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- PDB-6sdu: Xyloglucanase domain of NopAA, a type three effector from Sinorhi... -

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Basic information

Entry
Database: PDB / ID: 6sdu
TitleXyloglucanase domain of NopAA, a type three effector from Sinorhizobium fredii in complex with cellobiose
ComponentsType III effector NopAA
KeywordsCELL INVASION / Symbiotic Type Three Secretion System / Sinorhizobium fredii USDA 257 / xyloglucanase / secretion domain / Small Angle X-Ray Scattering (SAXS)
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-cellobiose / beta-D-glucopyranose / Uncharacterized protein / Type III effector NopAA
Similarity search - Component
Biological speciesSinorhizobium fredii USDA 257 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsDorival, D. / Philys, S. / Guintini, E. / Brailly, R. / de Ruyck, J. / Czjzek, M. / Biondi, E.
CitationJournal: Sci Rep / Year: 2020
Title: Structural and enzymatic characterisation of the Type III effector NopAA (=GunA) from Sinorhizobium fredii USDA257 reveals a Xyloglucan hydrolase activity.
Authors: Dorival, J. / Philys, S. / Giuntini, E. / Brailly, R. / de Ruyck, J. / Czjzek, M. / Biondi, E. / Bompard, C.
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III effector NopAA
B: Type III effector NopAA
C: Type III effector NopAA
D: Type III effector NopAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5296
Polymers104,0064
Non-polymers5222
Water6,161342
1
A: Type III effector NopAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1822
Polymers26,0021
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type III effector NopAA


Theoretical massNumber of molelcules
Total (without water)26,0021
Polymers26,0021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Type III effector NopAA


Theoretical massNumber of molelcules
Total (without water)26,0021
Polymers26,0021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Type III effector NopAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3442
Polymers26,0021
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.408, 108.319, 84.706
Angle α, β, γ (deg.)90.000, 113.110, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 17 through 42 or resid 44 through 236))
21(chain B and (resid 17 through 42 or resid 44 through 236))
31(chain C and (resid 17 through 42 or resid 44 through 236))
41(chain D and (resid 17 through 42 or resid 44 through 236))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 17 through 42 or resid 44 through 236))A17 - 42
121(chain A and (resid 17 through 42 or resid 44 through 236))A44 - 236
211(chain B and (resid 17 through 42 or resid 44 through 236))B17 - 42
221(chain B and (resid 17 through 42 or resid 44 through 236))B44 - 236
311(chain C and (resid 17 through 42 or resid 44 through 236))C17 - 42
321(chain C and (resid 17 through 42 or resid 44 through 236))C44 - 236
411(chain D and (resid 17 through 42 or resid 44 through 236))D17 - 42
421(chain D and (resid 17 through 42 or resid 44 through 236))D44 - 236

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Components

#1: Protein
Type III effector NopAA


Mass: 26001.615 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium fredii USDA 257 (bacteria)
Gene: nopAA / Production host: Escherichia coli (E. coli) / References: UniProt: M4PUR5, UniProt: A0A0T6ZV48*PLUS
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Sodium acetate 20mM pH 4.5, 4M Sodium formate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.19→44.47 Å / Num. obs: 57796 / % possible obs: 99.7 % / Redundancy: 4.18 % / Biso Wilson estimate: 37.69 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.163 / Χ2: 0.915 / Net I/σ(I): 7.59 / Num. measured all: 241563
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.19-2.344.1410.9531.334317010445104250.4711.09599.8
2.34-2.534.1930.7111.941143982698120.6240.81699.9
2.53-2.774.2440.453.1837706890788850.8410.51699.8
2.77-3.094.1080.2365.8232788801079820.9420.27299.7
3.09-3.574.0760.11910.6529442724272240.9830.13899.8
3.57-4.374.3720.07616.3326615610560870.9930.08799.7
4.37-6.154.1360.05919.5919438471847000.9960.06799.6
6.15-44.474.20.04923.5911261270426810.9970.05699.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.47 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 2879 5.05 %
Rwork0.1807 54118 -
obs0.1824 56997 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.91 Å2 / Biso mean: 46.8762 Å2 / Biso min: 4.25 Å2
Refinement stepCycle: final / Resolution: 2.2→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6774 0 35 342 7151
Biso mean--30.38 45.4 -
Num. residues----877
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2620X-RAY DIFFRACTION15.744TORSIONAL
12B2620X-RAY DIFFRACTION15.744TORSIONAL
13C2620X-RAY DIFFRACTION15.744TORSIONAL
14D2620X-RAY DIFFRACTION15.744TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.23610.2971600.26432564
2.2361-2.27460.31351500.26852518
2.2746-2.3160.30371330.26642567
2.316-2.36050.29341270.26622590
2.3605-2.40870.31041330.27612594
2.4087-2.46110.33111390.26682554
2.4611-2.51830.33061490.2692550
2.5183-2.58130.2781170.24692618
2.5813-2.65110.28541300.24212550
2.6511-2.72910.28951220.22292573
2.7291-2.81720.25861310.22812582
2.8172-2.91780.27131420.22992559
2.9178-3.03460.27931550.21552549
3.0346-3.17270.21351450.19592566
3.1727-3.33990.21171430.16862567
3.3399-3.54910.20491260.15592582
3.5491-3.8230.16911520.14392578
3.823-4.20740.15351450.13062588
4.2074-4.81560.12621270.10592602
4.8156-6.06480.16611230.13382614
6.0648-44.470.17621300.17752653
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)
10.09230.0591-0.0380.0735-0.04550.0205-0.12690.2269-0.00370.04340.04490.0278-0.0132-0.1975-00.248-0.0031-0.02060.36-0.00680.255842.748766.838225.954
20.1530.12090.04450.09150.06990.0994-0.0626-0.02110.0073-0.0448-0.0041-0.0025-0.0046-0.0709-0.00030.26230.02250.00150.2698-00.234253.576467.073930.4688
30.8238-0.07530.11740.16410.23990.63130.0020.09510.1895-0.0449-0.0194-0.0269-0.1693-0.043300.25870.01830.0030.19080.06820.232457.366478.409716.6878
40.04550.01220.04490.0112-0.01670.0601-0.0566-0.19010.02040.07740.0652-0.0446-0.1242-0.215-0.00060.5009-0.01950.05020.39410.02970.361255.44447.778133.2771
50.06170.05280.05540.0440.0450.0407-0.0359-0.0172-0.20290.19360.06470.12660.11220.0111-0.00020.387-0.03780.07440.24920.04230.395856.307442.741225.7025
60.1803-0.01310.15260.0658-0.04710.1346-0.03250.14120.04140.0806-0.10320.0895-0.0124-0.13360.00030.2918-0.03420.04220.31080.00240.306354.555549.480922.0434
70.0011-0.0040.00940.0157-0.0280.0392-0.26930.0054-0.33120.1516-0.08980.13470.1944-0.0731-0.07780.0452-0.46070.4222-0.03710.06040.523142.536733.098428.1989
80.02150.03180.0590.11270.19830.3393-0.04640.451-0.4128-0.1371-0.22410.249-0.0657-0.2521-0.05970.3231-0.11320.11140.35860.00030.521743.892243.552819.129
90.9117-0.0227-0.52560.1145-0.08170.3981-0.23290.5975-0.6329-0.24220.1784-0.0760.1556-0.09810.02270.4816-0.16860.06890.4878-0.20790.629748.517934.762210.2945
100.14470.0407-0.06560.0237-0.00870.0556-0.29770.1892-0.47140.39880.02590.00570.4924-0.2799-0.01050.7419-0.30150.05710.926-0.46791.069443.246231.36669.0255
110.18080.1525-0.4440.3265-0.07211.5284-0.03620.2848-0.2789-0.03480.01420.0558-0.0136-0.33480.20250.392-0.2424-0.07040.6388-0.17790.779541.653738.35311.7767
120.0157-0.00310.00640.16240.02730.091-0.14150.3339-0.0944-0.0251-0.02890.07240.1763-0.245-0.09940.3736-0.42780.27640.4856-0.27481.083534.957630.574818.1182
130.24630.01160.09840.15410.08710.2859-0.07580.321-0.3364-0.1825-0.10950.24880.066-0.299-0.01960.2926-0.09920.10540.2949-0.03160.526845.369339.951422.2398
140.0480.00640.04060.03570.05670.0925-0.1546-0.0863-0.14820.2752-0.18940.1583-0.1090.271900.35720.0623-0.06860.39240.01820.420291.31148.515332.4845
150.02850.02630.04860.1152-0.00090.0918-0.0076-0.02340.1777-0.01690.0424-0.0743-0.04580.133800.2795-0.0092-0.00560.27510.04030.342584.587153.052428.1045
160.00890.02270.00260.05790.010.04460.03770.035-0.15810.0167-0.05790.04530.07430.2471-0.00030.30630.06830.03070.33450.00030.339888.039143.509426.6981
170.1405-0.00990.13520.23220.07040.4337-0.00530.0509-0.04320.01510.0394-0.0240.07550.1382-00.21180.00990.01320.26740.00010.250386.020553.596915.8652
180.00340.0034-0.00390.00770.00410.015-0.00180.1795-0.0377-0.10570.02160.1956-0.0219-0.0170.00050.3097-0.0242-0.00240.28560.00290.248370.984250.28649.4805
190.1105-0.1009-0.04260.0953-0.04020.2145-0.02830.23150.01460.12890.0171-0.02630.04110.0365-0.00010.2229-0.01640.01290.32160.01390.21677.936657.75196.0705
200.0931-0.0189-0.03520.0081-0.00010.0107-0.03760.3023-0.0772-0.15220.0719-0.0570.16180.197-0.00010.3240.02850.03820.4440.01840.340291.557256.81753.1403
210.102-0.05420.06240.027-0.02160.08150.06160.1117-0.16330.0031-0.1117-0.0457-0.0463-0.025-0.00010.21970.0053-0.00230.29790.02560.32485.669856.866115.5502
220.06950.0050.101-0.0011-0.00210.13270.00260.0983-0.2020.02920.0697-0.07480.28380.2216-0.00150.30740.0734-0.00690.3554-0.01720.343991.046245.022917.7222
230.50360.40870.14540.47460.43040.8580.0954-0.0887-0.01210.07590.0166-0.03140.11760.11990.00150.1603-0.0288-0.01890.1333-0.00670.12681.937669.89944.6427
240.50410.495-0.08870.69180.14840.32230.1512-0.0587-0.07690.1409-0.0003-0.13690.06510.23810.00010.2271-0.0484-0.06830.2886-0.05240.214589.656875.25549.7416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 39 )A15 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 70 )A40 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 236 )A71 - 236
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 30 )B20 - 30
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 46 )B31 - 46
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 70 )B47 - 70
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 87 )B71 - 87
8X-RAY DIFFRACTION8chain 'B' and (resid 88 through 110 )B88 - 110
9X-RAY DIFFRACTION9chain 'B' and (resid 111 through 141 )B111 - 141
10X-RAY DIFFRACTION10chain 'B' and (resid 146 through 172 )B146 - 172
11X-RAY DIFFRACTION11chain 'B' and (resid 173 through 184 )B173 - 184
12X-RAY DIFFRACTION12chain 'B' and (resid 185 through 200 )B185 - 200
13X-RAY DIFFRACTION13chain 'B' and (resid 201 through 236 )B201 - 236
14X-RAY DIFFRACTION14chain 'C' and (resid 16 through 30 )C16 - 30
15X-RAY DIFFRACTION15chain 'C' and (resid 31 through 46 )C31 - 46
16X-RAY DIFFRACTION16chain 'C' and (resid 47 through 61 )C47 - 61
17X-RAY DIFFRACTION17chain 'C' and (resid 62 through 124 )C62 - 124
18X-RAY DIFFRACTION18chain 'C' and (resid 125 through 134 )C125 - 134
19X-RAY DIFFRACTION19chain 'C' and (resid 135 through 184 )C135 - 184
20X-RAY DIFFRACTION20chain 'C' and (resid 185 through 200 )C185 - 200
21X-RAY DIFFRACTION21chain 'C' and (resid 201 through 223 )C201 - 223
22X-RAY DIFFRACTION22chain 'C' and (resid 224 through 236 )C224 - 236
23X-RAY DIFFRACTION23chain 'D' and (resid 16 through 144 )D16 - 144
24X-RAY DIFFRACTION24chain 'D' and (resid 145 through 236 )D145 - 236

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