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- PDB-5yhe: The crystal structure of Staphylococcus aureus CntA in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5yhe
TitleThe crystal structure of Staphylococcus aureus CntA in complex with staphylopine and cobalt
ComponentsNickel ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / receptor
Function / homology
Function and homology information


nickel cation transport / zinc ion transport / cobalt ion transport / peptide transport / peptide transmembrane transporter activity / nickel cation binding / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / heme binding
Similarity search - Function
Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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. ...Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8UX / ACETATE ION / : / Nickel ABC transporter substrate-binding protein / Metal-staphylopine-binding protein CntA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.465 Å
AuthorsSong, L. / Ji, Q.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanistic insights into staphylopine-mediated metal acquisition
Authors: Song, L. / Zhang, Y. / Chen, W. / Gu, T. / Zhang, S.Y. / Ji, Q.
History
DepositionSep 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,31310
Polymers115,3262
Non-polymers9878
Water7,116395
1
A: Nickel ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2046
Polymers57,6631
Non-polymers5415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area21060 Å2
MethodPISA
2
B: Nickel ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1094
Polymers57,6631
Non-polymers4463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.605, 76.659, 85.673
Angle α, β, γ (deg.)90.68, 91.25, 104.57
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nickel ABC transporter substrate-binding protein


Mass: 57663.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: opp-1A, AYM28_13740, AYM37_13740, ERS072738_00487, ERS074020_00717, HMPREF3211_02361
Production host: Escherichia coli (E. coli) / References: UniProt: A0A068A9N4, UniProt: Q2FVE7*PLUS

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Non-polymers , 5 types, 403 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-8UX / (2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid / staphylopine


Mass: 328.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M BICINE pH 8.5, 8%(w/v) Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.465→50 Å / Num. obs: 37030 / % possible obs: 98 % / Redundancy: 3.5 % / Net I/σ(I): 11.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.465→36.776 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.99 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.2345 1839 4.97 %
Rwork0.1612 --
obs0.1649 37019 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.465→36.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 61 395 8525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078269
X-RAY DIFFRACTIONf_angle_d0.99511092
X-RAY DIFFRACTIONf_dihedral_angle_d17.8425089
X-RAY DIFFRACTIONf_chiral_restr0.0551177
X-RAY DIFFRACTIONf_plane_restr0.0061444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4647-2.53140.32581390.23882620X-RAY DIFFRACTION94
2.5314-2.60580.28511460.21542708X-RAY DIFFRACTION98
2.6058-2.68990.30581360.20932687X-RAY DIFFRACTION97
2.6899-2.7860.28991440.19392710X-RAY DIFFRACTION98
2.786-2.89750.30171510.19552660X-RAY DIFFRACTION98
2.8975-3.02930.281110.19372761X-RAY DIFFRACTION98
3.0293-3.1890.29551520.19272661X-RAY DIFFRACTION98
3.189-3.38860.26161290.17712769X-RAY DIFFRACTION98
3.3886-3.650.24911360.16052710X-RAY DIFFRACTION98
3.65-4.0170.22221480.14962727X-RAY DIFFRACTION99
4.017-4.59730.21071470.12282742X-RAY DIFFRACTION99
4.5973-5.78840.17691560.13422699X-RAY DIFFRACTION99
5.7884-36.77990.16621440.13282726X-RAY DIFFRACTION98

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