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- PDB-4ofj: Crystal structure of NikA from Staphylococcus aureus in complex w... -

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Basic information

Entry
Database: PDB / ID: 4ofj
TitleCrystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2
ComponentsExtracytoplasmic Nickel-Binding Protein SaNikA
KeywordsTRANSPORT PROTEIN / Extracytoplasmic / Nickel import / Metal transport / ABC-type importer / extracytoplasmic nickel-binding protein
Function / homology
Function and homology information


nickel cation transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll ...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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / NICKEL (II) ION / Nickel-binding protein NikA / ABC transporter, substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLebrette, H. / Cavazza, C.
CitationJournal: Metallomics / Year: 2015
Title: Novel insights into nickel import in Staphylococcus aureus: the positive role of free histidine and structural characterization of a new thiazolidine-type nickel chelator.
Authors: Lebrette, H. / Borezee-Durant, E. / Martin, L. / Richaud, P. / Boeri Erba, E. / Cavazza, C.
History
DepositionJan 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: Extracytoplasmic Nickel-Binding Protein SaNikA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,72022
Polymers53,5451
Non-polymers2,17521
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.900, 67.720, 115.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Extracytoplasmic Nickel-Binding Protein SaNikA / SaNikA


Mass: 53545.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: subsp. aureus COL / Gene: SACOL0217 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HJE1, UniProt: Q2G2P5*PLUS

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Non-polymers , 5 types, 436 molecules

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


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 27 % PEG 3350, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→45.69 Å / Num. all: 54220 / Num. obs: 53990 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.079 / Net I/σ(I): 17.04
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.23 / Num. unique all: 8418 / Rsym value: 0.652 / % possible all: 99.4

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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 3RQT

3rqt


Resolution: 1.7→45.689 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2700 5 %Random
Rwork0.1483 ---
obs0.1501 53988 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 140 415 4263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153977
X-RAY DIFFRACTIONf_angle_d1.5645355
X-RAY DIFFRACTIONf_dihedral_angle_d15.9531540
X-RAY DIFFRACTIONf_chiral_restr0.128584
X-RAY DIFFRACTIONf_plane_restr0.008685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73090.32271390.27332649X-RAY DIFFRACTION99
1.7309-1.76420.27811410.23982670X-RAY DIFFRACTION99
1.7642-1.80020.22571390.19382644X-RAY DIFFRACTION99
1.8002-1.83940.23211390.1682640X-RAY DIFFRACTION99
1.8394-1.88220.20041410.15972686X-RAY DIFFRACTION100
1.8822-1.92920.21611410.14982661X-RAY DIFFRACTION99
1.9292-1.98140.19871390.14692645X-RAY DIFFRACTION99
1.9814-2.03970.20331410.14832680X-RAY DIFFRACTION100
2.0397-2.10550.17911410.15052679X-RAY DIFFRACTION100
2.1055-2.18080.18991410.13862674X-RAY DIFFRACTION100
2.1808-2.26810.17431410.13972686X-RAY DIFFRACTION100
2.2681-2.37130.17941420.13952690X-RAY DIFFRACTION100
2.3713-2.49630.17771420.14882711X-RAY DIFFRACTION100
2.4963-2.65270.19591420.14922695X-RAY DIFFRACTION100
2.6527-2.85750.20061440.14572732X-RAY DIFFRACTION100
2.8575-3.1450.15971440.13882732X-RAY DIFFRACTION100
3.145-3.60.1691440.13352738X-RAY DIFFRACTION100
3.6-4.53490.14121460.1272776X-RAY DIFFRACTION100
4.5349-45.70570.19841530.16032900X-RAY DIFFRACTION99
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)
10.7958-0.3292-0.32692.36661.38372.5352-0.02340.0601-0.0599-0.0159-0.02160.0963-0.0287-0.1130.040.07890.00770.02440.11690.0210.116242.909643.397511.9214
21.02730.09890.18393.41460.46221.4659-0.0781-0.0810.0880.34580.0752-0.1379-0.04460.15130.00590.11560.0241-0.0130.15980.00930.094548.412457.641629.0537
30.8906-0.33410.20521.3181-0.11170.9672-0.01730.03910.0837-0.0673-0.0089-0.0782-0.04890.05910.02490.0831-0.02120.01390.10910.00110.101338.360770.51937.7028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 145 )
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 230 )
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 472 )

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