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- PDB-5tzf: Structure of the BldD CTD(D116A)-(c-di-GMP)2 intermediate, form 1 -

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Basic information

Entry
Database: PDB / ID: 5tzf
TitleStructure of the BldD CTD(D116A)-(c-di-GMP)2 intermediate, form 1
ComponentsDNA-binding protein
KeywordsDNA BINDING PROTEIN / BldD / c-di-GMP / assembly intermediate
Function / homology
Function and homology information


nucleotide binding / negative regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #1930 / DNA-binding protein BldD-like, C-terminal domain / BldD, C-terminal / BldD-like, C-terminal domain superfamily / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #1930 / DNA-binding protein BldD-like, C-terminal domain / BldD, C-terminal / BldD-like, C-terminal domain superfamily / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C2E / DNA-binding protein
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex.
Authors: Schumacher, M.A. / Zeng, W. / Findlay, K.C. / Buttner, M.J. / Brennan, R.G. / Tschowri, N.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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
J: DNA-binding protein
B: DNA-binding protein
E: DNA-binding protein
D: DNA-binding protein
I: DNA-binding protein
H: DNA-binding protein
N: DNA-binding protein
M: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,43016
Polymers80,9078
Non-polymers5,5238
Water3,081171
1
J: DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,1131
Polymers10,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4943
Polymers10,1131
Non-polymers1,3812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8042
Polymers10,1131
Non-polymers6901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8042
Polymers10,1131
Non-polymers6901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8042
Polymers10,1131
Non-polymers6901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
H: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8042
Polymers10,1131
Non-polymers6901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
N: DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,1131
Polymers10,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
M: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4943
Polymers10,1131
Non-polymers1,3812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.133, 93.061, 94.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DNA-binding protein /


Mass: 10113.378 Da / Num. of mol.: 8 / Mutation: D166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_1089 / Production host: Escherichia coli (E. coli) / References: UniProt: F2RCL8
#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.6 M sodium/potassium phosphate, 100 mM Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→66.2 Å / Num. obs: 30442 / % possible obs: 99.58 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / CC1/2: 0.998 / Rsym value: 0.054 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.6 / Num. measured obs: 2940 / CC1/2: 0.908 / % possible all: 68.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZD

5tzd


Resolution: 2.4→66.166 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.57
RfactorNum. reflection% reflection
Rfree0.2719 1485 4.88 %
Rwork0.2294 --
obs0.2315 30442 99.58 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 47.049 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 173.86 Å2 / Biso mean: 58.59 Å2 / Biso min: 17.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.2017 Å20 Å2-0 Å2
2--1.4629 Å20 Å2
3----2.6646 Å2
Refinement stepCycle: final / Resolution: 2.4→66.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 368 171 5361
Biso mean--38.09 48.02 -
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115316
X-RAY DIFFRACTIONf_angle_d1.0967320
X-RAY DIFFRACTIONf_chiral_restr0.408856
X-RAY DIFFRACTIONf_plane_restr0.003886
X-RAY DIFFRACTIONf_dihedral_angle_d39.372372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.48580.36331520.302328362988100
2.4858-2.58530.30711540.280728473001100
2.5853-2.7030.29881490.265928753024100
2.703-2.84550.34781490.256428613010100
2.8455-3.02380.30051340.262628913025100
3.0238-3.25720.3071550.251528803035100
3.2572-3.5850.30041450.248428983043100
3.585-4.10370.2511520.201329163068100
4.1037-5.16990.24531470.192829523099100
5.1699-66.19140.22031480.21343001314997
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)
10.03150.01290.0358-0.0106-0.0036-0.01420.32940.25880.50680.1175-0.11250.326-0.44620.1131-0.00010.69380.1080.07430.6269-0.0690.3469-0.060831.16513.0696
21.008-0.5599-0.7530.75470.76760.881-0.0681-1.7073-0.8829-0.10991.0461-0.4654-0.3566-0.50510.59260.08510.0025-0.08160.81580.16020.45815.679618.463221.5788
30.4138-0.2218-0.27030.74570.25080.61920.2723-0.09420.1683-0.4538-0.1004-0.49140.3754-0.2115-0.00050.392-0.01540.07150.3548-0.0380.26973.142319.217810.8365
40.7799-0.0095-0.19380.7190.31480.8289-0.4444-0.846-0.2239-0.32510.08280.2197-0.27020.0348-0.03060.1881-0.12710.04320.5921-0.06730.2408-6.228222.490518.8836
50.78010.0753-0.6730.02360.01591.0991-1.1503-0.31780.07551.05670.2741-0.0771-0.01790.2636-0.04820.30370.0914-0.06620.63760.03540.3066-12.564463.127312.1487
6-0.0292-0.0390.00120.01360.00520.03780.57430.0482-0.58490.0518-0.557-1.16930.76750.0653-00.72090.17190.17490.29190.18410.3751-18.067852.393519.8984
70.98460.41970.5809-0.25591.0610.64120.01780.0065-0.0259-0.09030.06140.06260.2820.2276-00.2820.0587-0.05670.247-0.01020.4102-21.099960.4059.3573
80.3595-0.1272-0.00980.19520.02560.10060.0449-0.23050.4086-0.188-0.1317-0.03610.13260.38290.11380.1670.1051-0.14180.32790.02260.2982-15.508766.440719.1811
90.2527-0.05950.1030.0394-0.26580.05170.68560.44660.88390.4356-0.0734-0.38230.3813-0.13190.0870.2066-0.2198-0.13020.728-0.2075-0.0631-18.167266.5581-16.6401
10-0.0138-0.05670.0157-0.018-0.0472-0.02911.04630.04470.4187-0.0232-0.014-0.3557-0.39130.83260.00030.39810.0644-0.06020.68660.56870.6823-19.782480.5426-22.658
110.1210.3359-0.10141.06220.28130.971-0.0180.3541-0.00870.39220.1799-0.3062-0.28130.18140.01060.1986-0.1236-0.05880.44620.12280.3166-17.95773.3887-9.4404
120.2937-0.06920.2056-0.013-0.18780.7989-0.350.62760.3923-0.19940.50630.0061-0.41440.31310.00440.2041-0.072-0.02360.75890.01720.2872-27.79870.7366-18.6876
130.7245-0.04570.47370.0927-0.05620.30890.0787-0.65810.67530.1975-0.45040.3285-0.00360.3382-0.01420.5943-0.0410.13950.4669-0.06630.1467-0.760181.1094-1.2758
140.39680.21590.2990.4322-0.17130.62350.30930.2487-0.1554-0.5712-0.40810.09490.1505-0.24920.06670.2620.1329-0.00850.2077-0.0920.19831.792983.7622-16.1208
150.1764-0.3536-0.39710.5110.17020.38710.226-0.50630.02940.7052-0.04240.2870.77820.0999-0.00080.27630.0388-0.02440.3002-0.0660.24313.374579.3053-7.4029
160.158-0.09990.21950.5949-0.37110.3205-0.2457-0.1554-0.14110.21320.1549-0.3556-0.7340.11850.00290.3290.0182-0.06530.1981-0.08540.35295.040290.5401-5.1219
170.3483-0.21440.33250.3393-0.22350.2996-0.00080.2337-0.7853-1.0726-0.91550.0370.37570.60840.00120.7259-0.2050.2278-0.0614-0.13520.33395.813858.6384-9.6842
180.05470.0289-0.11030.1179-0.02880.1048-0.4913-0.54-0.2974-0.11390.43280.2440.77830.13390.00081.5321-0.03270.45820.31680.06890.93483.514549.06524.8276
191.7937-0.3412-0.67651.3497-0.51690.55870.18620.1099-0.23480.7477-0.0883-0.12330.0301-0.02590.00460.4604-0.05560.13320.1116-0.01480.19743.829161.83861.0637
201.05180.1769-1.42150.15890.01242.0295-0.4133-0.2676-0.7624-0.5044-0.1885-0.36151.31680.53960.00051.06310.13990.17530.18470.09520.550312.340152.3256-3.8601
210.2226-0.14540.07250.17050.22440.21640.4876-0.58170.1006-1.152-0.62970.22820.53980.7024-00.547-0.15830.11730.41060.00650.3358.398832.1318-13.5344
220.00390.00430.00590.01240.0106-0.00320.11030.1708-0.27440.34-0.0697-0.0592-0.1469-0.067200.78620.0101-0.08860.62320.07070.7085-0.269641.4338-20.917
230.6446-0.58960.0190.42190.12590.69360.04390.0828-0.07290.1806-0.1049-0.1515-0.1741-0.0497-00.3777-0.14160.14870.2352-0.04610.31530.524332.994-8.6587
240.15790.1022-0.14040.21130.14840.2160.37820.1229-0.1497-0.3787-0.6567-0.2543-0.21010.678700.2903-0.00810.15370.46130.01560.2875.267226.8907-19.1288
250.09780.19390.07110.08640.04510.025-0.4675-0.39950.80280.0462-0.21971.3354-0.50650.0929-00.86970.0097-0.11320.34890.04590.6902-23.15241.5239-12.4243
26-0.0336-0.3195-0.47220.34590.17150.18190.43970.39620.1208-0.4743-0.18990.4968-0.41760.026100.37790.0028-0.01390.3171-0.04650.3214-20.180531.8048-14.9355
27-0.00180.03580.0325-0.0135-0.0180.042-0.247-0.51570.0438-0.02790.5349-0.5-0.9460.373300.47430.01750.09890.4093-0.13520.3327-13.247432.9587-3.2882
280.2653-0.01930.16170.3053-0.0933-0.00480.3041-0.58470.9551-0.5935-0.1488-0.0333-0.682-0.08610.00140.63080.00050.27380.1851-0.14230.6635-16.874643.4016-5.0465
290.5284-0.02960.95310.43030.44112.0396-0.7827-0.3374-0.4616-1.5449-0.45150.3454-0.99281.0412-0.07680.29030.13250.1240.2582-0.06360.571-15.665311.784-9.2796
300.4521-0.0115-0.50710.0057-0.33370.3457-0.4458-0.4483-0.46481.70930.31331.10670.328-0.40690.42820.85150.13560.6630.3310.20380.6991-20.28259.70814.2556
312.93261.22420.70171.13980.59690.988-0.65862.12821.95650.3670.9261.28180.52371.30890.02540.22640.06070.1885-0.1535-0.2773-0.1499-9.698714.0554-0.6046
320.1465-0.47830.04660.8876-0.40372.70240.1678-0.0032-0.15050.4003-0.26440.63290.17780.4327-0.10640.31770.05010.12220.1423-0.07910.3023-10.00254.3771-5.1725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 83:86)B83 - 86
2X-RAY DIFFRACTION2(chain B and resid 87:97)B87 - 97
3X-RAY DIFFRACTION3(chain B and resid 98:130)B98 - 130
4X-RAY DIFFRACTION4(chain B and resid 131:158)B131 - 158
5X-RAY DIFFRACTION5(chain D and resid 82:91)D82 - 91
6X-RAY DIFFRACTION6(chain D and resid 92:99)D92 - 99
7X-RAY DIFFRACTION7(chain D and resid 100:143)D100 - 143
8X-RAY DIFFRACTION8(chain D and resid 144:158)D144 - 158
9X-RAY DIFFRACTION9(chain E and resid 82:91)E82 - 91
10X-RAY DIFFRACTION10(chain E and resid 92:100)E92 - 100
11X-RAY DIFFRACTION11(chain E and resid 101:130)E101 - 130
12X-RAY DIFFRACTION12(chain E and resid 131:158)E131 - 158
13X-RAY DIFFRACTION13(chain H and resid 83:86)H83 - 86
14X-RAY DIFFRACTION14(chain H and resid 87:117)H87 - 117
15X-RAY DIFFRACTION15(chain H and resid 118:131)H118 - 131
16X-RAY DIFFRACTION16(chain H and resid 132:158)H132 - 158
17X-RAY DIFFRACTION17(chain I and resid 81:88)I81 - 88
18X-RAY DIFFRACTION18(chain I and resid 89:100)I89 - 100
19X-RAY DIFFRACTION19(chain I and resid 101:133)I101 - 133
20X-RAY DIFFRACTION20(chain I and resid 134:158)I134 - 158
21X-RAY DIFFRACTION21(chain J and resid 81:96)J81 - 96
22X-RAY DIFFRACTION22(chain J and resid 97:100)J97 - 100
23X-RAY DIFFRACTION23(chain J and resid 101:141)J101 - 141
24X-RAY DIFFRACTION24(chain J and resid 142:158)J142 - 158
25X-RAY DIFFRACTION25(chain M and resid 83:99)M83 - 99
26X-RAY DIFFRACTION26(chain M and resid 100:124)M100 - 124
27X-RAY DIFFRACTION27(chain M and resid 125:130)M125 - 130
28X-RAY DIFFRACTION28(chain M and resid 131:158)M131 - 158
29X-RAY DIFFRACTION29(chain N and resid 81:88)N81 - 88
30X-RAY DIFFRACTION30(chain N and resid 89:120)N89 - 120
31X-RAY DIFFRACTION31(chain N and resid 121:138)N121 - 138
32X-RAY DIFFRACTION32(chain N and resid 139:158)N139 - 158

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