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- PDB-2fn9: Thermotoga maritima Ribose Binding Protein Unliganded Form -

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Basic information

Entry
Database: PDB / ID: 2fn9
TitleThermotoga maritima Ribose Binding Protein Unliganded Form
Componentsribose ABC transporter, periplasmic ribose-binding protein
KeywordsSUGAR BINDING PROTEIN / RBP / ribose binding protein / periplasmic binding protein / thermophilic proteins
Function / homology
Function and homology information


monosaccharide binding / transmembrane transport / outer membrane-bounded 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
: / Ribose ABC transporter, periplasmic ribose-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCuneo, M.J. / Changela, A. / Tian, Y. / Beese, L.S. / Hellinga, H.W.
CitationJournal: Bmc Struct.Biol. / Year: 2008
Title: Ligand-induced conformational changes in a thermophilic ribose-binding protein.
Authors: Cuneo, M.J. / Beese, L.S. / Hellinga, H.W.
History
DepositionJan 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 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 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ribose ABC transporter, periplasmic ribose-binding protein
B: ribose ABC transporter, periplasmic ribose-binding protein


Theoretical massNumber of molelcules
Total (without water)64,4052
Polymers64,4052
Non-polymers00
Water11,295627
1
A: ribose ABC transporter, periplasmic ribose-binding protein


Theoretical massNumber of molelcules
Total (without water)32,2021
Polymers32,2021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ribose ABC transporter, periplasmic ribose-binding protein


Theoretical massNumber of molelcules
Total (without water)32,2021
Polymers32,2021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.901, 136.826, 144.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

DetailsThe biological assembly is a monomer.

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Components

#1: Protein ribose ABC transporter, periplasmic ribose-binding protein


Mass: 32202.428 Da / Num. of mol.: 2 / Mutation: M114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0958 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta / References: GenBank: 4981496, UniProt: Q9X053*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 290 K / Method: microbatch / pH: 5.9
Details: 0.2M NaCl, 0.1M Bis-Tris pH5.9, 25% PEG 3350, MICRO-BATCH, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.997 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 115461 / Num. obs: 115461 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.05 / Χ2: 0.996
Reflection shellResolution: 1.4→1.45 Å / % possible obs: 91.4 % / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.7 / Num. measured obs: 10575 / Rsym value: 0.515 / Χ2: 0.727 / % possible all: 91.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DRI

2dri


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.98 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5767 5 %RANDOM
Rwork0.18 ---
all0.181 115460 --
obs0.181 115460 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.38 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 0 627 4989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224456
X-RAY DIFFRACTIONr_bond_other_d0.0010.024012
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9456044
X-RAY DIFFRACTIONr_angle_other_deg0.75539324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2235558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2524.811212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.615730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4661522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
X-RAY DIFFRACTIONr_nbd_refined0.2080.2922
X-RAY DIFFRACTIONr_nbd_other0.1740.23901
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22230
X-RAY DIFFRACTIONr_nbtor_other0.0820.22448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2449
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.253
X-RAY DIFFRACTIONr_mcbond_it1.0521.53621
X-RAY DIFFRACTIONr_mcbond_other0.1731.51140
X-RAY DIFFRACTIONr_mcangle_it1.11924458
X-RAY DIFFRACTIONr_scbond_it2.14432003
X-RAY DIFFRACTIONr_scangle_it2.9144.51586
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 380 -
Rwork0.28 7237 -
all-7617 -
obs--88.88 %

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