[English] 日本語
Yorodumi
- PDB-5tzd: Structure of the WT S. venezulae BldD-(CTD-c-di-GMP)2 assembly in... -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more