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- PDB-5er3: Crystal structure of ABC transporter system solute-binding protei... -

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Basic information

Entry
Database: PDB / ID: 5er3
TitleCrystal structure of ABC transporter system solute-binding protein from Rhodopirellula baltica SH 1
ComponentsSugar ABC transporter, periplasmic sugar-binding protein
Keywordssolute-binding protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ABC transporter
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / Sugar ABC transporter, periplasmic sugar-binding protein
Function and homology information
Biological speciesRhodopirellula baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.105 Å
AuthorsChang, C. / Duke, N. / Endres, M. / Mack, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of ABC transporter system solute-binding protein from Rhodopirellula baltica SH 1
Authors: Chang, C. / Duke, N. / Endres, M. / Mack, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8104
Polymers36,5861
Non-polymers2243
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules

A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6208
Polymers73,1722
Non-polymers4496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3510 Å2
ΔGint-22 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.755, 95.576, 46.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Sugar ABC transporter, periplasmic sugar-binding protein


Mass: 36585.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1) (bacteria)
Strain: DSM 10527 / NCIMB 13988 / SH1 / Gene: RB10898 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7UK26
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Calcium Chloride, HEPES, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 19830 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 24.68 Å2 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.057 / Rrim(I) all: 0.163 / Χ2: 0.823 / Net I/av σ(I): 11.437 / Net I/σ(I): 6.2 / Num. measured all: 163470
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.60.5849330.7410.2380.6340.83596.3
2.14-2.1870.5869490.8080.2350.6340.88799.4
2.18-2.227.40.5529740.8120.2190.5960.84799.1
2.22-2.267.70.5029730.8650.1930.540.8399.6
2.26-2.318.10.4769950.8870.180.510.864100
2.31-2.378.30.4589550.8930.1710.490.84100
2.37-2.428.50.3919950.9220.1450.4180.821100
2.42-2.498.70.3999680.9180.1460.4260.813100
2.49-2.568.80.3289870.9470.1190.3490.816100
2.56-2.658.80.2829760.9520.1030.3010.829100
2.65-2.748.70.2419930.9640.0880.2570.819100
2.74-2.858.80.2049830.9710.0740.2170.838100
2.85-2.988.70.1679790.9850.0610.1780.817100
2.98-3.148.70.1339980.9880.0480.1420.823100
3.14-3.338.70.11310020.9860.0410.1210.837100
3.33-3.598.50.09310020.9870.0340.0990.824100
3.59-3.958.50.08310040.9910.030.0880.834100
3.95-4.528.40.07610150.990.0280.0820.775100
4.52-5.78.20.0710410.9850.0270.0750.683100
5.7-507.80.08211080.9910.0320.0890.84599.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.105→34.81 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2076 1672 4.96 %
Rwork0.1764 32068 -
obs0.178 33740 90.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.05 Å2 / Biso mean: 30.5357 Å2 / Biso min: 13.19 Å2
Refinement stepCycle: final / Resolution: 2.105→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 13 98 2442
Biso mean--50.12 31.98 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052393
X-RAY DIFFRACTIONf_angle_d0.6783247
X-RAY DIFFRACTIONf_chiral_restr0.051370
X-RAY DIFFRACTIONf_plane_restr0.005430
X-RAY DIFFRACTIONf_dihedral_angle_d11.3051444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1051-2.16710.2585990.21021798189761
2.1671-2.2370.2406920.20422046213870
2.237-2.31690.2241130.19732375248880
2.3169-2.40970.21211670.2022556272388
2.4097-2.51930.23191620.21322747290995
2.5193-2.65210.26521140.20032934304898
2.6521-2.81820.25121380.211329743112100
2.8182-3.03570.25211440.196329283072100
3.0357-3.34090.23541400.182729443084100
3.3409-3.82390.20051870.157729303117100
3.8239-4.81560.14941410.131129243065100
4.8156-34.8150.17641750.167329123087100
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)
11.96421.0083-0.64452.35680.20911.50320.0565-0.01330.16530.14080.00190.3914-0.048-0.0973-0.04090.16720.00070.01150.18840.00410.222118.29522.06559.6976
21.34990.2965-0.27012.2871-1.27071.81270.02930.0479-0.01380.0078-0.116-0.2491-0.04230.16350.06150.1232-0.0112-0.00530.17180.01470.199338.884316.9372-3.5653
31.5025-0.61950.67812.1464-0.65312.6951-0.10640.04170.20240.1833-0.0189-0.1093-0.3943-0.0070.12630.2276-0.0141-0.00090.16580.00010.173332.134928.0372-10.6933
42.76880.17660.51631.69521.09952.4348-0.24250.12680.024-0.37370.1179-0.0084-0.0881-0.03680.11980.23410.01130.00860.20210.00580.171828.631523.1307-21.8209
50.9051-0.79591.49771.7694-0.81312.70580.00790.0248-0.0111-0.0056-0.01550.01720.1433-0.23510.01610.2536-0.00130.02130.2407-0.02030.16930.51614.4465-17.1967
62.25090.0223-0.70382.0039-0.50261.9391-0.03730.2892-0.0161-0.1723-0.028-0.03490.0181-0.05130.03620.199-0.0228-0.01010.19290.00450.181625.6205-2.5472-1.1098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 138 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 200 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 261 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 292 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 293 through 309 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 310 through 364 )A0

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