[English] 日本語
Yorodumi
- PDB-6d9m: T4-Lysozyme fusion to Geobacter GGDEF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d9m
TitleT4-Lysozyme fusion to Geobacter GGDEF
ComponentsFusion protein of Endolysin,Response receiver sensor diguanylate cyclase, GAF domain-containing
KeywordsHYDROLASE / Cyclic dinucleotide / GGDEF
Function / homology
Function and homology information


phosphorelay signal transduction system / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / GAF-like domain superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
ACETATE ION / GUANOSINE / GUANOSINE-5'-TRIPHOSPHATE / PYROPHOSPHATE 2- / Endolysin / Endolysin / Response receiver sensor diguanylate cyclase, GAF domain-containing
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Geobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsHallberg, Z. / Doxzen, K. / Kranzusch, P.J. / Hammond, M.
CitationJournal: Elife / Year: 2019
Title: Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration.
Authors: Hallberg, Z.F. / Chan, C.H. / Wright, T.A. / Kranzusch, P.J. / Doxzen, K.W. / Park, J.J. / Bond, D.R. / Hammond, M.C.
History
DepositionApr 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 17, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fusion protein of Endolysin,Response receiver sensor diguanylate cyclase, GAF domain-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8318
Polymers38,1501
Non-polymers1,6817
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.677, 111.645, 55.336
Angle α, β, γ (deg.)90.000, 122.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-655-

HOH

21A-703-

HOH

31A-736-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Fusion protein of Endolysin,Response receiver sensor diguanylate cyclase, GAF domain-containing / / Lysis protein / Lysozyme / Muramidase


Mass: 38149.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria)
Gene: e, T4Tp126, Gmet_1914 / Strain: GS-15 / ATCC 53774 / DSM 7210 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: D9IEF7, UniProt: Q39UD1, UniProt: P00720*PLUS, lysozyme

-
Non-polymers , 7 types, 447 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG 4,000; 0.03M HEPES-KOH, pH 7.5; 0.3M Na(OAc)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115820, 2.254180
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.115821
22.254181
ReflectionResolution: 1.35→35.75 Å / Num. obs: 77765 / % possible obs: 97.8 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Net I/σ(I): 21.6 / Num. measured all: 512201 / Scaling rejects: 338
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.374 / Num. measured all: 8093 / Num. unique all: 2643 / CC1/2: 0.862 / Rpim(I) all: 0.222 / Rrim(I) all: 0.439 / Net I/σ(I) obs: 2.9 / % possible all: 67.7

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→35.747 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1701 1561 2.01 %
Rwork0.1545 76202 -
obs0.1548 77763 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.23 Å2 / Biso mean: 21.1363 Å2 / Biso min: 8.71 Å2
Refinement stepCycle: final / Resolution: 1.35→35.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 83 440 3100
Biso mean--28.03 33.87 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162932
X-RAY DIFFRACTIONf_angle_d1.5643992
X-RAY DIFFRACTIONf_chiral_restr0.103436
X-RAY DIFFRACTIONf_plane_restr0.011515
X-RAY DIFFRACTIONf_dihedral_angle_d18.861117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.38940.21451160.20525653576980
1.3894-1.4390.19921480.18516926707498
1.439-1.49660.1781270.16996991711899
1.4966-1.56480.21440.15916988713299
1.5648-1.64720.16951530.15077040719399
1.6472-1.75050.15981450.15270437188100
1.7505-1.88560.16151470.153470887235100
1.8856-2.07530.16751390.149771027241100
2.0753-2.37560.15911480.148470967244100
2.3756-2.99280.18661480.162571007248100
2.9928-35.75970.16031460.147271757321100
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)
11.28650.84520.11091.5194-1.71685.9476-0.2213-0.015-0.14110.09680.1102-0.12810.19220.22650.09130.1190.00850.00920.1597-0.00280.1339-0.66276.12135.239
21.6463-0.44240.11513.01030.84781.8652-0.00540.02940.0402-0.05610.02990.0245-0.08390.0105-0.01720.0711-0.00530.00920.10980.02310.10273.34985.1620.432
31.1451-0.8646-0.31820.79161.04415.447-0.22290.19560.0044-0.51120.6595-1.0670.30730.39310.89590.1792-0.04220.05770.2415-0.06750.26813.479.8421.508
43.2603-1.9561-2.30473.47323.42645.30770.0667-0.12340.1465-0.06890.1726-0.3588-0.09880.3647-0.17810.1452-0.0189-0.03390.190.00430.16096.23187.39236.287
51.76170.038-0.63573.6363-0.82742.42720.007-0.27440.2063-0.0009-0.0340.0848-0.074-0.0202-0.02980.15240.0484-0.04920.2013-0.06330.1791-4.9192.43547.721
62.2053-0.8323-0.45760.66730.85741.7304-0.1790.150.3959-0.0070.094-0.1578-0.31680.04720.0380.1187-0.0079-0.03320.14280.01530.1595-7.43988.67239.089
71.34240.1437-0.30861.15590.47683.3677-0.1974-0.21410.11140.22280.01050.3098-0.1849-0.38420.14450.1480.07380.01140.2052-0.02480.1346-16.96188.26348.241
88.1304-0.6390.56773.42523.42634.3322-0.0810.20730.3349-0.216-0.1319-0.0601-0.48070.01590.17980.0924-0.0046-0.02360.14840.00510.1149-17.61283.93632.425
92.2074-1.1747-0.04932.66230.31012.0749-0.1824-0.0415-0.07940.32720.09470.21450.1246-0.12370.02720.11430.0270.0340.14420.00070.1083-10.89976.68841.864
103.8167-2.83610.5165.37410.471.6603-0.1035-0.082-0.22230.58570.18620.43890.1346-0.0244-0.03610.16760.04210.01880.1187-0.02170.1732-3.79763.33638.393
110.4903-0.00520.24993.4923-1.24293.36650.0179-0.00310.0360.0040.00750.20180.1192-0.1096-0.07240.11960.004-0.0120.15550.00710.1846-7.52471.17324.155
120.3172-0.3280.4742.1577-1.25210.73530.04940.03020.02710.0545-0.04380.18180.016-0.0511-0.0460.1930.01670.03460.1143-0.00740.126-0.46550.86727.875
131.80770.8972-0.90325.3105-3.58895.3457-0.10430.00380.03110.338-0.122-0.3918-0.14410.05350.24720.14710.0143-0.01120.1289-0.02090.16235.77453.03436.809
140.80610.31990.23261.7722-1.25762.3129-0.1144-0.05470.02950.0313-0.1039-0.1549-0.13430.13550.08160.20080.0191-0.01820.1574-0.00770.21560.3961.65128.659
150.3311-0.316-0.05730.32310.24220.71210.0230.10150.1473-0.19910.03530.03240.0152-0.0031-0.00010.15030.02240.01530.145-0.00750.1667-0.55660.91524.381
160.4661-0.3130.69650.8194-0.54842.4030.04420.20710.1033-0.0904-0.3119-0.27330.17390.49990.08680.14260.04140.04450.20370.03420.183210.18552.825.147
171.0028-0.51150.82821.5319-0.65991.77560.0650.090.1119-0.1315-0.1381-0.07290.23140.0961-0.06090.1510.02710.0130.1259-0.00250.12290.64654.32421.338
180.4959-0.8530.7097.0574-1.18820.94510.0921-0.0645-0.4466-0.10870.0250.65310.4169-0.22470.04850.23930.0066-0.02530.1914-0.02970.2371-8.72553.30618.321
190.5462-0.0926-0.43533.116-2.63752.74080.20040.3217-0.0707-1.0264-0.05580.35830.8657-0.27520.07670.39260.0517-0.03210.2451-0.01120.2178-0.25848.30915.474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -160:-149 )A-160 - -149
2X-RAY DIFFRACTION2( CHAIN A AND RESID -148:-110 )A-148 - -110
3X-RAY DIFFRACTION3( CHAIN A AND RESID -109:-101 )A-109 - -101
4X-RAY DIFFRACTION4( CHAIN A AND RESID -100:-81 )A-100 - -81
5X-RAY DIFFRACTION5( CHAIN A AND RESID -80:-68 )A-80 - -68
6X-RAY DIFFRACTION6( CHAIN A AND RESID -67:-46 )A-67 - -46
7X-RAY DIFFRACTION7( CHAIN A AND RESID -45:-26 )A-45 - -26
8X-RAY DIFFRACTION8( CHAIN A AND RESID -25:-18 )A-25 - -18
9X-RAY DIFFRACTION9( CHAIN A AND RESID -17:0 )A-17 - 0
10X-RAY DIFFRACTION10( CHAIN A AND RESID 1:12 )A1 - 12
11X-RAY DIFFRACTION11( CHAIN A AND RESID 13:30 )A13 - 30
12X-RAY DIFFRACTION12( CHAIN A AND RESID 31:52 )A31 - 52
13X-RAY DIFFRACTION13( CHAIN A AND RESID 53:69 )A53 - 69
14X-RAY DIFFRACTION14( CHAIN A AND RESID 70:81 )A70 - 81
15X-RAY DIFFRACTION15( CHAIN A AND RESID 82:93 )A82 - 93
16X-RAY DIFFRACTION16( CHAIN A AND RESID 94:117 )A94 - 117
17X-RAY DIFFRACTION17( CHAIN A AND RESID 118:138 )A118 - 138
18X-RAY DIFFRACTION18( CHAIN A AND RESID 139:155 )A139 - 155
19X-RAY DIFFRACTION19( CHAIN A AND RESID 156:163 )A156 - 163

+
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