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- PDB-4fc9: Structure of the C-terminal domain of the type III effector Xcv32... -

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Basic information

Entry
Database: PDB / ID: 4fc9
TitleStructure of the C-terminal domain of the type III effector Xcv3220 (XopL)
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / all-helical bilobal / secreted into plant host
Function / homology: / Type III effector Xcv3220, C-terminal domain / : / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / cytoplasm / Type III effector Xcv3220-like C-terminal domain-containing protein
Function and homology information
Biological speciesXanthomonas campestris pv. vesicatoria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSinger, A.U. / Xu, X. / Cui, H. / Tan, K. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of the C-terminal domain of the type III effector Xcv3220 (XopL)
Authors: Singer, A.U. / Schulze, S. / Xu, X. / Skarina, T. / Cui, H. / Egler, M. / Srikumar, T. / Raught, B. / Savchenko, A. / Bonas, U.
History
DepositionMay 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: uncharacterized protein
A: uncharacterized protein
C: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3859
Polymers70,0923
Non-polymers2936
Water7,062392
1
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5244
Polymers23,3641
Non-polymers1603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4623
Polymers23,3641
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3992
Polymers23,3641
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.198, 119.198, 38.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Detailsaccording to PISA

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Components

#1: Protein uncharacterized protein


Mass: 23364.004 Da / Num. of mol.: 3 / Fragment: UNP residues 474-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. vesicatoria (bacteria)
Strain: 85-10 / Gene: XCV3220 / Plasmid: p15Tvlic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q3BQL2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium Acetate, 30% PEG 4K, 4% ethylene glycol, 0.1 M Tris 8.5, cryoprotected with Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 13, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 110283 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 25
Reflection shellResolution: 1.8→1.8309 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.85 / Num. unique all: 2854 / Rsym value: 0.519 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXCDphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→28.63 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.02 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 3944 3.58 %random
Rwork0.1518 ---
obs0.154 110283 96.53 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.541 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.7071 Å20 Å20 Å2
2---0.7071 Å2-0 Å2
3---1.4142 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 15 392 4430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044235
X-RAY DIFFRACTIONf_angle_d0.7595769
X-RAY DIFFRACTIONf_dihedral_angle_d13.8621580
X-RAY DIFFRACTIONf_chiral_restr0.05636
X-RAY DIFFRACTIONf_plane_restr0.003770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7999-1.83090.31611880.31524875506384
1.8309-1.86420.27151960.28515006520288
1.8642-1.90.36411900.26965221541192
1.9-1.93880.25321750.24475288546393
1.9388-1.98090.24441840.23235402558695
1.9809-2.0270.25172090.22385428563795
2.027-2.07760.23882030.21925270547394
2.0776-2.13370.23431920.19655478567095
2.1337-2.19650.21652030.18885361556494
2.1965-2.26730.20891870.18035412559995
2.2673-2.34820.21681900.17695371556194
2.3482-2.44210.20081820.17125448563094
2.4421-2.55310.21571700.16635377554796
2.5531-2.68750.21031960.16815416561295
2.6875-2.85550.20642130.16125401561495
2.8555-3.07540.2481970.15295395559295
3.0754-3.38380.17522000.13625429562994
3.3838-3.87090.15051800.10535295547594
3.8709-4.86760.13871980.09195051524989
4.8676-21.46890.1731770.12255328550594
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)
16.52347.6072-3.86939.0603-4.66842.41220.63-0.2290.33251.0803-0.38710.2109-0.4637-0.0705-0.23620.3988-0.0203-0.00180.2835-0.01150.1943-5.69072.72139.2752
29.4007-7.5637-4.59157.95964.61023.6120.18760.42570.2589-0.4728-0.23310.0625-0.449-0.1070.02480.18160.0084-0.0260.23650.1010.182715.987.9799-3.7044
34.6407-0.5291-2.27093.12120.93262.53980.0114-0.15920.0229-0.0317-0.0046-0.2011-0.11250.0754-0.00430.1171-0.0055-0.0070.17810.03680.117430.27490.2090.8087
41.95220.50910.43038.13662.03720.55870.0034-0.55220.21990.4717-0.01450.409-0.3944-0.4735-0.0070.30420.0460.10090.38620.04140.213611.00712.107715.5539
58.36646.10053.98064.663.82045.8302-0.48420.15220.4986-0.59380.22080.0022-0.22240.63680.31810.244-0.0110.03380.2726-0.02110.2584-7.5253-7.694610.2973
62.55162.7051.0293.08660.33962.9907-0.23620.0574-0.1722-0.19940.1996-0.0406-0.00290.03040.01170.1834-0.00760.03260.23450.0220.2228-1.4264-7.56634.6492
75.296-0.70640.85374.9626-2.93413.0223-0.1308-0.3994-0.9545-0.112-0.14010.14180.44970.16490.27410.18610.04090.0720.24710.09110.298117.3213-10.37310.1943
85.2091.1039-1.95262.10850.75791.955-0.2854-0.7085-0.48050.2686-0.1092-0.11740.1260.30770.40360.15350.04350.02130.25110.11450.203325.8376-9.0557.7817
94.9113-0.513-0.5844.5571.04541.48880.0414-0.22030.50510.24820.0222-0.086-0.1997-0.0348-0.09130.14450.02150.00340.16220.03010.130718.90817.2575.2314
106.59083.08527.25951.43923.39157.95630.0331-0.3389-0.03620.0241-0.14910.12890.04-0.23870.0670.2622-0.0953-0.00030.30040.03290.227961.5723-40.2943-9.7196
111.5949-0.58330.83499.4293-4.74553.8095-0.05640.3584-0.3486-0.56390.13370.26130.3489-0.229-0.06750.25720.0136-0.00360.2894-0.1090.235542.8306-28.8912-22.9678
122.1931-0.2050.36643.5813-1.49255.22170.08710.45490.05-0.3458-0.12090.2298-0.2154-0.49220.05230.20370.1056-0.05220.3297-0.01150.158536.721-11.65-22.5469
137.1494-4.0739-0.8012.56240.43850.0796-0.29-0.2931-0.45870.32660.24810.16290.06330.0720.12620.23270.0131-0.00580.19750.0120.150451.1249-25.5237-6.1333
143.3238-4.3556-0.04175.7267-0.19552.63130.13320.3653-0.0207-0.1767-0.0938-0.079-0.09270.0626-0.0010.19850.0053-0.03850.238-0.05050.172566.2319-30.8314-14.864
152.6875-1.0017-0.51654.4883-0.37581.3113-0.0583-0.05910.06280.22260.008-0.21190.0375-0.0120.04620.16440.0207-0.01180.156800.115747.6259-18.7091-12.1808
166.384-4.38311.57727.9876-5.98495.2204-0.0162-0.3618-0.57270.2330.3580.76370.2428-0.5694-0.36830.2495-0.06590.04620.2302-0.03070.308337.4074-28.6523-10.4837
172.0006-0.1659-4.8130.1416-0.48034.5301-0.39510.6718-0.3173-0.0826-0.4733-0.2614-0.19670.04980.62940.52070.0606-0.17920.40350.01250.667558.964641.1134-20.7957
181.8305-2.53143.03054.4738-5.73537.4614-0.2823-0.23910.22860.4390.0952-0.2242-0.2203-0.56190.20520.2846-0.06970.08070.3659-0.16530.436744.863824.6861-7.9995
192.06230.6847-0.99792.5362-1.04851.6541-0.01270.2211-0.0209-0.3195-0.0379-0.2461-0.0078-0.03910.04630.3291-0.09990.19750.3306-0.11310.391546.39712.2731-15.9065
208.18635.93740.08356.3439-0.02252.8208-0.093-0.51330.3059-0.1596-0.32010.26290.17050.04170.40210.25960.02160.10770.27280.03350.540967.618533.6236-18.4317
211.411-0.299-0.491.6683-0.00822.004-0.18850.3332-0.1264-0.5659-0.2043-0.54240.2762-0.2923-0.31410.2362-0.11690.44090.249-0.09610.457952.60115.3721-18.6072
224.0458-0.54292.90375.6566-1.218.4069-0.19830.51850.0982-0.54010.12560.34690.293-1.15170.12790.2376-0.04140.01750.3336-0.09280.325239.472521.9682-19.0162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 468:483)
2X-RAY DIFFRACTION2chain 'B' and (resseq 484:501)
3X-RAY DIFFRACTION3chain 'B' and (resseq 502:541)
4X-RAY DIFFRACTION4chain 'B' and (resseq 542:553)
5X-RAY DIFFRACTION5chain 'B' and (resseq 554:563)
6X-RAY DIFFRACTION6chain 'B' and (resseq 564:581)
7X-RAY DIFFRACTION7chain 'B' and (resseq 582:591)
8X-RAY DIFFRACTION8chain 'B' and (resseq 592:603)
9X-RAY DIFFRACTION9chain 'B' and (resseq 604:642)
10X-RAY DIFFRACTION10chain 'A' and (resseq 469:483)
11X-RAY DIFFRACTION11chain 'A' and (resseq 484:501)
12X-RAY DIFFRACTION12chain 'A' and (resseq 502:530)
13X-RAY DIFFRACTION13chain 'A' and (resseq 531:563)
14X-RAY DIFFRACTION14chain 'A' and (resseq 564:581)
15X-RAY DIFFRACTION15chain 'A' and (resseq 582:623)
16X-RAY DIFFRACTION16chain 'A' and (resseq 624:639)
17X-RAY DIFFRACTION17chain 'C' and (resseq 469:483)
18X-RAY DIFFRACTION18chain 'C' and (resseq 484:501)
19X-RAY DIFFRACTION19chain 'C' and (resseq 502:553)
20X-RAY DIFFRACTION20chain 'C' and (resseq 554:581)
21X-RAY DIFFRACTION21chain 'C' and (resseq 582:623)
22X-RAY DIFFRACTION22chain 'C' and (resseq 624:640)

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