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

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Basic information

Entry
Database: PDB / ID: 4xkr
TitleCrystal structure of NikA from Staphylococcus aureus in complex with Ni-(L-His)(2-methyl-thiazolidine dicarboxylate) (co-crystallization with Ni(II) and CDdeltaHis 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
Chem-41K / HISTIDINE / NICKEL (II) ION / Nickel-binding protein NikA / :
Similarity search - Component
Biological speciesStaphylococcus aureus USA300-ISMMS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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_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.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.value / _struct_conn.pdbx_dist_value / _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

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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)55,87024
Polymers53,5451
Non-polymers2,32523
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-14 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.803, 67.373, 115.566
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 , 7 types, 546 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.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Chemical ChemComp-41K / (2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid


Mass: 191.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO4S
#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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 45.25 % / 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 CDdeltaHis medium supernatant.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→45.54 Å / Num. obs: 47766 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 0.078 / Net I/σ(I): 14.6
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.36 / Rsym value: 0.616 / % possible all: 96.4

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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: 1.75→45.543 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 2388 5 %Random selection
Rwork0.1716 ---
obs0.1732 47756 96.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→45.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 148 523 4375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083967
X-RAY DIFFRACTIONf_angle_d1.1255343
X-RAY DIFFRACTIONf_dihedral_angle_d14.3771561
X-RAY DIFFRACTIONf_chiral_restr0.053586
X-RAY DIFFRACTIONf_plane_restr0.005680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78570.23761390.22312632X-RAY DIFFRACTION96
1.7857-1.82460.25421380.22722625X-RAY DIFFRACTION96
1.8246-1.8670.23871370.21942600X-RAY DIFFRACTION96
1.867-1.91370.25821360.20022583X-RAY DIFFRACTION95
1.9137-1.96550.23171380.18872629X-RAY DIFFRACTION97
1.9655-2.02330.21141410.17282676X-RAY DIFFRACTION97
2.0233-2.08860.17651390.16732636X-RAY DIFFRACTION97
2.0886-2.16320.21061410.16542670X-RAY DIFFRACTION97
2.1632-2.24990.19111380.1662632X-RAY DIFFRACTION96
2.2499-2.35220.22691400.16892660X-RAY DIFFRACTION97
2.3522-2.47630.22011420.17052700X-RAY DIFFRACTION98
2.4763-2.63140.20291410.16572671X-RAY DIFFRACTION97
2.6314-2.83450.21061420.16862700X-RAY DIFFRACTION97
2.8345-3.11970.1991420.16562690X-RAY DIFFRACTION97
3.1197-3.5710.19651430.15772726X-RAY DIFFRACTION98
3.571-4.49840.16661420.14732717X-RAY DIFFRACTION96
4.4984-45.55880.19671490.18782821X-RAY DIFFRACTION95
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)
10.4504-0.1603-0.10110.92880.30070.6798-0.0209-0.0003-0.04790.013-0.00880.05710.0207-0.0236-0.00030.08820.00210.01740.10110.00570.101742.789243.068611.6063
20.6494-0.21580.12320.6305-0.090.7103-0.0889-0.09130.0140.23830.0672-0.0084-0.02930.0933-0.04790.10370.0136-0.01270.1221-0.00660.074748.222357.469128.9519
30.1268-0.1214-0.06910.52780.03290.5277-0.03480.08730.1008-0.0166-0.014-0.0312-0.08820.03610.01020.0971-0.0201-0.01020.08540.00460.124538.506675.41927.2556
40.21740.166-0.03770.65730.3490.7470.00270.01360.2335-0.36830.1019-0.0627-0.16020.06770.2150.1945-0.02110.00220.1390.03880.1935.838281.65251.2043
50.2809-0.0111-0.17590.15460.20570.50020.0043-0.07340.06070.17860.02540.0554-0.0669-0.07690.00350.1142-0.0056-0.00460.1046-0.00690.121330.79276.072316.5743
60.4586-0.2343-0.11080.7788-0.00850.3067-0.01210.05320.0078-0.0622-0.0046-0.0546-0.02770.0240.00150.0871-0.00870.00380.106-0.00670.097542.569560.92675.5522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 145 )
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 230 )
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 280 )
4X-RAY DIFFRACTION4chain 'A' and (resid 281 through 314 )
5X-RAY DIFFRACTION5chain 'A' and (resid 315 through 365 )
6X-RAY DIFFRACTION6chain 'A' and (resid 366 through 472 )

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