACTIONf_plane_restr0.0051434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45580.28691330.23742530X-RAY DIFFRACTION99
2.4558-2.51720.2721330.22522532X-RAY DIFFRACTION100
2.5172-2.58530.24761350.21582556X-RAY DIFFRACTION100
2.5853-2.66140.28821340.21222559X-RAY DIFFRACTION100
2.6614-2.74720.24361350.2112554X-RAY DIFFRACTION100
2.7472-2.84540.25281330.21042544X-RAY DIFFRACTION100
2.8454-2.95930.26211370.20232592X-RAY DIFFRACTION100
2.9593-3.0940.26081360.20612586X-RAY DIFFRACTION100
3.094-3.25710.24891350.1932560X-RAY DIFFRACTION100
3.2571-3.46110.18931360.1722580X-RAY DIFFRACTION100
3.4611-3.72820.2061360.162596X-RAY DIFFRACTION100
3.7282-4.10320.18761370.14892592X-RAY DIFFRACTION100
4.1032-4.69640.18041380.13942633X-RAY DIFFRACTION100
4.6964-5.9150.19561400.16682656X-RAY DIFFRACTION100
5.915-46.06640.19531460.16812766X-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)
13.6329-3.08750.67074.87970.95491.15460.1022-0.20550.3897-0.3989-0.2403-0.6935-0.01190.10450.12290.25350.00910.03430.2756-0.00990.197735.814264.860620.9181
21.7986-0.10630.44831.3829-0.79911.9144-0.0454-0.28110.27990.05950.02020.1004-0.178-0.24920.04340.17530.0155-0.00740.249-0.07530.307225.633974.826710.1003
31.28960.39490.23070.9721-0.20440.889-0.0084-0.0284-0.0108-0.0156-0.0266-0.1085-0.08220.01260.04320.18210.02140.00330.1283-0.0320.136454.151774.686510.347
41.65841.04462.05993.22532.03212.76840.00610.1469-0.22460.0699-0.0145-0.1502-0.11570.21010.07440.2923-0.05020.07830.31060.01050.232279.858469.832533.1453
51.2180.474-0.20440.92560.5362.64140.03590.23360.0484-0.09690.2582-0.2433-0.36510.5215-0.26090.2024-0.06020.04270.3173-0.06380.342487.171171.304549.2588
61.0410.26831.01371.19850.19672.58550.0668-0.1509-0.0609-0.01970.03390.10490.1032-0.4163-0.07390.1824-0.03080.00470.1750.03130.203360.230664.241644.1971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 494 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 27 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 178 )
6X-RAY DIFFRACTION6chain 'B' and (resid 179 through 494 )

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