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- PDB-4kvf: The crystal structure of a rhamnose ABC transporter, periplasmic ... -

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Basic information

Entry
Database: PDB / ID: 4kvf
TitleThe crystal structure of a rhamnose ABC transporter, periplasmic rhamnose-binding protein from Kribbella flavida DSM 17836
ComponentsRhamnose ABC transporter, periplasmic rhamnose-binding protein
KeywordsTRANSPORT PROTEIN / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


rhamnose transmembrane transport / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
Rhamnose ABC transporter, substrate-binding protein RhaS / : / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Rhamnose ABC transporter, periplasmic rhamnose-binding protein
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.722 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a rhamnose ABC transporter, periplasmic rhamnose-binding protein from Kribbella flavida DSM 17836
Authors: Tan, K. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Rhamnose ABC transporter, periplasmic rhamnose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8743
Polymers35,6901
Non-polymers1842
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.274, 78.451, 49.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

21A-660-

HOH

DetailsExperimentally unknown. It is predicted to be a monomer.

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Components

#1: Protein Rhamnose ABC transporter, periplasmic rhamnose-binding protein


Mass: 35689.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_0259 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2PT67
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.81 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.01M sodium citrate, 33% (w/v) PEG6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.72→27.5 Å / Num. all: 30087 / Num. obs: 30087 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 42.5
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1476 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.722→27.17 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1518 5.05 %random
Rwork0.1782 ---
obs0.1798 30042 99.41 %-
all-30042 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.722→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 12 162 2485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062364
X-RAY DIFFRACTIONf_angle_d1.0083208
X-RAY DIFFRACTIONf_dihedral_angle_d13.599857
X-RAY DIFFRACTIONf_chiral_restr0.072369
X-RAY DIFFRACTIONf_plane_restr0.004422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7215-1.77710.31461410.23372535X-RAY DIFFRACTION99
1.7771-1.84060.24441160.21552565X-RAY DIFFRACTION100
1.8406-1.91430.25681410.19972591X-RAY DIFFRACTION100
1.9143-2.00140.26571440.2022527X-RAY DIFFRACTION100
2.0014-2.10690.25881540.19992573X-RAY DIFFRACTION100
2.1069-2.23880.26731360.1982587X-RAY DIFFRACTION100
2.2388-2.41160.23391270.18852596X-RAY DIFFRACTION100
2.4116-2.65410.22821440.1962623X-RAY DIFFRACTION100
2.6541-3.03770.24431320.20242615X-RAY DIFFRACTION100
3.0377-3.82540.21161380.17092632X-RAY DIFFRACTION99
3.8254-27.17320.15741450.15222680X-RAY DIFFRACTION97
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)
14.83560.46970.18664.85740.7852.32920.0608-0.02730.3230.16360.06660.33710.0463-0.1418-0.15030.15370.02590.03680.19520.0170.2582-6.302917.719226.2495
21.2518-0.72630.88662.3475-2.52133.8186-0.1263-0.13120.09710.4166-0.0159-0.2888-0.35110.23580.08370.2352-0.0018-0.03150.2262-0.06670.242913.65247.785340.0282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 363 )

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