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- PDB-4joq: Putative ribose ABC transporter, periplasmic solute-binding prote... -

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Basic information

Entry
Database: PDB / ID: 4joq
TitlePutative ribose ABC transporter, periplasmic solute-binding protein from Rhodobacter sphaeroides
ComponentsABC ribose transporter, periplasmic solute-binding protein
KeywordsTRANSPORT PROTEIN / structural genomics / ribose / ABC transporter / solute-binding protein / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Periplasmic binding protein / Periplasmic binding protein domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Response regulator / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Transcriptional regulators-like protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Tesar, C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Putative ribose ABC transporter, periplasmic solute-binding protein from Rhodobacter sphaeroides.
Authors: Osipiuk, J. / Tesar, C. / Endres, M. / Joachimiak, A.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,1654
Polymers65,0442
Non-polymers1212
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-8 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.096, 86.096, 199.986
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-619-

HOH

21B-655-

HOH

31B-656-

HOH

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Components

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


Mass: 32522.012 Da / Num. of mol.: 2 / Mutation: N153H, S214P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17025 / Gene: RbsB, Rsph17025_2685 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4WW08
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M calcium acetate, 0.1 M Tris buffer, 20% PEG-3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.569
11-h,-k,l20.431
ReflectionResolution: 1.9→42.1 Å / Num. all: 68031 / Num. obs: 68031 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.755 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.938.70.9632.2333100.928100
1.93-1.979.50.83733390.968100
1.97-2.0110.40.67833601.047100
2.01-2.0511.10.55933891.121100
2.05-2.09110.43933741.262100
2.09-2.1411.10.39333591.344100
2.14-2.19110.32433471.51100
2.19-2.25110.28933811.593100
2.25-2.32110.25333641.763100
2.32-2.3910.90.22333831.874100
2.39-2.4810.90.18633642.025100
2.48-2.5810.90.16733792.129100
2.58-2.710.80.14734132.2100
2.7-2.8410.70.13133732.287100
2.84-3.0210.60.11134202.275100
3.02-3.2510.30.09534302.158100
3.25-3.58100.08234391.904100
3.58-4.099.40.07134581.847100
4.09-5.169.40.06334962.023100
5.16-509.20.05636532.70998.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.08 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.13 / SU B: 2.751 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.017 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1425 3437 5.1 %RANDOM
Rwork0.1248 ---
all0.1257 67964 --
obs0.1257 67964 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.28 Å2 / Biso mean: 37.7712 Å2 / Biso min: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.36 Å20 Å20 Å2
2--4.36 Å20 Å2
3----8.72 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 8 306 4808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194709
X-RAY DIFFRACTIONr_bond_other_d0.0020.024455
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9686432
X-RAY DIFFRACTIONr_angle_other_deg0.854310275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63625.409220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6491523
X-RAY DIFFRACTIONr_chiral_restr0.1020.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021042
LS refinement shellResolution: 1.905→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 285 -
Rwork0.204 4631 -
all-4916 -
obs-4916 99.41 %
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)
10.3144-0.0283-0.37810.14320.07431.18050.02050.02370.002-0.02510.0106-0.0040.1754-0.0316-0.03110.095-0.0004-0.02990.0039-0.00130.017932.975-25.162-27.488
20.2921-0.3914-0.06481.0260.25160.15360.0273-0.01020.0211-0.0171-0.0149-0.03520.0151-0.0113-0.01240.0214-0.01270.00910.0178-0.00420.006635.37690.0662-8.2474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 319
2X-RAY DIFFRACTION2B25 - 319

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