[English] 日本語
Yorodumi
- PDB-6gyy: Crystal structure of DacA from Staphylococcus aureus, N166C/T172C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gyy
TitleCrystal structure of DacA from Staphylococcus aureus, N166C/T172C double mutant
ComponentsDiadenylate cyclase
KeywordsTRANSFERASE / c-di-AMP / diadenylate cyclase / protein engineering
Function / homologyYojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsTosi, T. / Freemont, P.S. / Grundling, A.
CitationJournal: PLoS Pathog. / Year: 2019
Title: Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM.
Authors: Tosi, T. / Hoshiga, F. / Millership, C. / Singh, R. / Eldrid, C. / Patin, D. / Mengin-Lecreulx, D. / Thalassinos, K. / Freemont, P. / Grundling, A.
History
DepositionJul 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diadenylate cyclase
B: Diadenylate cyclase


Theoretical massNumber of molelcules
Total (without water)38,7802
Polymers38,7802
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-16 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.862, 79.773, 98.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 111 through 259)
21(chain B and resid 111 through 259)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 111 - 259 / Label seq-ID: 17 - 165

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 111 through 259)AA
2(chain B and resid 111 through 259)BB

-
Components

#1: Protein Diadenylate cyclase / / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase


Mass: 19390.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dacA, C7J94_12115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P7CAT2, diadenylate cyclase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M LiCl, 0.1M Na-Cacodylate pH 6.5, 30% Peg400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.77→98.91 Å / Num. obs: 9512 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.2
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1345 / CC1/2: 0.892 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GYW

6gyw


Resolution: 2.77→42.003 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.36
RfactorNum. reflection% reflection
Rfree0.2312 467 4.93 %
Rwork0.2101 --
obs0.2113 9471 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 192.53 Å2 / Biso mean: 92.3439 Å2 / Biso min: 54.98 Å2
Refinement stepCycle: final / Resolution: 2.77→42.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 0 0 2316
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082353
X-RAY DIFFRACTIONf_angle_d1.1993177
X-RAY DIFFRACTIONf_chiral_restr0.081371
X-RAY DIFFRACTIONf_plane_restr0.007405
X-RAY DIFFRACTIONf_dihedral_angle_d8.511433
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1330X-RAY DIFFRACTION10.92TORSIONAL
12B1330X-RAY DIFFRACTION10.92TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7702-3.17090.33021340.278629453079
3.1709-3.99450.27051510.249729753126
3.9945-42.00760.2071820.185830843266
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)
17.60643.7771-1.25313.0446-0.57511.3066-0.60390.24430.2389-0.88670.1691-1.55450.89120.7760.02770.8756-0.00720.21380.9646-0.15440.9827-1.6687-3.2485-0.4943
23.88522.23310.46459.46182.78358.21570.1042-0.31530.1420.28320.1376-0.0908-0.2650.2543-0.180.50310.00020.03250.5723-0.1110.5205-11.98021.78388.3467
30.0657-0.05330.13310.38160.82932.01541.0590.0547-0.22333.2466-1.06731.01591.4844-1.3168-0.06360.927-0.2321-0.01231.054-0.11771.0416-24.4753-10.48569.3775
46.60621.35360.58375.33261.98981.58210.3414-0.5007-0.44860.2316-0.17040.55310.5859-0.6111-0.33090.77770.0167-0.15160.7224-0.14230.5778-17.9099-9.48514.7265
54.12582.53640.48266.63872.81835.21150.0760.4617-0.7691-0.90860.2323-0.42920.3418-0.0064-0.3990.99710.1089-0.00420.8359-0.14940.818-11.4794-9.6069-4.4091
63.8621.17150.1881.56760.56671.47830.1801-0.1366-0.17180.30820.1651.5929-0.254-0.9557-0.17270.6962-0.01770.03650.7874-0.01040.8859-9.135116.411125.1437
74.0032-0.83811.75386.37152.62947.70270.01130.59990.2728-0.4420.1512-0.2238-0.09010.3079-0.20090.6361-0.08870.11250.5764-0.05540.80550.918413.277816.1072
84.497-3.77072.69136.2141-3.17514.8137-0.19180.3729-1.3997-0.1673-0.2155-3.02882.32821.52640.34520.9170.07220.32250.8505-0.04061.07672.99192.569618.8838
93.5114-3.06892.60726.05411.4485.9692-0.49171.2783-0.955-0.8781-0.14790.3087-2.28461.00840.75681.1166-0.13640.11990.6143-0.14780.8036-1.14316.581912.9267
102.871-3.2238-2.78422.0210.41833.8292-2.3543-0.27720.4535-0.61260.0493-0.77091.05372.0429-0.14080.78060.00110.16731.4730.02421.569214.805113.141618.6051
114.4636-4.0314-0.31185.19310.9330.35-0.0721.88390.5202-1.99910.95150.46520.6607-0.2655-0.32111.62310.1259-0.30161.53650.30131.656918.502213.082932.3049
127.3893-0.555-0.9917.15681.77747.02620.2226-0.51220.85030.16670.6002-0.7774-0.2231.1375-0.31060.566-0.13130.03610.9413-0.19880.89058.707515.581625.998
133.93635.30511.07057.24521.75951.5751-0.5523-0.56611.31070.53420.2624-0.73340.37192.1216-0.63460.73980.01930.05981.1964-0.22880.91097.990320.871732.1025
146.79831.00913.49458.91685.32475.1726-0.3358-0.1991.0138-0.2714-0.5574-1.00990.3935-0.77510.21330.65180.04530.01390.7917-0.02241.0243-3.184124.017327.225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 110 through 130 )A110 - 130
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 188 )A131 - 188
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 206 )A189 - 206
4X-RAY DIFFRACTION4chain 'A' and (resid 207 through 237 )A207 - 237
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 259 )A238 - 259
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 130 )B111 - 130
7X-RAY DIFFRACTION7chain 'B' and (resid 131 through 167 )B131 - 167
8X-RAY DIFFRACTION8chain 'B' and (resid 168 through 178 )B168 - 178
9X-RAY DIFFRACTION9chain 'B' and (resid 179 through 188 )B179 - 188
10X-RAY DIFFRACTION10chain 'B' and (resid 189 through 198 )B189 - 198
11X-RAY DIFFRACTION11chain 'B' and (resid 199 through 206 )B199 - 206
12X-RAY DIFFRACTION12chain 'B' and (resid 207 through 237 )B207 - 237
13X-RAY DIFFRACTION13chain 'B' and (resid 238 through 246 )B238 - 246
14X-RAY DIFFRACTION14chain 'B' and (resid 247 through 260 )B247 - 260

+
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