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

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Basic information

Entry
Database: PDB / ID: 4xkq
TitleCrystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2 (co-crystallization with Ni(II) and CD 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)55,07615
Polymers53,5451
Non-polymers1,53014
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.500, 67.220, 116.040
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 19-461
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, 379 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.: 10 / 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.: 365 / 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: 2.28 Å3/Da / Density % sol: 45.96 % / 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 CD medium supernatant.

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Data collection

DiffractionMean temperature: 100 K
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: 1.9→45.77 Å / Num. obs: 39047 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rsym value: 0.11 / Net I/σ(I): 13.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.14 / Rsym value: 0.799 / % possible all: 97.7

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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→45.77 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1951 5 %Random selection
Rwork0.155 ---
obs0.157 39040 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 98 365 4171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013968
X-RAY DIFFRACTIONf_angle_d1.2495360
X-RAY DIFFRACTIONf_dihedral_angle_d14.2721536
X-RAY DIFFRACTIONf_chiral_restr0.056586
X-RAY DIFFRACTIONf_plane_restr0.005692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94760.28571320.24692504X-RAY DIFFRACTION96
1.9476-2.00020.2691380.19222626X-RAY DIFFRACTION99
2.0002-2.05910.25521380.1792611X-RAY DIFFRACTION100
2.0591-2.12560.23331370.17322600X-RAY DIFFRACTION100
2.1256-2.20150.22621380.16852621X-RAY DIFFRACTION100
2.2015-2.28970.21311380.16092635X-RAY DIFFRACTION99
2.2897-2.39390.20491390.15272635X-RAY DIFFRACTION100
2.3939-2.52010.19541380.15252621X-RAY DIFFRACTION100
2.5201-2.67790.20071400.15092657X-RAY DIFFRACTION100
2.6779-2.88470.20031400.14772654X-RAY DIFFRACTION100
2.8847-3.17490.17041400.14262673X-RAY DIFFRACTION100
3.1749-3.63420.19041420.13792698X-RAY DIFFRACTION100
3.6342-4.5780.1551430.13062716X-RAY DIFFRACTION100
4.578-45.78520.18051480.16872838X-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)
10.2203-0.0598-0.08510.28490.05850.3009-0.0598-0.0297-0.02970.04590.02390.03830.05980.0271-0.02440.09780.01830.01730.10140.00740.095844.074645.737617.0741
20.1544-0.09710.11660.49810.01760.3459-0.02240.01220.0353-0.03080.0085-0.0446-0.06660.04510.00230.0797-0.0166-0.00130.09030.00190.090540.181469.85839.7601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 8 THROUGH 201 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 202 THROUGH 472 )

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