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- PDB-3c7j: Crystal structure of transcriptional regulator (GntR family membe... -

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Basic information

Entry
Database: PDB / ID: 3c7j
TitleCrystal structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000
ComponentsTranscriptional regulator, GntR familyTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / transcriptional regulator / GntR family / structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
GntR ligand-binding domain-like / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Four Helix Bundle (Hemerythrin (Met), subunit A) ...GntR ligand-binding domain-like / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Regulatory protein GntR / Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsNocek, B. / Sather, A. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000.
Authors: Nocek, B. / Sather, A. / Gu, M. / Joachimiak, A.
History
DepositionFeb 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, GntR family
B: Transcriptional regulator, GntR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7034
Polymers53,5852
Non-polymers1172
Water6,377354
1
A: Transcriptional regulator, GntR family
B: Transcriptional regulator, GntR family
hetero molecules

A: Transcriptional regulator, GntR family
B: Transcriptional regulator, GntR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4068
Polymers107,1714
Non-polymers2354
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.954, 132.768, 170.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Transcriptional regulator, GntR family / Transcriptional regulation


Mass: 26792.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: PSPTO5454 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q87U60, UniProt: Q19AK4*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% Propanol, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. all: 37685 / Num. obs: 37612 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.5 / % possible all: 96

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
Cootmodel building
MLPHAREphasing
PHENIXphasing
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.315 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.179 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1838 5 %RANDOM
Rwork0.18 ---
all0.182 ---
obs0.182 36788 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.956 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 2 354 4018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223740
X-RAY DIFFRACTIONr_bond_other_d0.0010.022577
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9785046
X-RAY DIFFRACTIONr_angle_other_deg1.0236264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2995467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30223.871186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19215688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8881539
X-RAY DIFFRACTIONr_chiral_restr0.0850.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02745
X-RAY DIFFRACTIONr_nbd_refined0.2220.2796
X-RAY DIFFRACTIONr_nbd_other0.1920.22700
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21822
X-RAY DIFFRACTIONr_nbtor_other0.0870.21907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.212
X-RAY DIFFRACTIONr_mcbond_it0.991.52904
X-RAY DIFFRACTIONr_mcbond_other0.1891.5937
X-RAY DIFFRACTIONr_mcangle_it1.18523714
X-RAY DIFFRACTIONr_scbond_it2.46631520
X-RAY DIFFRACTIONr_scangle_it3.2144.51328
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 138 -
Rwork0.205 2448 -
all-2586 -
obs--94.21 %
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)
121.1581-3.40963.27626.518114.730942.17020.18920.2577-0.36720.4625-0.46160.26470.1091-1.33340.27240.07460.17470.11650.0630.01030.031532.5802103.045647.1021
23.8243-2.71.28292.2037-1.54991.82530.0620.14060.4879-0.0516-0.1857-0.1069-0.464-0.05790.12370.17970.03160.1266-0.021-0.00040.131138.8036107.833757.6973
36.80870.8328-3.43931.71470.6312.42310.2347-0.49180.110.0841-0.0544-0.1539-0.22580.2667-0.18030.0429-0.03780.04490.1131-0.05830.08150.4328100.755465.7696
48.0205-4.8267-2.55826.26280.58181.08910.1976-0.69150.40770.1106-0.1727-0.0433-0.1243-0.0672-0.02490.0589-0.03550.04670.0779-0.07350.107636.4083101.732170.1073
53.2844-0.41530.62990.1342-0.35581.05470.21830.16130.0737-0.1001-0.12210.0417-0.09350.0267-0.09620.09910.04060.0840.0546-0.03690.099842.005100.02756.7453
614.49685.0466-10.663.8459-6.469611.6455-0.4889-0.1054-0.8218-0.2305-0.1265-0.42980.38860.25190.61540.06710.01730.05830.058-0.06340.1247.655592.559860.3206
717.69891.28565.00644.8074.143512.1004-0.1579-0.2734-0.4542-0.00460.02820.1383-0.0730.2170.12970.0354-0.01840.05340.01660.01760.055938.293890.691766.5117
814.615-8.7556-20.17218.46811.480762.7339-0.78232.0887-0.76170.0013-0.83760.02661.8432-5.69061.61990.0202-0.19730.09870.4514-0.18080.094131.117189.136553.9695
97.4545-1.1293-6.16850.27670.32438.62980.1398-0.2555-0.2828-0.1036-0.3290.1390.12480.06880.18920.0657-0.04360.0250.0722-0.07020.084230.543393.994966.345
1018.46464.7954-1.32911.55750.14840.87650.09480.1559-0.18750.05570.0789-0.10890.00790.0441-0.17370.0194-0.05160.00480.1-0.03560.082217.370391.134371.1717
110.24040.3718-0.35241.0942-0.1580.8048-0.03070.1042-0.00160.0070.0548-0.01290.14380.0543-0.02410.0441-0.0243-0.00850.09530.01440.08691.664479.256677.9893
121.06490.77811.00221.0767-0.31685.86710.04070.05230.0262-0.0274-0.2061-0.24330.00060.25080.16530.025-0.0058-0.03580.07420.03110.110711.114679.975786.3694
138.98952.4788-8.07391.6247-3.73429.6673-0.56080.222-0.2274-0.1940.1097-0.01640.9093-0.39960.45110.1101-0.04320.04660.0975-0.03230.07516.440874.956266.9443
146.1103-0.566610.30125.5854-0.750317.37420.30910.2178-0.1772-0.3533-0.3203-0.43880.6290.63010.01120.04290.0015-0.0050.11750.02960.091915.034378.534271.8349
1520.3009-1.31638.306116.3146-5.449112.9441-0.51420.7241-0.26240.4239-0.3682-0.6926-0.87750.790.8824-0.0454-0.0519-0.16460.08640.05290.121520.528182.996279.8723
169.19452.2062-2.76161.6914-3.64688.4930.5361-1.1298-0.3396-0.4435-0.28870.19840.32090.5582-0.24740.0216-0.1022-0.14320.19920.05780.084222.085287.728287.9214
179.01734.29513.03934.24241.43494.81990.01590.00570.20360.1392-0.10350.028-0.30230.05070.08760.10030.00190.00120.00240.04040.08033.412188.121787.6794
188.17184.9151-2.00399.05631.77616.05790.0272-0.25190.2627-0.1667-0.04980.42930.07-0.24390.0226-0.0019-0.0139-0.01850.08820.04320.0741-5.850885.71877.203
1921.1795.6374.31391.54621.0791.4370.2027-0.21260.47820.1078-0.10030.1856-0.10750.0298-0.10240.053-0.02940.00610.0842-0.02960.058312.700294.607779.143
2020.43193.91465.69716.681415.560329.02390.54990.2396-0.41510.49140.39620.01420.99590.3836-0.9461-0.1142-0.0539-0.08610.02120.01240.137231.052498.249284.9615
210.11460.2331-0.41612.94772.88957.1520.0701-0.0689-0.0183-0.0656-0.35230.1075-0.4234-0.46950.28230.08770.0578-0.02040.0632-0.0540.0831-7.12962.555675.9626
221.25261.84571.601414.24651.18915.59790.0140.0827-0.2628-0.4958-0.15850.67020.4469-0.62050.14450.1349-0.1717-0.00720.0933-0.1610.0341-10.993145.627965.4311
233.18080.366-0.013214.5244-6.32232.76490.02240.873-0.2495-0.3632-0.36010.0547-0.0576-0.84120.33770.15620.0188-0.00670.1543-0.108-0.033-5.389356.291659.9177
240.71040.6715-1.54173.3607-0.69573.5584-0.02860.1363-0.0492-0.0426-0.21010.08120.0738-0.21910.23870.09670.02020.0190.0358-0.04220.0819-3.99852.622872.0545
253.62233.15-1.9418.0994-2.11193.8668-0.14910.1277-0.3325-0.1935-0.1592-0.40080.15760.06550.30840.14160.00360.0925-0.0202-0.03230.07463.508150.770763.9685
269.7282-3.74887.97432.1169-1.371639.0129-0.88410.5740.41731.1479-0.849-0.6316-2.93341.59011.7330.3957-0.151-0.0796-0.08220.10010.14339.71560.97673.3513
270.67021.0046-1.19355.6688-3.70243.0047-0.2-0.0167-0.0165-0.47430.0982-0.0983-0.21490.41780.10180.2074-0.01550.0451-0.0068-0.02070.06044.098361.25464.3206
281.46141.48960.881821.5796-0.94120.7009-0.21740.03170.0691-0.12350.3035-0.10720.3983-0.0399-0.08610.2095-0.07710.05170.0516-0.00160.00186.737973.245356.2867
295.67871.7783-2.22744.7574-2.07081.3226-0.08810.0737-0.3181-0.05340.185-0.1302-0.0805-0.0805-0.09680.078-0.0237-0.00660.09530.00140.06379.600386.311358.3342
300.52990.35350.31661.84731.02433.13150.0079-0.0176-0.0204-0.12180.0082-0.1008-0.05820.3513-0.01610.0487-0.03580.04810.09110.02630.059316.201992.271343.5235
310.988-0.12632.517313.06770.27556.44110.0564-0.06020.01840.0573-0.2797-0.10380.3280.24210.22320.0064-0.00390.08830.12290.01420.089117.712286.788744.6665
320.09950.7184-0.77675.1856-5.60646.0614-0.0537-0.15190.18210.0934-0.1729-0.0362-0.29260.59210.22660.0437-0.04640.02850.1665-0.04370.055518.190594.228655.8211
330.85192.38054.37487.935710.172425.7459-0.24310.0075-0.01060.0789-0.0362-0.14470.36870.97270.2792-0.02420.01030.01670.1877-0.00030.046919.25185.293659.063
343.9133-0.2225-6.06766.585411.345428.2804-0.50080.4214-0.33960.424-0.1050.02360.88490.12750.60580.07980.04750.1070.032-0.0120.059218.196577.711249.9043
350.38560.3956-1.423716.4894-0.6245.3007-0.2280.16560.147-1.38790.2141-0.1250.94110.11110.01390.1226-0.09240.08520.0671-0.05120.012612.171377.191741.3679
364.2634-6.35180.63059.8434-1.39689.501-0.00890.0130.0369-0.2598-0.17590.2-0.0905-0.43810.18480.0377-0.0090.05260.09840.01470.05057.449794.841442.4061
3711.08873.8831-3.501517.2741-2.19681.16490.05810.59541.0219-0.53490.17860.187-0.0655-0.0843-0.23670.12620.01430.00590.05620.00230.05577.4187101.849147.9952
381.14123.43160.093523.5693.89211.55960.09610.21810.2323-0.00610.05690.15030.1437-0.4039-0.1530.0448-0.01310.01120.12520.00840.04263.44891.044651.661
390.8607-0.8981-2.428829.63244.24226.95550.2641-0.02860.0766-1.3235-0.3340.83190.2471-0.92080.06990.2211-0.0707-0.06510.1116-0.0084-0.01362.678276.605247.9636
4023.0444-6.71832.247923.8641-3.31247.21260.5443-0.2795-1.4955-1.4188-0.26880.11870.8068-0.3864-0.27550.3155-0.05050.0149-0.059-0.0154-0.01955.300466.003645.9605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 31 - 6
2X-RAY DIFFRACTION2AA4 - 177 - 20
3X-RAY DIFFRACTION3AA18 - 3221 - 35
4X-RAY DIFFRACTION4AA33 - 4036 - 43
5X-RAY DIFFRACTION5AA41 - 6044 - 63
6X-RAY DIFFRACTION6AA61 - 6864 - 71
7X-RAY DIFFRACTION7AA69 - 7772 - 80
8X-RAY DIFFRACTION8AA78 - 8281 - 85
9X-RAY DIFFRACTION9AA83 - 9186 - 94
10X-RAY DIFFRACTION10AA92 - 10295 - 105
11X-RAY DIFFRACTION11AA103 - 130106 - 133
12X-RAY DIFFRACTION12AA131 - 153134 - 156
13X-RAY DIFFRACTION13AA154 - 161157 - 164
14X-RAY DIFFRACTION14AA162 - 169165 - 172
15X-RAY DIFFRACTION15AA170 - 174173 - 177
16X-RAY DIFFRACTION16AA175 - 185178 - 188
17X-RAY DIFFRACTION17AA186 - 197189 - 200
18X-RAY DIFFRACTION18AA198 - 205201 - 208
19X-RAY DIFFRACTION19AA206 - 228209 - 231
20X-RAY DIFFRACTION20AA229 - 234232 - 237
21X-RAY DIFFRACTION21BB-2 - 131 - 16
22X-RAY DIFFRACTION22BB14 - 2717 - 30
23X-RAY DIFFRACTION23BB28 - 4131 - 44
24X-RAY DIFFRACTION24BB42 - 6145 - 64
25X-RAY DIFFRACTION25BB62 - 7765 - 80
26X-RAY DIFFRACTION26BB78 - 8281 - 85
27X-RAY DIFFRACTION27BB83 - 8986 - 92
28X-RAY DIFFRACTION28BB90 - 9993 - 102
29X-RAY DIFFRACTION29BB100 - 107103 - 110
30X-RAY DIFFRACTION30BB108 - 141111 - 144
31X-RAY DIFFRACTION31BB142 - 148145 - 151
32X-RAY DIFFRACTION32BB149 - 158152 - 161
33X-RAY DIFFRACTION33BB159 - 168162 - 171
34X-RAY DIFFRACTION34BB169 - 173172 - 176
35X-RAY DIFFRACTION35BB174 - 191177 - 194
36X-RAY DIFFRACTION36BB192 - 197195 - 200
37X-RAY DIFFRACTION37BB198 - 203201 - 206
38X-RAY DIFFRACTION38BB204 - 215207 - 218
39X-RAY DIFFRACTION39BB216 - 224219 - 227
40X-RAY DIFFRACTION40BB225 - 229228 - 232

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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