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- PDB-5kc4: Structure of TmRibU, orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 5kc4
TitleStructure of TmRibU, orthorhombic crystal form
ComponentsRiboflavin transporter RibU
KeywordsTransport Protein / Membrane Protein / Active transport / vitamins / substrate capture
Function / homology
Function and homology information


riboflavin transport / riboflavin transmembrane transporter activity / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKarpowich, N.K. / Wang, D.N. / Song, J.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK099023 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK053973 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM093825 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01- MH083840 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01-DA019676 United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin.
Authors: Karpowich, N.K. / Song, J. / Wang, D.N.
History
DepositionJun 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Riboflavin transporter RibU
E: Riboflavin transporter RibU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9616
Polymers39,5962
Non-polymers1,3664
Water0
1
A: Riboflavin transporter RibU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4813
Polymers19,7981
Non-polymers6832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Riboflavin transporter RibU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4813
Polymers19,7981
Non-polymers6832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.769, 80.784, 118.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer confirmed by static light scattering

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Components

#1: Protein Riboflavin transporter RibU / Riboflavin ECF transporter S component RibU


Mass: 19797.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: ribU, TM_1455 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1G6
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O6
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 3.96 Å3/Da / Density % sol: 68.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 30% PEG400, 100 mM NaCl, 0.5% NG, and 1% hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.4→19.916 Å / Num. obs: 8513 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Redundancy: 14.1 % / Rsym value: 0.078 / Net I/σ(I): 24.6
Reflection shellResolution: 3.4→3.48 Å / Rsym value: 0.89

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KC0

5kc0


Resolution: 3.4→19.916 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.97
RfactorNum. reflection% reflection
Rfree0.2696 428 5.03 %
Rwork0.2491 --
obs0.2501 8513 94.15 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 3.4→19.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 96 0 2640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042721
X-RAY DIFFRACTIONf_angle_d0.7523682
X-RAY DIFFRACTIONf_dihedral_angle_d12.8631532
X-RAY DIFFRACTIONf_chiral_restr0.043438
X-RAY DIFFRACTIONf_plane_restr0.007431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.88880.34751330.2862446X-RAY DIFFRACTION87
3.8888-4.88750.26281410.2352727X-RAY DIFFRACTION96
4.8875-19.91680.24961540.24682912X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -45.6323 Å / Origin y: -0.7384 Å / Origin z: 10.2115 Å
111213212223313233
T1.0646 Å20.0035 Å2-0.0289 Å2-0.9467 Å2-0 Å2--0.9642 Å2
L9.7778 °21.3895 °2-0.0999 °2-1.5396 °20.3138 °2--0.8051 °2
S0.0415 Å °-0.1188 Å °0.5728 Å °0.0646 Å °-0.0897 Å °0.3979 Å °0.0421 Å °0.0081 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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