[English] 日本語
Yorodumi
- PDB-5tzf: Structure of the BldD CTD(D116A)-(c-di-GMP)2 intermediate, form 1 -

+
Open data


ID or keywords:

Loading...

-
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


negative regulation of DNA-templated transcription / nucleotide binding / 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.35 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

-
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

-
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: 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

+
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://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