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

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Basic information

Entry
Database: PDB / ID: 4xkp
TitleCrystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2 (co-crystallization with Ni(II) and BHI medium supernatant)
ComponentsNickel ABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / Extracytoplasmic Nickel-Binding Protein / Nickel import / ABC-type importer
Function / homology
Function and homology information


nickel cation transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / 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. ...: / 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 / :
Similarity search - Component
Biological speciesStaphylococcus aureus USA300-ISMMS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nickel ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,98314
Polymers53,5451
Non-polymers1,43813
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)62.340, 67.240, 115.210
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 Nickel ABC transporter substrate-binding protein


Mass: 53545.285 Da / Num. of mol.: 1 / Fragment: UNP residues 19-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus USA300-ISMMS1 (bacteria)
Gene: AZ30_01190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W6DY02, UniProt: Q2G2P5*PLUS

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Non-polymers , 5 types, 428 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#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: 2.25 Å3/Da / Density % sol: 45.45 % / Description: plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 27% PEG 3350, 0.1 M HEPES pH 7.0 - protein pre-incubated with NiCl2 and BHI medium supernatant.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97901 Å
DetectorType: DECTRIS PILATUS 6M-F / 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: 1.9→45.72 Å / Num. obs: 38955 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.12 / Net I/σ(I): 13.13
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.58 / Rsym value: 0.714 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OFJ

4ofj


Resolution: 1.9→45.72 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1945 5 %Random selection
Rwork0.158 ---
obs0.16 38891 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 92 415 4215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053963
X-RAY DIFFRACTIONf_angle_d0.9415355
X-RAY DIFFRACTIONf_dihedral_angle_d13.6271534
X-RAY DIFFRACTIONf_chiral_restr0.039586
X-RAY DIFFRACTIONf_plane_restr0.004692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.25341370.21432598X-RAY DIFFRACTION100
1.9475-2.00020.21161360.18772595X-RAY DIFFRACTION100
2.0002-2.0590.21431370.17472590X-RAY DIFFRACTION100
2.059-2.12550.21421370.17282614X-RAY DIFFRACTION100
2.1255-2.20150.21591370.15622593X-RAY DIFFRACTION100
2.2015-2.28960.20181380.15922628X-RAY DIFFRACTION100
2.2896-2.39380.20411380.16282625X-RAY DIFFRACTION100
2.3938-2.520.18641370.16172603X-RAY DIFFRACTION100
2.52-2.67790.19681390.16412638X-RAY DIFFRACTION100
2.6779-2.88460.19181380.15712625X-RAY DIFFRACTION100
2.8846-3.17480.20981390.15582649X-RAY DIFFRACTION100
3.1748-3.63410.15131410.14222665X-RAY DIFFRACTION100
3.6341-4.57790.17081420.13462704X-RAY DIFFRACTION100
4.5779-45.72850.1881490.1662819X-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)
10.3219-0.14-0.11580.71130.02280.6491-0.0516-0.00540.00060.0990.0285-0.00540.02040.0413-00.10780.020.01060.13030.01260.125445.480348.928118.348
20.3917-0.09240.03240.68080.07390.5453-0.01670.01590.0417-0.05220.0077-0.0241-0.07240.031600.0926-0.01560.00490.10220.00610.107638.411670.10067.6077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 8 THROUGH 233 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 234 THROUGH 472 )

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