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- PDB-5vvh: Crystal Structure of the Effector Binding Domain of LysR-type Tra... -

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Basic information

Entry
Database: PDB / ID: 5vvh
TitleCrystal Structure of the Effector Binding Domain of LysR-type Transcriptional Regulator, OccR from Agrobacterium tumefaciens
ComponentsOctopine catabolism/uptake operon regulatory protein OccR
KeywordsTRANSCRIPTION / alpha-beta structure / type 2 periplasmic binding fold / Structural Genomics / MCSG / PSI-Biology / Midwest Center for Structural Genomics
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Octopine catabolism/uptake operon regulatory protein OccR, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Octopine catabolism/uptake operon regulatory protein OccR
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKim, Y. / Chhor, G. / Jedrzejczak, R. / Winans, S.C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Mol. Microbiol. / Year: 2018
Title: Crystal Structure of the Ligand-Binding Domain of a LysR-type Transcriptional Regulator: Transcriptional Activation via a Rotary Switch.
Authors: Kim, Y. / Chhor, G. / Tsai, C.S. / Winans, J.B. / Jedrzejczak, R. / Joachimiak, A. / Winans, S.C.
History
DepositionMay 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Octopine catabolism/uptake operon regulatory protein OccR
B: Octopine catabolism/uptake operon regulatory protein OccR
C: Octopine catabolism/uptake operon regulatory protein OccR
D: Octopine catabolism/uptake operon regulatory protein OccR
E: Octopine catabolism/uptake operon regulatory protein OccR
F: Octopine catabolism/uptake operon regulatory protein OccR
G: Octopine catabolism/uptake operon regulatory protein OccR
H: Octopine catabolism/uptake operon regulatory protein OccR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,92917
Polymers186,3658
Non-polymers5649
Water1,45981
1
A: Octopine catabolism/uptake operon regulatory protein OccR
B: Octopine catabolism/uptake operon regulatory protein OccR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8256
Polymers46,5912
Non-polymers2344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-11 kcal/mol
Surface area18550 Å2
MethodPISA
2
C: Octopine catabolism/uptake operon regulatory protein OccR
D: Octopine catabolism/uptake operon regulatory protein OccR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7334
Polymers46,5912
Non-polymers1422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-26 kcal/mol
Surface area18050 Å2
MethodPISA
3
E: Octopine catabolism/uptake operon regulatory protein OccR
F: Octopine catabolism/uptake operon regulatory protein OccR


Theoretical massNumber of molelcules
Total (without water)46,5912
Polymers46,5912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-10 kcal/mol
Surface area18310 Å2
MethodPISA
4
G: Octopine catabolism/uptake operon regulatory protein OccR
H: Octopine catabolism/uptake operon regulatory protein OccR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7795
Polymers46,5912
Non-polymers1883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-36 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.392, 106.330, 215.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Octopine catabolism/uptake operon regulatory protein OccR


Mass: 23295.623 Da / Num. of mol.: 8 / Fragment: UNP residues 92-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: occR / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) / Strain (production host): BL21(DE3) gold / References: UniProt: P0A4T3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.3 M Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.5→45.7 Å / Num. obs: 57897 / % possible obs: 99.9 % / Redundancy: 4 % / Rsym value: 0.093 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.9 % / Num. unique obs: 2844 / CC1/2: 0.612 / Rsym value: 0.773 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.742 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.58 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 2764 5.04 %random
Rwork0.2181 ---
obs0.2201 54787 94.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12779 0 33 81 12893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413131
X-RAY DIFFRACTIONf_angle_d0.9917791
X-RAY DIFFRACTIONf_dihedral_angle_d21.8474924
X-RAY DIFFRACTIONf_chiral_restr0.042055
X-RAY DIFFRACTIONf_plane_restr0.0032345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54320.3285980.29481731X-RAY DIFFRACTION64
2.5432-2.58940.36031020.28861896X-RAY DIFFRACTION71
2.5894-2.63920.34881060.29212231X-RAY DIFFRACTION81
2.6392-2.69310.31561460.27762380X-RAY DIFFRACTION90
2.6931-2.75160.31371440.27732625X-RAY DIFFRACTION96
2.7516-2.81560.28451320.27382643X-RAY DIFFRACTION99
2.8156-2.8860.36881560.27232710X-RAY DIFFRACTION99
2.886-2.9640.35071430.28372719X-RAY DIFFRACTION100
2.964-3.05120.32431390.27162698X-RAY DIFFRACTION100
3.0512-3.14970.31421440.26042706X-RAY DIFFRACTION100
3.1497-3.26220.28661480.25192723X-RAY DIFFRACTION100
3.2622-3.39280.23851300.24262759X-RAY DIFFRACTION100
3.3928-3.54720.26311340.22232736X-RAY DIFFRACTION100
3.5472-3.73410.24921540.21882713X-RAY DIFFRACTION100
3.7341-3.96790.25131370.20022755X-RAY DIFFRACTION100
3.9679-4.27410.24481420.18892744X-RAY DIFFRACTION100
4.2741-4.70380.22991420.16642767X-RAY DIFFRACTION100
4.7038-5.38360.22251350.17762797X-RAY DIFFRACTION100
5.3836-6.77920.19771490.19432807X-RAY DIFFRACTION100
6.7792-45.75010.18421830.15992883X-RAY DIFFRACTION98
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)
13.6040.9605-2.49579.4706-2.61972.58450.20510.1232-0.1073-0.26420.0004-0.72170.1460.0064-0.1870.28910.0106-0.00050.24610.00530.216654.107619.49163.4233
26.3066-1.54814.85392.0647-1.4123.98470.26940.1839-0.0458-0.1906-0.10280.10330.19570.0374-0.18790.19030.0260.08040.26680.01410.203333.458417.61560.9953
36.189-2.5489-1.01756.3010.13944.72290.13760.08620.0267-0.1193-0.1858-0.31440.01260.4209-0.02360.2526-0.0134-0.02250.40950.08060.261930.922223.382151.0651
45.1764-1.00762.42753.2736-1.32173.2081-0.1256-0.48760.3677-0.09740.1427-0.1925-0.1744-0.1908-0.0020.30040.03590.01430.2434-0.02810.146945.152623.732370.6018
55.4172-1.7532-1.00526.8367-1.46884.0302-0.15310.49330.54430.6977-0.04190.8218-0.0095-0.58350.20630.3805-0.03420.06060.5043-0.03370.408437.379.772541.22
64.7392.69290.16783.54361.12611.88050.04470.1796-0.6613-0.0338-0.1006-0.07510.1368-0.33290.06870.32020.0030.0230.36890.03070.20541.47088.108939.0621
70.9471.07760.18136.7190.29732.6348-0.1241-0.08850.2081-0.12450.1514-0.5177-0.06850.4582-0.08380.20730.03320.00490.28620.0260.442964.030517.888647.1662
84.76180.4982-2.26983.6450.44468.97470.03030.1975-0.1893-0.0345-0.1176-0.0324-0.06650.3062-0.04070.26160.0506-0.03630.2349-0.0070.262158.381619.488548.2573
94.7381.85210.19124.6657-1.12793.3-0.05240.56920.0484-0.3810.04180.20260.1134-0.22540.01870.45630.03190.0210.4313-0.02820.187944.318211.179331.1704
105.9664-0.68221.49992.6987-2.53293.84570.23950.1320.07520.08830.1553-0.0921-0.1454-0.1669-0.31320.4209-0.01730.06260.2557-0.07820.309986.6195-8.494849.9979
114.23970.0997-1.77891.89620.05781.56170.220.26660.3648-0.161-0.09340.1122-0.1659-0.168-0.14890.3180.027-0.09230.2764-0.04770.314272.2228-4.893251.3634
123.74862.83332.19686.51440.44516.81250.31840.16080.10060.1753-0.3937-0.1145-0.36850.13260.00670.26810.06440.0320.2726-0.0420.323266.5654-8.938962.1043
133.4432-0.60081.22523.9472-0.63492.15430.03970.2848-0.0951-0.1982-0.04290.1014-0.0657-0.01750.04970.3380.00340.00150.2568-0.07390.188479.4916-12.009442.694
142.28230.06190.4657.4342-0.31263.01440.5589-0.217-0.4246-0.1942-0.2233-0.01730.18790.0276-0.3620.33760.019-0.05050.4639-0.10790.472.27821.585473.0081
157.6952-1.371-0.42322.76541.19342.13060.19220.49870.4878-0.1838-0.20420.196-0.1909-0.45310.11580.332-0.00870.00610.552-0.09080.398971.72067.967870.9443
164.1919-1.6641-1.05741.47271.39891.4505-0.0863-0.38921.51720.17890.0356-0.8992-0.12840.3605-0.05750.3554-0.08580.05180.3204-0.08930.641685.564913.471376.7544
174.5392-1.14360.66078.52050.41483.44290.23960.3227-0.1874-0.414-0.2201-0.61130.18750.39350.07450.212-0.03280.030.2458-0.01160.294699.4074-4.110263.4441
184.7294-1.1292-0.10035.15840.01152.9459-0.0578-0.2347-0.49160.3377-0.11920.87880.3088-0.58390.15770.355-0.09850.03530.3453-0.03220.419389.624-8.88466.0332
194.5361-3.6128-0.88213.6461.7591.50080.0292-0.8750.73640.2083-0.0087-0.3514-0.0336-0.0334-0.04460.4406-0.08560.0890.3252-0.07730.430485.41429.369376.4722
209.0126-0.9004-0.95086.0030.24663.8067-0.0062-1.6152-0.09010.0943-0.13270.13830.33670.1640.1640.4579-0.13140.03720.5467-0.0960.232180.07690.10182.3173
217.8384-0.68351.46233.7515-0.55463.3688-0.067-0.78470.79420.23840.05830.00160.025-0.4621-0.01040.37120.05270.0130.4982-0.10740.340374.829324.506316.7492
225.62010.32110.25057.3481.30234.03920.0281-0.1143-0.01190.10470.0635-0.58140.1307-0.0378-0.08520.3076-0.0186-0.05550.2180.02560.291996.255213.74267.5133
235.30210.3913-1.65092.55240.6434.8889-0.2804-1.94650.32880.5760.3241-0.06290.4804-0.1431-0.03330.58960.12-0.11270.9476-0.11670.393979.087720.383924.1817
245.5429-0.82570.86095.5761-0.54492.37230.09450.1038-0.15160.52050.2135-0.3878-0.2157-0.09590.01530.3540.0270.05030.24220.04830.205889.136814.5682-8.3256
256.38461.1262-1.82441.0438-0.5281.9585-0.01230.28230.1199-0.22920.02770.21330.2102-0.11970.02680.28520.0436-0.0620.23560.05820.284470.939215.2123-8.3469
265.28910.93131.57164.0317-1.355.66790.2112-0.6971-0.09010.2909-0.2568-0.0539-0.15810.21370.17630.2709-0.02280.04640.31060.04050.343765.50912.22083.4039
276.5660.1531-1.32290.64030.50810.72520.03410.5859-0.37350.03760.05820.04150.2657-0.10440.110.3552-0.0235-0.03010.28450.0050.27878.096210.8418-15.0859
285.87140.9091-1.79695.3404-1.18193.9392-0.0755-0.3928-0.8432-0.5462-0.1619-0.34620.33060.10620.03190.3464-0.0263-0.03490.241-0.11760.262672.78922.0311125.5787
293.7319-2.7977-0.78483.10730.86141.5558-0.0627-0.01050.18180.10980.0317-0.26340.0631-0.0633-0.04630.282-0.0312-0.0180.181-0.0090.204786.046424.2936122.004
303.01020.04060.98567.1721.50013.98140.15870.1255-0.28910.0449-0.25170.06980.26210.01220.01280.2589-0.00580.04290.3151-0.05710.267194.560616.4775117.5894
313.648-0.60270.06173.2794-0.85354.1306-0.0371-0.25020.0656-0.24470.1301-0.0108-0.02230.2138-0.04120.2722-00.00540.2121-0.06320.115979.612325.9096132.8184
327.6163-1.64132.66918.9411-2.97945.47410.0213-0.06520.39890.25990.14530.09050.01750.1132-0.17140.2656-0.03350.01120.2566-0.10680.163987.04215.4991100.5073
333.79971.9373-1.42812.4964-0.32633.031-0.03730.4660.09140.46760.04580.4928-0.141-0.18070.03940.1682-0.0202-0.10450.2933-0.02420.3565.260511.1377107.8764
342.09750.83952.20465.0457-0.87415.9663-0.0581-0.05940.05240.2228-0.0606-0.0844-0.0354-0.26880.12050.20640.02840.03450.2286-0.10470.309265.802312.7286113.5978
355.69571.4291-0.07197.5099-2.75074.8694-0.14150.51120.00680.09620.25510.29840.1394-0.2295-0.10150.285-0.00880.01750.3055-0.0740.250680.07587.17196.2398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 90 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 297 )
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 104 )
6X-RAY DIFFRACTION6chain 'B' and (resid 105 through 169 )
7X-RAY DIFFRACTION7chain 'B' and (resid 170 through 206 )
8X-RAY DIFFRACTION8chain 'B' and (resid 207 through 258 )
9X-RAY DIFFRACTION9chain 'B' and (resid 259 through 298 )
10X-RAY DIFFRACTION10chain 'C' and (resid 91 through 115 )
11X-RAY DIFFRACTION11chain 'C' and (resid 116 through 206 )
12X-RAY DIFFRACTION12chain 'C' and (resid 207 through 258 )
13X-RAY DIFFRACTION13chain 'C' and (resid 259 through 298 )
14X-RAY DIFFRACTION14chain 'D' and (resid 89 through 113 )
15X-RAY DIFFRACTION15chain 'D' and (resid 114 through 147 )
16X-RAY DIFFRACTION16chain 'D' and (resid 148 through 163 )
17X-RAY DIFFRACTION17chain 'D' and (resid 164 through 220 )
18X-RAY DIFFRACTION18chain 'D' and (resid 221 through 253 )
19X-RAY DIFFRACTION19chain 'D' and (resid 254 through 273 )
20X-RAY DIFFRACTION20chain 'D' and (resid 274 through 298 )
21X-RAY DIFFRACTION21chain 'E' and (resid 90 through 163 )
22X-RAY DIFFRACTION22chain 'E' and (resid 164 through 258 )
23X-RAY DIFFRACTION23chain 'E' and (resid 259 through 297 )
24X-RAY DIFFRACTION24chain 'F' and (resid 90 through 128 )
25X-RAY DIFFRACTION25chain 'F' and (resid 129 through 185 )
26X-RAY DIFFRACTION26chain 'F' and (resid 186 through 253 )
27X-RAY DIFFRACTION27chain 'F' and (resid 254 through 297 )
28X-RAY DIFFRACTION28chain 'G' and (resid 91 through 115 )
29X-RAY DIFFRACTION29chain 'G' and (resid 116 through 197 )
30X-RAY DIFFRACTION30chain 'G' and (resid 198 through 258 )
31X-RAY DIFFRACTION31chain 'G' and (resid 259 through 298 )
32X-RAY DIFFRACTION32chain 'H' and (resid 90 through 147 )
33X-RAY DIFFRACTION33chain 'H' and (resid 148 through 197 )
34X-RAY DIFFRACTION34chain 'H' and (resid 198 through 258 )
35X-RAY DIFFRACTION35chain 'H' and (resid 259 through 298 )

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