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- PDB-4kq9: Crystal structure of periplasmic ribose ABC transporter from Cone... -

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Basic information

Entry
Database: PDB / ID: 4kq9
TitleCrystal structure of periplasmic ribose ABC transporter from Conexibacter woesei DSM 14684
ComponentsRibose ABC transporter, substrate binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / ribose binding / PSI-Biology / MCSG / Structural Genomics / Midwest Center for Structural Genomics / ribose transporter
Function / homology
Function and homology information


cell envelope / carbohydrate binding
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribose ABC transporter, substrate binding protein
Similarity search - Component
Biological speciesConexibacter woesei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsNocek, B. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of periplasmic ribose ABC transporter from Conexibacter woesei DSM 14684
Authors: Nocek, B. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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

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Assembly

Deposited unit
A: Ribose ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9444
Polymers31,6671
Non-polymers2763
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.469, 60.536, 88.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribose ABC transporter, substrate binding protein


Mass: 31667.428 Da / Num. of mol.: 1 / Mutation: V262M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conexibacter woesei (bacteria) / Strain: DSM 14684 / Gene: Cwoe_4347 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: D3F6W3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.1 M DL-Malic Acid, pH 7, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 27010 / Num. obs: 26570 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.4
Reflection shellResolution: 1.9→1.93 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
DMmodel building
SHELXmodel building
ARP/wARPmodel building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.555 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.156 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23436 1266 5.1 %RANDOM
Rwork0.19012 ---
all0.2 24853 --
obs0.19249 23587 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 18 179 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192242
X-RAY DIFFRACTIONr_bond_other_d0.0010.022150
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.9793040
X-RAY DIFFRACTIONr_angle_other_deg0.9013.0014928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42724.04394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89615336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3481519
X-RAY DIFFRACTIONr_chiral_restr0.1140.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02482
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.906→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 48 -
Rwork0.23 932 -
obs--50.57 %

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