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

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Basic information

Entry
Database: PDB / ID: 4xkn
TitleCrystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2 (co-crystallization with Ni(II) and L-Histidine)
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: 1.85 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)55,72022
Polymers53,5451
Non-polymers2,17521
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint1 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.490, 67.200, 115.530
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, 517 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.: 496 / 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: 2.27 Å3/Da / Density % sol: 45.7 % / 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 2 and 4 molar equivalents of NiCl2 and L-histidine, respectively.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979621 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979621 Å / Relative weight: 1
ReflectionResolution: 1.85→45.76 Å / Num. obs: 42182 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.11 / Net I/σ(I): 16.89
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.94 / Rsym value: 0.669 / % possible all: 99.2

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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: 1.85→45.76 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2109 5 %Random selection
Rwork0.15 ---
obs0.152 42158 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 140 496 4344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083957
X-RAY DIFFRACTIONf_angle_d1.1065325
X-RAY DIFFRACTIONf_dihedral_angle_d14.1191534
X-RAY DIFFRACTIONf_chiral_restr0.047582
X-RAY DIFFRACTIONf_plane_restr0.005680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.89310.261380.22882608X-RAY DIFFRACTION99
1.8931-1.94040.27191380.19082624X-RAY DIFFRACTION100
1.9404-1.99290.23371390.18732649X-RAY DIFFRACTION100
1.9929-2.05150.21921380.17712615X-RAY DIFFRACTION100
2.0515-2.11780.24791380.18862609X-RAY DIFFRACTION99
2.1178-2.19340.17151390.14732640X-RAY DIFFRACTION100
2.1934-2.28130.19411390.14232656X-RAY DIFFRACTION100
2.2813-2.38510.19781400.14152653X-RAY DIFFRACTION100
2.3851-2.51080.19281410.15072671X-RAY DIFFRACTION100
2.5108-2.66810.20331390.14522659X-RAY DIFFRACTION100
2.6681-2.87410.18481410.14912678X-RAY DIFFRACTION100
2.8741-3.16330.17491420.13882699X-RAY DIFFRACTION100
3.1633-3.62080.16111430.12852706X-RAY DIFFRACTION100
3.6208-4.56120.15291440.12032733X-RAY DIFFRACTION100
4.5612-45.77570.20981500.15972849X-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)
10.5405-0.2191-0.04551.13990.50381.164-0.03660.012-0.03430.02970.00190.05510.0567-0.01140.0280.09080.00870.02010.1020.01250.108943.326343.223412.0013
20.77850.07560.20361.51610.17291.023-0.0761-0.09890.06880.20110.0426-0.1109-0.04980.210.03550.13230.0123-0.02010.16930.00560.106548.883457.496828.9888
30.5221-0.0920.07690.95590.04330.8256-0.0040.02130.0685-0.07840.0025-0.0599-0.10450.05090.00690.0919-0.01470.00470.1010.00390.105438.5370.13837.6562
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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