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- PDB-5tzd: Structure of the WT S. venezulae BldD-(CTD-c-di-GMP)2 assembly in... -

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Basic information

Entry
Database: PDB / ID: 5tzd
TitleStructure of the WT S. venezulae BldD-(CTD-c-di-GMP)2 assembly intermediate
ComponentsDNA-binding protein
KeywordsDNA BINDING PROTEIN / BldD / assembly intermediate / antibiotics / c-di-GMP / Streptomyces
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 / BldD, C-terminal / BldD-like, C-terminal domain superfamily / DNA-binding protein BldD-like, C-terminal domain / 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 / BldD, C-terminal / BldD-like, C-terminal domain superfamily / DNA-binding protein BldD-like, C-terminal domain / 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: 1.749 Å
AuthorsSchumacher, M.
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
C: DNA-binding protein
A: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4638
Polymers40,7024
Non-polymers2,7624
Water5,621312
1
J: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5563
Polymers10,1751
Non-polymers1,3812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,1751
Polymers10,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5563
Polymers10,1751
Non-polymers1,3812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,1751
Polymers10,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.300, 108.300, 49.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
DNA-binding protein


Mass: 10175.426 Da / Num. of mol.: 4 / Mutation: L92M
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


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 1500, 100 mM sodium acetate, pH 5.0

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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: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.038
ReflectionResolution: 1.749→93.827 Å / Num. obs: 31775 / % possible obs: 94.7 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rsym value: 0.049 / Net I/σ(I): 17
Reflection shellResolution: 1.749→1.94 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3808 / CC1/2: 0.978 / % possible all: 79.5

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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: 5khd

5khd


Resolution: 1.749→43.888 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.07
RfactorNum. reflection% reflection
Rfree0.2396 2033 6.4 %
Rwork0.2074 --
obs0.2151 31775 94.17 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Bsol: 46.744 Å2 / ksol: 0.429 e/Å3
Displacement parametersBiso max: 120.26 Å2 / Biso mean: 31.26 Å2 / Biso min: 5.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.0131 Å20 Å20 Å2
2--0.0131 Å2-0 Å2
3----0.0262 Å2
Refinement stepCycle: final / Resolution: 1.749→43.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 276 312 2923
Biso mean--22.2 35.13 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0242601
X-RAY DIFFRACTIONf_angle_d2.393573
X-RAY DIFFRACTIONf_chiral_restr0.448416
X-RAY DIFFRACTIONf_plane_restr0.007434
X-RAY DIFFRACTIONf_dihedral_angle_d38.8161163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7503-1.7910.31211050.29011480158567
1.791-1.83580.31261170.27291741185877
1.8358-1.88540.30151350.26411982211789
1.8854-1.94090.53281130.42551766187980
1.9409-2.00360.27261390.24922106224594
2.0036-2.07520.30341370.23172093223094
2.0752-2.15830.20621420.22812106224894
2.1583-2.25650.33831170.3021815193281
2.2565-2.37540.23681380.21422026216491
2.3754-2.52430.26551420.20942109225194
2.5243-2.71910.2281420.21082094223694
2.7191-2.99270.27261450.20322099224494
2.9927-3.42560.19961410.17822130227194
3.4256-4.31530.1741420.15182095223793
4.3153-43.90150.24941390.19052113225290
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)
1-0.0125-0.0201-0.0071-0.00610.0122-0.03140.1669-0.0313-0.04060.1344-0.09910.1748-0.22860.0334-00.3590.10060.05820.167-0.01330.2753-36.19741.33663.601
20.011-0.0380.02110.07260.01060.0396-0.06360.07510.3410.09640.07510.0480.316-0.01860.01410.10880.04230.08050.0963-0.03130.2591-37.327234.956710.0541
30.00470.04480.03780.02970.00560.0043-0.2180.1220.0806-0.14410.1831-0.17770.2446-0.100.223-0.03850.07670.1484-0.00310.1546-36.85729.3486-1.3754
4-0.0014-0.0032-0.00140.0009-0.00090.00110.125-0.040.0278-0.04880.1352-0.10530.04740.035500.3960.02190.09330.26580.10840.3423-34.924938.9359-5.4151
5-0.0095-0.0012-0.0024-0.0051-0.00170.0415-0.3051-0.1347-0.04220.01820.11470.13920.1569-0.165800.1373-0.05190.020.3420.00830.2656-54.473611.23596.9264
60.04830.0443-0.00470.00970.02030.06790.07750.1071-0.1218-0.0552-0.03620.2522-0.0403-0.0040.00870.08770.0372-0.02630.1761-0.02690.2259-50.043815.15980.2771
70.013-0.0224-0.00740.0131-0.04630.09610.22-0.2849-0.0449-0.1169-0.13180.1828-0.11050.20480.00240.0816-0.00580.06610.1472-0.03360.2123-43.052520.15128.8085
80.00510.0018-0.00510.0016-0.00410.01450.0962-0.1718-0.020.22090.03120.2913-0.3018-0.220100.1995-0.00330.08890.47590.04210.2475-50.620615.704116.2738
90.02160.0111-0.01620.03580.06390.02970.2528-0.2915-0.16080.1034-0.12280.1176-0.38980.35910.00820.1794-0.0988-0.02990.2744-0.02330.1188-9.485818.177418.6681
100.09470.0264-0.09030.0272-0.06350.03160.13860.02050.05740.0391-0.0759-0.0672-0.0576-0.0590.01360.0708-0.00660.0370.08020.02180.1111-13.421220.610710.507
11-0.0074-0.0068-0.02540.01450.01630.01390.0560.05550.06050.1853-0.02580.0120.1245-0.1437-00.0845-0.009-0.00740.0636-0.0090.0785-20.827910.199211.8123
120.0179-0.0086-0.00340.01330.01110.0610.29330.0206-0.06090.4649-0.15560.08530.05450.10710.03140.2041-0.03630.02640.1124-0.00390.071-17.64313.25123.0668
130.0305-0.0329-0.00680.03540.0010.06770.0110.02540.2670.10130.0374-0.09070.4217-0.02060.00930.10660.04140.03220.1164-0.01950.0873-18.96131.528-5.8281
140.0193-0.01690.05540.0476-0.08010.0985-0.0306-0.0621-0.1212-0.02490.0857-0.0249-0.0449-0.03850.01980.0664-0.00070.00580.06480.0120.0898-26.29351.28913.2938
150.0527-0.0121-0.0543-0.01420.02080.0863-0.1004-0.092-0.0248-0.09750.0205-0.0281-0.0137-0.0735-0.03080.08120.0238-0.0130.0766-0.00250.1193-28.01439.7978-2.5611
160.0590.03970.02730.0607-0.09420.0614-0.13210.0403-0.0135-0.04680.051-0.0147-0.0384-0.0074-0.01830.0566-0.0192-0.00380.0697-0.00020.0627-18.716111.5281-7.8875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 84:96)A84 - 96
2X-RAY DIFFRACTION2(chain A and resid 97:120)A97 - 120
3X-RAY DIFFRACTION3(chain A and resid 121:146)A121 - 146
4X-RAY DIFFRACTION4(chain A and resid 147:158)A147 - 158
5X-RAY DIFFRACTION5(chain B and resid 83:96)B83 - 96
6X-RAY DIFFRACTION6(chain B and resid 97:122)B97 - 122
7X-RAY DIFFRACTION7(chain B and resid 123:137)B123 - 137
8X-RAY DIFFRACTION8(chain B and resid 138:158)B138 - 158
9X-RAY DIFFRACTION9(chain C and resid 83:97)C83 - 97
10X-RAY DIFFRACTION10(chain C and resid 98:126)C98 - 126
11X-RAY DIFFRACTION11(chain C and resid 127:138)C127 - 138
12X-RAY DIFFRACTION12(chain C and resid 139:158)C139 - 158
13X-RAY DIFFRACTION13(chain J and resid 84:99)J84 - 99
14X-RAY DIFFRACTION14(chain J and resid 100:119)J100 - 119
15X-RAY DIFFRACTION15(chain J and resid 120:130)J120 - 130
16X-RAY DIFFRACTION16(chain J and resid 131:158)J131 - 158

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