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- PDB-3p5n: Structure and mechanism of the S component of a bacterial ECF tra... -

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Basic information

Entry
Database: PDB / ID: 3p5n
TitleStructure and mechanism of the S component of a bacterial ECF transporter
ComponentsRiboflavin uptake protein
KeywordsTRANSPORT PROTEIN / transporter / alpha-helical bundle
Function / homology
Function and homology information


riboflavin transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
ECF transporter, Riboflavin transporter RibU / ECF transporter, substrate-specific component / ECF transporter, substrate-specific component / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RIBOFLAVIN / : / Riboflavin transporter RibU
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.6 Å
AuthorsZhang, P. / Wang, J. / Shi, Y.
CitationJournal: Nature / Year: 2010
Title: Structure and mechanism of the S component of a bacterial ECF transporter
Authors: Zhang, P. / Wang, J. / Shi, Y.
History
DepositionOct 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Riboflavin uptake protein
B: Riboflavin uptake protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8044
Polymers42,0512
Non-polymers7532
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-21 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.434, 94.244, 115.402
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNMETMETchain A and (resseq 10:141 or resseq 153:188 )AA10 - 14110 - 141
12LYSLYSARGARGchain A and (resseq 10:141 or resseq 153:188 )AA153 - 188153 - 188
21GLNGLNMETMETchain B and (resseq 10:141 or resseq 153:188 )BB10 - 14110 - 141
22LYSLYSARGARGchain B and (resseq 10:141 or resseq 153:188 )BB153 - 188153 - 188

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Components

#1: Protein Riboflavin uptake protein / RibU


Mass: 21025.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: TCH60 / Gene: HMPREF0772_2174 / Production host: Escherichia coli (E. coli) / References: UniProt: C2GB05, UniProt: E5QVT2*PLUS
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O6

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Mosaicity (°)
13.2662.280.647
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop8.6pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop8.6pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.075
SYNCHROTRONNSLS X29A20.9791, 0.9793, 0.9600
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 3, 2010
ADSC QUANTUM 3152CCDFeb 3, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
20.97911
30.97931
40.961
ReflectionResolution: 3.6→50 Å / Num. obs: 6783 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.065 / Χ2: 1.033 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.6-3.7370.8316490.881100
3.73-3.887.10.5016610.787100
3.88-4.057.20.3746540.901100
4.05-4.277.10.2096770.894100
4.27-4.547.10.1266630.984100
4.54-4.8970.0846671.065100
4.89-5.3870.0846751.106100
5.38-6.156.90.0936891.206100
6.15-7.756.60.057041.148100
7.75-506.20.0297441.38197.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 3.6→49.21 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7392 / SU ML: 0.64 / σ(F): 0.18 / Stereochemistry target values: MLHL
Details: Ligand RBF has high real space R value due to the high B factor.
RfactorNum. reflection% reflection
Rfree0.2892 362 5.61 %
Rwork0.2646 --
obs0.266 6457 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 147.254 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 247.48 Å2 / Biso mean: 142.7039 Å2 / Biso min: 78.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.0701 Å20 Å2-0 Å2
2--11.8841 Å20 Å2
3----20.9542 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 54 0 2660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0392940
X-RAY DIFFRACTIONf_angle_d1.873936
X-RAY DIFFRACTIONf_chiral_restr0.08470
X-RAY DIFFRACTIONf_plane_restr0.007432
X-RAY DIFFRACTIONf_dihedral_angle_d22.3461600
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1303X-RAY DIFFRACTIONPOSITIONAL0.028
12B1303X-RAY DIFFRACTIONPOSITIONAL0.028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6002-4.12090.3871100.29441853196390
4.1209-5.1910.27671090.21662072218198
5.191-49.21480.27631430.27682170231398

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