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- PDB-4ry0: Crystal structure of ribose transporter solute binding protein RH... -

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Basic information

Entry
Database: PDB / ID: 4ry0
TitleCrystal structure of ribose transporter solute binding protein RHE_PF00037 from Rhizobium etli CFN 42, TARGET EFI-511357, in complex with D-ribose
ComponentsProbable ribose ABC transporter, substrate-binding protein
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORTER / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


carbohydrate binding / periplasmic space
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
beta-D-ribopyranose / D-apiose import binding protein
Similarity search - Component
Biological speciesRhizobium etli CFN 42 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Hillerich, B. / Siedel, R.D. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal Structure of Ribose Transporter Solute Binding Protein from Rhizobium Etly, Target Efi-511357
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Morisco, L.L. / Wasserman, S.R. / ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Morisco, L.L. / Wasserman, S.R. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Structure summary
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ribose ABC transporter, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8584
Polymers30,6321
Non-polymers2263
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.110, 36.766, 95.480
Angle α, β, γ (deg.)90.00, 117.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-723-

HOH

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Components

#1: Protein Probable ribose ABC transporter, substrate-binding protein


Mass: 30632.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli CFN 42 (bacteria) / Strain: CFN 42 / ATCC 51251 / Gene: RHE_PF00037 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2JZQ5
#2: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growpH: 8.5
Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-RIBOSE); RESERVOIR: 0.2 M CALCIUM CHLORIDE, 0.1 M TRIS-HCL, PH 8.5, 20% (w/v) PEG 4000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% D-GLUCOSE ...Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-RIBOSE); RESERVOIR: 0.2 M CALCIUM CHLORIDE, 0.1 M TRIS-HCL, PH 8.5, 20% (w/v) PEG 4000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% D-GLUCOSE SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 5, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 57304 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 22.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.57 / % possible all: 96.6

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Processing

Software
NameVersionClassification
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→24 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.851 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18106 1724 3.1 %RANDOM
Rwork0.14341 ---
obs0.1446 53653 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-1.08 Å2
2--3.84 Å2-0 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.4→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 0 12 261 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192173
X-RAY DIFFRACTIONr_bond_other_d0.0020.022098
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9622944
X-RAY DIFFRACTIONr_angle_other_deg1.44834838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67426.95792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73615376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.484155
X-RAY DIFFRACTIONr_chiral_restr0.090.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022532
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02443
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_it3.1961.9221156
X-RAY DIFFRACTIONr_mcbond_other3.2321.9151155
X-RAY DIFFRACTIONr_mcangle_it3.3143.2461446
X-RAY DIFFRACTIONr_mcangle_other3.3373.2521447
X-RAY DIFFRACTIONr_scbond_it7.9592.6961017
X-RAY DIFFRACTIONr_scbond_other7.9592.6961017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.984.0991497
X-RAY DIFFRACTIONr_long_range_B_refined6.43410.0062704
X-RAY DIFFRACTIONr_long_range_B_other6.349.5342577
X-RAY DIFFRACTIONr_rigid_bond_restr4.40434271
X-RAY DIFFRACTIONr_sphericity_free30.549578
X-RAY DIFFRACTIONr_sphericity_bonded15.75454428
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 144 -
Rwork0.253 3842 -
obs--96.35 %

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