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- PDB-3uor: The structure of the sugar-binding protein MalE from the phytopat... -

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Basic information

Entry
Database: PDB / ID: 3uor
TitleThe structure of the sugar-binding protein MalE from the phytopathogen Xanthomonas citri
ComponentsABC transporter sugar binding protein
KeywordsSUGAR BINDING PROTEIN / alfa/beta protein / periplasmic-binding protein / maltose
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / ABC transporter sugar binding protein
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.202 Å
AuthorsMedrano, F.J. / Souza, C.S. / Balan, A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structure determination of a sugar-binding protein from the phytopathogenic bacterium Xanthomonas citri.
Authors: Medrano, F.J. / de Souza, C.S. / Romero, A. / Balan, A.
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter sugar binding protein
B: ABC transporter sugar binding protein


Theoretical massNumber of molelcules
Total (without water)102,7722
Polymers102,7722
Non-polymers00
Water6,233346
1
A: ABC transporter sugar binding protein


Theoretical massNumber of molelcules
Total (without water)51,3861
Polymers51,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter sugar binding protein


Theoretical massNumber of molelcules
Total (without water)51,3861
Polymers51,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.971, 122.971, 304.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ABC transporter sugar binding protein


Mass: 51385.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: malE, XAC2310 / Plasmid: pET28_MalE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) / References: UniProt: Q8PK66
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.2361.93
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, sitting drop80.1 M Tris HCl pH 8.0, 3.5 M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
2982vapor diffusion, sitting drop80.1 M Tris HCl pH 8.0; 3.5 M Sodium Formate; heavy atom soaking with 1 mM mersalyl acid, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111.00662
SYNCHROTRONESRF ID23-121.00591
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDDec 6, 2010mirrors
ADSC QUANTUM 315r2CCDDec 6, 2010mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiliconSINGLE WAVELENGTHMx-ray1
2SiliconSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.006621
21.005911
ReflectionResolution: 2.2→50 Å / Num. obs: 68944 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 41.76 Å2 / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
MxCuBEdata collection
SHARPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.202→47.818 Å / SU ML: 0.35 / σ(F): 0.02 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 3254 5.06 %RANDOM
Rwork0.189 ---
all0.2282 68944 --
obs0.191 64277 92.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.632 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.152 Å20 Å2-0 Å2
2--4.152 Å20 Å2
3----8.304 Å2
Refinement stepCycle: LAST / Resolution: 2.202→47.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6373 0 0 346 6719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076553
X-RAY DIFFRACTIONf_angle_d1.0788910
X-RAY DIFFRACTIONf_dihedral_angle_d17.0192368
X-RAY DIFFRACTIONf_chiral_restr0.076925
X-RAY DIFFRACTIONf_plane_restr0.0051170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2025-2.28120.34852690.28764612X-RAY DIFFRACTION72
2.2812-2.37250.30392630.24865309X-RAY DIFFRACTION82
2.3725-2.48050.27353070.21635759X-RAY DIFFRACTION89
2.4805-2.61130.26353150.20746016X-RAY DIFFRACTION92
2.6113-2.77490.28013240.21546234X-RAY DIFFRACTION95
2.7749-2.98910.28073340.23036367X-RAY DIFFRACTION97
2.9891-3.28980.26213600.20566435X-RAY DIFFRACTION98
3.2898-3.76570.19443880.16496542X-RAY DIFFRACTION99
3.7657-4.74370.17863340.13576717X-RAY DIFFRACTION100
4.7437-47.82970.18473600.16587032X-RAY DIFFRACTION99
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)
11.8434-0.29161.02483.39190.79911.67240.24960.22940.0706-0.0521-0.23550.7897-0.4202-0.3022-00.34550.09780.10340.3542-0.01930.5435-28.8172-18.3047-5.5724
20.9586-0.7109-0.70591.1943-0.15330.71450.0354-0.1132-0.08730.2486-0.08580.21930.01170.17830.00010.2760.01010.08740.20930.01210.2487-12.6421-29.0983-3.1312
3-0.0012-0.3327-0.03162.6262-0.83561.09230.03080.1182-0.009-0.2134-0.21540.00490.22280.190900.23140.15360.06640.24480.0270.2173-4.8741-37.4172-20.1745
41.1679-0.5071-0.99981.98851.28682.31450.1284-0.1028-0.1910.3874-0.29290.34730.13180.07480.00010.24820.03880.12470.16820.02150.2769-17.1314-32.5127-2.5314
50.1233-0.1090.43341.3741-0.26620.3651-0.08980.01140.1032-0.4290.06120.1469-0.04780.10240.00010.27350.08380.03630.33020.11950.24-4.3248-21.9285-27.3478
6-0.0057-0.24860.30140.3138-0.33720.2137-0.41410.28610.0608-0.15470.18680.2264-0.23360.6380.00010.35650.0698-0.05720.28010.06820.3-5.6428-3.2664-19.6924
71.8347-0.88350.44940.6929-0.29731.0324-0.29211.59310.0155-0.8360.2187-0.12060.0446-0.305500.7794-0.40390.13591.09820.01490.41-42.0163-49.9482-29.7689
82.79390.5971-1.21530.8760.67650.6185-0.2243-0.1154-0.5415-0.0207-0.0807-0.1066-0.15140.06460.00010.3701-0.175-0.00330.32790.0910.3755-46.4628-54.6703-1.209
92.24120.2329-1.30751.2903-1.86321.88680.04740.31280.16890.02010.22250.0760.01750.1405-0.00010.3971-0.1851-0.0340.29690.1320.3156-57.8999-47.292-1.3759
103.612-0.2054-2.12871.7197-0.73041.0277-0.0095-0.18030.2918-0.054-0.0969-0.13050.12020.21-00.4219-0.1912-0.00960.40840.13120.4405-40.3587-47.6639-2.6544
111.40960.637-0.01511.01990.20031-0.38290.6943-0.8249-0.22420.0732-0.27260.2927-0.035-0.00020.5486-0.13480.20260.6744-0.13210.5651-38.354-57.4773-19.6781
120.7451-0.57110.90231.0121-0.64020.6934-0.19560.610.5753-0.25250.23050.2971-0.2071-0.2934-0.00020.5111-0.2158-0.12590.61640.31230.5119-66.913-43.4578-14.1332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 27:107)
2X-RAY DIFFRACTION2(chain A and resid 108:154)
3X-RAY DIFFRACTION3(chain A and resid 155:270)
4X-RAY DIFFRACTION4(chain A and resid 271:371)
5X-RAY DIFFRACTION5(chain A and resid 372:408)
6X-RAY DIFFRACTION6(chain A and resid 409:423)
7X-RAY DIFFRACTION7(chain B and resid 28:128)
8X-RAY DIFFRACTION8(chain B and resid 129:174)
9X-RAY DIFFRACTION9(chain B and resid 175:244)
10X-RAY DIFFRACTION10(chain B and resid 245:306)
11X-RAY DIFFRACTION11(chain B and resid 307:371)
12X-RAY DIFFRACTION12(chain B and resid 372:422)

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