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- PDB-3urm: Crystal structure of the periplasmic sugar binding protein ChvE -

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Basic information

Entry
Database: PDB / ID: 3urm
TitleCrystal structure of the periplasmic sugar binding protein ChvE
ComponentsMultiple sugar-binding periplasmic receptor ChvE
KeywordsSUGAR BINDING PROTEIN / periplasmic binding protein / SUGAR-BINDING PROTEIN / sugar / periplasmic
Function / homology
Function and homology information


chemotaxis / 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-galactopyranose / Multiple sugar-binding periplasmic receptor ChvE
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsHu, X. / Zhao, J. / Binns, A. / Degrado, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals.
Authors: Hu, X. / Zhao, J. / Degrado, W.F. / Binns, A.N.
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Multiple sugar-binding periplasmic receptor ChvE
B: Multiple sugar-binding periplasmic receptor ChvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0974
Polymers71,7372
Non-polymers3602
Water11,872659
1
A: Multiple sugar-binding periplasmic receptor ChvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0492
Polymers35,8681
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multiple sugar-binding periplasmic receptor ChvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0492
Polymers35,8681
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.076, 130.076, 64.676
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Multiple sugar-binding periplasmic receptor ChvE


Mass: 35868.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_C_4267, Atu2348, chvE / Plasmid: pJZ01 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21(DE3) / References: UniProt: P25548
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 32% PEG4000, 0.2M Magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 54466 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.082 / Net I/σ(I): 34.55
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 952 / Rsym value: 0.494 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1drk
Resolution: 1.801→42.577 Å / SU ML: 0.21 / σ(F): 0.09 / σ(I): 0 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 2689 5.09 %random
Rwork0.1492 ---
obs0.1514 52840 91.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.818 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4439 Å20 Å2-0 Å2
2--0.4439 Å20 Å2
3----0.8878 Å2
Refinement stepCycle: LAST / Resolution: 1.801→42.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 0 24 659 5707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045157
X-RAY DIFFRACTIONf_angle_d0.8916994
X-RAY DIFFRACTIONf_dihedral_angle_d13.7441894
X-RAY DIFFRACTIONf_chiral_restr0.064803
X-RAY DIFFRACTIONf_plane_restr0.004905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8014-1.86570.2312340.18934526X-RAY DIFFRACTION83
1.8657-1.94040.22322480.17564876X-RAY DIFFRACTION89
1.9404-2.02880.22852700.1654972X-RAY DIFFRACTION91
2.0288-2.13570.22532760.15575128X-RAY DIFFRACTION94
2.1357-2.26950.20772830.15175125X-RAY DIFFRACTION94
2.2695-2.44470.20372830.15525116X-RAY DIFFRACTION94
2.4447-2.69070.22222890.15865139X-RAY DIFFRACTION94
2.6907-3.080.21072740.16215123X-RAY DIFFRACTION93
3.08-3.880.16942630.13835102X-RAY DIFFRACTION93
3.88-42.58920.16452690.12695044X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0226-0.30130.42121.65070.46512.2885-0.2244-0.1688-0.06440.25550.021-0.14510.18170.21570.07810.12320.0052-0.02570.192-0.01420.143-41.294850.79985.5979
22.0085-0.786-1.72680.9581.04164.41440.1097-0.05640.48450.0970.162-0.1973-0.42810.0034-0.23640.16860.0193-0.00390.1663-0.02030.1964-43.127557.51654.1971
31.07370.01640.63842.01690.14291.19330.0851-0.0859-0.12470.20460.0588-0.40970.24460.2184-0.15150.1520.0334-0.02940.1953-0.02920.1764-37.678543.08936.5018
41.6556-0.0776-0.31321.7861-0.02020.1993-0.1132-0.1827-0.02660.30520.19180.01210.19760.1649-0.07220.17060.05610.0030.18010.01050.1401-44.894244.1799.7864
52.08151.0902-1.18672.2365-0.75744.4101-0.0252-0.2688-0.34850.28010.1455-0.04010.9975-0.1351-0.10730.2542-0.0329-0.04550.19650.06180.2096-48.919635.32759.7092
60.4981-0.25560.08772.055-0.8551.2493-0.05040.04050.0240.07440.23270.33480.1686-0.2992-0.15850.1077-0.00910.0170.18060.03070.1624-51.713342.14324.5553
70.2399-0.1192-0.86340.85260.2181.9329-0.00750.1169-0.0075-0.15890.13340.1676-0.0304-0.4615-0.12210.1256-0.0424-0.02940.22970.03680.1438-53.504550.5681-15.8713
82.6055-2.2001-0.56944.04831.72795.0815-0.10780.49070.4466-0.9249-0.57240.6245-1.1293-1.4720.5330.4534-0.0188-0.17110.57080.00360.2779-55.378151.1944-37.0903
90.37720.0092-0.50580.527-0.07171.1331-0.10860.1647-0.1231-0.19590.14760.06920.3044-0.436-0.02080.2177-0.1142-0.01330.23110.00460.1404-51.522941.6972-22.9201
104.98323.6254-3.67582.7186-2.68536.5113-0.84560.1379-0.1839-0.82970.6073-0.05431.22890.61210.02790.4376-0.19270.00720.2346-0.01650.2121-46.644234.6486-28.3172
110.99470.1783-0.99161.42660.56294.0832-0.09770.0423-0.127-0.1850.0509-0.09930.66650.29110.07010.2757-0.01970.03670.1925-0.03990.1986-38.570437.7648-22.0213
121.02020.28210.43631.6589-0.32780.28390.00560.3302-0.0587-0.29850.0579-0.13120.13080.229-0.05340.1928-0.05750.0350.2448-0.03250.1208-39.000745.8121-26.022
131.4305-0.2915-1.32223.10911.40761.96580.00530.34720.2291-0.74640.216-0.3853-0.71960.3935-0.24720.3124-0.14660.06620.316-0.05640.1924-34.663450.3107-34.1987
140.6501-0.4564-0.19321.0213-0.22181.5443-0.06870.05520.0437-0.15060.0728-0.23220.16120.0524-0.01890.1394-0.0360.0170.1775-0.00130.1696-39.583956.0721-20.1924
150.32670.06670.13750.4203-0.17941.3356-0.03410.04250.21930.04130.1309-0.0223-0.175-0.2695-0.07620.14050.03150.00650.16930.00950.2183-50.70157.4463-0.3335
161.285-0.42761.71282.80871.6786.8291-0.3088-0.79220.20910.41050.04040.6282-0.2038-1.7398-0.0190.25760.08060.0520.48360.05740.2379-60.619653.27857.743
170.50850.99210.43944.8881-1.15451.6249-0.0202-0.14630.0341-0.35690.37640.82980.2038-0.4066-0.31280.1252-0.0671-0.01860.32640.11670.2528-60.54640.3257-1.9757
180.5340.1464-0.14090.6791-0.25550.09920.0793-0.23360.2337-0.07020.22920.2517-0.0398-0.0547-0.26120.1230.0023-0.00530.23390.06170.1884-54.373355.2855-9.4828
191.0256-0.0895-0.5020.2683-0.57371.4707-0.01520.08010.3673-0.0541-0.0367-0.0493-0.0005-0.21070.0740.1353-0.0147-0.00160.15450.02310.2538-43.426666.0156-15.7925
200.5893-1.0069-0.19721.98970.24070.16540.32950.48490.3463-0.5379-0.0559-0.4081-0.14140.0868-0.17970.1643-0.05570.04510.27410.00280.3411-33.818767.7849-13.5731
211.6826-0.155-0.87380.25390.1410.4065-0.1366-0.24580.23260.1555-0.00630.02280.24620.12790.00540.20030.0586-0.01440.2995-0.05340.2891-56.400971.3373-5.2456
220.2815-0.2387-0.18050.45790.63452.5687-0.12880.07790.4584-0.08830.1123-0.333-0.04010.52550.01290.1470.02180.00180.245-0.03790.3665-51.765573.4469-10.9308
232.0111-2.5598-0.18883.48160.69272.8760.0293-0.3809-0.02120.41410.2637-0.94460.29730.5674-0.35160.20290.0094-0.03720.4014-0.06450.3117-52.924570.9694-2.5455
243.8053-0.9746-2.59390.78960.50332.0535-0.1882-0.5376-0.14450.2541-0.00920.1340.14840.13340.0990.2320.00580.04720.23550.02370.2751-66.502564.9759-4.5963
250.96270.45360.00191.08820.59482.23190.0338-0.65280.39430.0270.05150.25080.0192-0.0893-0.02410.14050.0420.04720.3449-0.09560.2999-66.479472.5199-1.9793
260.6171-2.02750.09517.49570.68566.92710.1135-1.5370.44610.79470.51070.18710.31140.0654-0.38520.22780.08340.09090.7294-0.24880.3685-68.854877.13525.3828
270.3123-0.5087-0.24960.79750.7372.95420.071-0.0630.5565-0.10070.0775-0.0232-0.2865-0.0855-0.10150.161-0.00030.02780.2334-0.01380.4842-64.603182.3518-16.7466
282.279-1.02853.03291.3083-2.08319.6876-0.17240.65841.106-0.78170.20940.2325-1.39410.04480.16530.6649-0.0026-0.00340.58970.29770.6376-62.063586.9153-44.8579
290.978-0.6726-0.0151.51830.50731.39940.10040.17930.3301-0.2933-0.1740.1726-0.3794-0.24110.00970.17030.0576-0.00250.25080.06710.3777-70.198479.5086-29.8065
302.3309-2.73730.57063.677-0.43991.84020.21640.98670.4098-0.7193-0.26370.3973-0.3837-0.7165-0.05370.44120.1973-0.10570.4910.14480.4108-74.243980.8795-41.5835
310.1694-0.63330.44993.0493-1.83166.6691-0.0943-0.3859-0.0418-0.18970.14050.31940.353-0.87070.02650.13290.00250.00130.29790.01560.375-72.435371.0609-26.0844
321.616-0.3751.01722.03630.17910.78530.02710.1541-0.0019-0.3578-0.12440.2892-0.13050.00930.08970.18860.0211-0.01080.29870.01710.2664-66.704467.7801-37.1295
337.09362.7708-0.94388.22662.10481.24960.25971.92490.2061-1.7601-0.3456-0.3775-0.5516-0.20820.03520.35050.09880.06460.56690.06780.2159-59.11867.3726-46.3195
340.75970.02150.33370.3926-0.06010.09800.13220.406-0.04710.0042-0.1475-0.2649-0.1688-0.0460.13950.00460.04840.29210.09050.266-53.760673.0817-32.7372
351.3683-0.2686-0.05910.2756-0.35780.4624-0.0145-0.31270.68850.17760.0053-0.1457-0.18260.23050.00590.1659-0.02350.04420.3065-0.07940.4687-52.897282.041-12.2229
361.06720.81980.39771.40351.5492.6532-0.1511-0.49251.03540.55250.20130.026-1.29570.7214-0.29280.3614-0.02790.01650.428-0.27090.5966-58.409690.2082-2.0901
371.3072.2031-0.94093.9784-1.42132.22720.4813-0.43781.23620.35470.32621.8011-0.2758-0.3069-0.74710.2120.04670.07910.22510.00620.8457-71.889887.7572-11.6171
381.0083-0.4839-0.49450.73061.08193.10280.3302-0.27441.0983-0.1659-0.07690.0707-0.7750.4595-0.09540.2197-0.02760.10710.227-0.05840.6723-61.31487.4984-14.8067
391.815-1.8610.64212.5204-0.51471.3653-0.04340.0911.05910.02040.1499-0.7772-0.56620.24270.0810.1397-0.08480.13510.22750.10630.5615-45.191179.2446-28.4017
400.6174-1.0289-1.30896.06931.87413.8537-0.20250.49880.304-1.04050.5248-1.82740.03090.4218-0.34840.2293-0.04850.0890.34850.00080.5005-40.323370.1024-26.8817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:16)
2X-RAY DIFFRACTION2(chain A and resid 17:34)
3X-RAY DIFFRACTION3(chain A and resid 35:54)
4X-RAY DIFFRACTION4(chain A and resid 55:69)
5X-RAY DIFFRACTION5(chain A and resid 70:82)
6X-RAY DIFFRACTION6(chain A and resid 83:100)
7X-RAY DIFFRACTION7(chain A and resid 101:124)
8X-RAY DIFFRACTION8(chain A and resid 125:131)
9X-RAY DIFFRACTION9(chain A and resid 132:168)
10X-RAY DIFFRACTION10(chain A and resid 169:174)
11X-RAY DIFFRACTION11(chain A and resid 175:200)
12X-RAY DIFFRACTION12(chain A and resid 201:222)
13X-RAY DIFFRACTION13(chain A and resid 223:237)
14X-RAY DIFFRACTION14(chain A and resid 238:259)
15X-RAY DIFFRACTION15(chain A and resid 260:277)
16X-RAY DIFFRACTION16(chain A and resid 278:288)
17X-RAY DIFFRACTION17(chain A and resid 289:299)
18X-RAY DIFFRACTION18(chain A and resid 300:310)
19X-RAY DIFFRACTION19(chain A and resid 311:324)
20X-RAY DIFFRACTION20(chain A and resid 325:330)
21X-RAY DIFFRACTION21(chain B and resid 2:15)
22X-RAY DIFFRACTION22(chain B and resid 16:29)
23X-RAY DIFFRACTION23(chain B and resid 30:42)
24X-RAY DIFFRACTION24(chain B and resid 43:55)
25X-RAY DIFFRACTION25(chain B and resid 56:76)
26X-RAY DIFFRACTION26(chain B and resid 77:86)
27X-RAY DIFFRACTION27(chain B and resid 87:120)
28X-RAY DIFFRACTION28(chain B and resid 121:130)
29X-RAY DIFFRACTION29(chain B and resid 131:159)
30X-RAY DIFFRACTION30(chain B and resid 160:172)
31X-RAY DIFFRACTION31(chain B and resid 173:184)
32X-RAY DIFFRACTION32(chain B and resid 185:222)
33X-RAY DIFFRACTION33(chain B and resid 223:236)
34X-RAY DIFFRACTION34(chain B and resid 237:258)
35X-RAY DIFFRACTION35(chain B and resid 259:277)
36X-RAY DIFFRACTION36(chain B and resid 278:288)
37X-RAY DIFFRACTION37(chain B and resid 289:296)
38X-RAY DIFFRACTION38(chain B and resid 297:308)
39X-RAY DIFFRACTION39(chain B and resid 309:324)
40X-RAY DIFFRACTION40(chain B and resid 325:330)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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