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

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Basic information

Entry
Database: PDB / ID: 4oev
TitleCrystal structure of NikZ from Campylobacter jejuni in complex with Ni(II) ion
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
NICKEL (II) ION / OXALATE ION / Peptide ABC-transport system periplasmic peptide-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_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.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)114,47712
Polymers113,6312
Non-polymers84610
Water16,159897
1
A: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1465
Polymers56,8151
Non-polymers3314
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)57,3317
Polymers56,8151
Non-polymers5156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)246.120, 47.860, 140.460
Angle α, β, γ (deg.)90.00, 114.60, 90.00
Int Tables number5
Space group name H-MC121

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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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 897 / 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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 % PEG 6000, 0.1 M MES pH 6.0 + NiCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97964 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2013
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 1.9→45.24 Å / Num. all: 118346 / Num. obs: 117159 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.065 / Net I/σ(I): 13.65
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.14 / Num. unique all: 16740 / Rsym value: 0.425 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MXCUBEdata collection
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: 1.9→45.235 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 5854 5 %Random
Rwork0.2019 ---
obs0.2036 117047 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8050 0 50 897 8997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178312
X-RAY DIFFRACTIONf_angle_d1.40711210
X-RAY DIFFRACTIONf_dihedral_angle_d13.8673060
X-RAY DIFFRACTIONf_chiral_restr0.0741188
X-RAY DIFFRACTIONf_plane_restr0.0081438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.32621940.31423681X-RAY DIFFRACTION99
1.9216-1.94420.30611920.29063639X-RAY DIFFRACTION100
1.9442-1.96790.30451950.27313716X-RAY DIFFRACTION100
1.9679-1.99280.32781970.2763725X-RAY DIFFRACTION99
1.9928-2.01910.31921930.26953688X-RAY DIFFRACTION100
2.0191-2.04670.33371950.2683692X-RAY DIFFRACTION100
2.0467-2.0760.31311950.27653705X-RAY DIFFRACTION99
2.076-2.10690.33311930.26463668X-RAY DIFFRACTION100
2.1069-2.13990.311950.26473691X-RAY DIFFRACTION99
2.1399-2.17490.2781950.25273711X-RAY DIFFRACTION99
2.1749-2.21240.3181910.25963640X-RAY DIFFRACTION99
2.2124-2.25270.28961960.24883716X-RAY DIFFRACTION99
2.2527-2.2960.29261940.25773699X-RAY DIFFRACTION99
2.296-2.34290.32441930.25143664X-RAY DIFFRACTION99
2.3429-2.39380.30281980.23993755X-RAY DIFFRACTION99
2.3938-2.44950.29671900.22883615X-RAY DIFFRACTION99
2.4495-2.51070.29561980.2423755X-RAY DIFFRACTION99
2.5107-2.57860.27741910.22123623X-RAY DIFFRACTION99
2.5786-2.65450.23221970.22033742X-RAY DIFFRACTION99
2.6545-2.74020.26631920.22283648X-RAY DIFFRACTION99
2.7402-2.83810.25421950.22563708X-RAY DIFFRACTION99
2.8381-2.95170.24551950.22183696X-RAY DIFFRACTION99
2.9517-3.0860.25441950.20683716X-RAY DIFFRACTION99
3.086-3.24870.23371960.21313713X-RAY DIFFRACTION99
3.2487-3.45210.28411960.19873731X-RAY DIFFRACTION99
3.4521-3.71860.19681970.18063733X-RAY DIFFRACTION99
3.7186-4.09250.18991940.15753700X-RAY DIFFRACTION99
4.0925-4.68420.15331990.13723771X-RAY DIFFRACTION99
4.6842-5.89960.16482010.14133823X-RAY DIFFRACTION99
5.8996-45.24740.1592020.14973829X-RAY DIFFRACTION97
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)
11.3759-0.14960.12280.7354-0.19351.433-0.03810.82580.0302-0.00360.21360.12880.2062-1.0532-0.13630.1826-0.0357-0.04921.10280.1450.3478-44.89640.8343-11.4118
21.36520.0674-0.3650.3181-0.13061.64040.03910.6699-0.1335-0.12670.06490.00790.2466-0.2482-0.07060.249-0.0356-0.0360.67210.00180.3057-23.4553-2.6796-12.5819
30.8582-0.0996-0.15081.1046-0.78963.5022-0.00880.46990.5701-0.0266-0.1496-0.3665-0.69180.96520.02330.3743-0.08390.0650.46890.11450.4801-15.095114.75445.1026
41.6997-0.0075-0.67340.50970.02982.95120.12850.28040.0673-0.0321-0.0337-0.0171-0.18650.1796-0.07830.1745-0.0103-0.00480.29140.06680.2625-23.12274.16742.9967
52.1038-0.5715-0.91970.57270.29521.89080.00620.202-0.0382-0.055-0.08120.13910.0751-1.0620.07310.2543-0.0493-0.03990.57680.05140.2743-53.90630.63824.8632
61.43030.0056-0.32790.25790.04841.82140.0305-0.26890.03970.0398-0.03030.0929-0.061-0.5821-0.02420.24510.0038-0.01990.66010.02790.2771-48.29542.061845.8438
73.02540.1772-0.81530.8830.911.3399-0.0978-1.0566-0.59440.27270.2125-0.04980.88860.30920.0450.583-0.06240.00740.39310.23890.3902-29.3037-15.979746.8141
81.8435-0.1627-0.1850.59720.15832.606-0.084-0.5563-0.1098-0.00230.02390.00480.2526-0.02750.05070.2291-0.0346-0.00960.31470.06460.2229-33.5522-4.741640.7225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 313 )
4X-RAY DIFFRACTION4chain 'A' and (resid 314 through 494 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 151 )
6X-RAY DIFFRACTION6chain 'B' and (resid 152 through 264 )
7X-RAY DIFFRACTION7chain 'B' and (resid 265 through 313 )
8X-RAY DIFFRACTION8chain 'B' and (resid 314 through 494 )

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