[English] 日本語
Yorodumi
- PDB-3zec: Fic protein from SHEWANELLA ONEIDENSIS (E73G mutant) in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zec
TitleFic protein from SHEWANELLA ONEIDENSIS (E73G mutant) in complex with AMPPNP
ComponentsADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC
KeywordsTRANSFERASE / AMPYLATION / ADENYLYLATION
Function / homology
Function and homology information


AMPylase activity / protein adenylylation / protein adenylyltransferase / magnesium ion binding / protein homodimerization activity / ATP binding
Similarity search - Function
Fic/DOC N-terminal / Protein adenylyltransferase SoFic-like / : / Fic/DOC family N-terminal / Protein adenylyltransferase SoFic-like, C-terminal domain / Fido domain-containing protein / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile.
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein adenylyltransferase SoFic
Similarity search - Component
Biological speciesSHEWANELLA ONEIDENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGoepfert, A. / Schirmer, T.
CitationJournal: Plos One / Year: 2013
Title: Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold.
Authors: Goepfert, A. / Stanger, F.V. / Dehio, C. / Schirmer, T.
History
DepositionDec 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC
B: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1755
Polymers86,1392
Non-polymers1,0373
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-22.8 kcal/mol
Surface area32780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.320, 80.630, 141.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC / AMPYLATOR SOFIC / FIC DOMAIN CONTAINING TRANSCRIPTION REGULATOR


Mass: 43069.316 Da / Num. of mol.: 2 / Fragment: FIC DOMAIN RESIDUES 2-372 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): AI
References: UniProt: Q8E9K5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NONE
Crystal growpH: 7.1 / Details: 22% W/V PEG3350, 0.2M NAF PH 7.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.66 Å / Num. obs: 42250 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.57
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.33 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EQX

3eqx


Resolution: 2.2→14.993 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 19.68 / Stereochemistry target values: ML
Details: LOCAL TORSION-ANGLE NCS RESTRAINTS AS IMPLEMENTED IN PHENIX HAVE BEEN APPLIED FOR REFINEMENT
RfactorNum. reflection% reflection
Rfree0.2105 1992 4.7 %
Rwork0.1623 --
obs0.1645 42085 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→14.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 0 63 695 6680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116193
X-RAY DIFFRACTIONf_angle_d1.1928470
X-RAY DIFFRACTIONf_dihedral_angle_d16.9962381
X-RAY DIFFRACTIONf_chiral_restr0.07983
X-RAY DIFFRACTIONf_plane_restr0.0071074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27850.2961970.20043956X-RAY DIFFRACTION100
2.2785-2.36940.26311960.1943962X-RAY DIFFRACTION100
2.3694-2.47680.21681960.17423944X-RAY DIFFRACTION100
2.4768-2.60670.23831980.16673972X-RAY DIFFRACTION100
2.6067-2.76910.22141970.16793963X-RAY DIFFRACTION100
2.7691-2.98130.21871990.16894008X-RAY DIFFRACTION100
2.9813-3.27850.23541980.17433984X-RAY DIFFRACTION100
3.2785-3.74640.20712000.15564032X-RAY DIFFRACTION100
3.7464-4.69590.16922020.13724067X-RAY DIFFRACTION100
4.6959-14.99340.17832090.15294205X-RAY DIFFRACTION100
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)
11.0468-0.0004-0.26752.2312-0.71490.7179-0.0008-0.39680.01350.6015-0.03210.0209-0.15690.0370.00540.16920.00480.00910.17220.02920.068514.2105-22.44321.7806
20.6739-0.0777-0.00731.76120.36421.7179-0.03720.1033-0.0637-0.2373-0.0542-0.015-0.0409-0.09030.07340.046-0.00530.02790.0687-0.00760.081319.929-20.3618-7.3763
32.0848-0.8723-1.08422.85870.89612.0624-0.03470.165-0.239-0.2312-0.0423-0.03130.1546-0.23920.06420.1077-0.0362-0.01370.08360.00180.127113.0079-36.7761-6.958
40.1773-0.0530.15990.16160.3651.32530.0995-0.1649-0.59480.11550.0231-0.01740.4063-0.2354-0.11650.1462-0.01470.01680.11720.07810.329415.7473-40.643616.0666
50.82350.2861-0.21560.9595-0.04771.1650.0085-0.0288-0.04-0.01630.00910.0255-0.0373-0.0394-0.00740.02010.0202-0.00990.0376-0.00340.040118.5347-23.85021.6547
60.90150.40880.31180.98120.72841.4663-0.37170.3701-0.4916-0.3211-0.38010.14730.0536-0.52520.01070.2634-0.0380.04050.4488-0.40840.208821.1177-33.0688-30.0171
70.2551-0.4428-0.21881.73670.56380.2265-0.0964-0.05530.04510.3187-0.0016-0.0207-0.0451-0.0416-0.00390.2296-0.0079-0.11230.20820.01220.161927.770820.394212.4648
80.45380.10850.30180.85190.30941.5563-0.05950.0730.0902-0.12670.0117-0.0032-0.1142-0.04960.03320.09140.01020.02650.08730.02880.113617.72889.6141-15.7115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28 THROUGH 72 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 73 THROUGH 131 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 132 THROUGH 160 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 161 THROUGH 292 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 293 THROUGH 370 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 0 THROUGH 27 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 28 THROUGH 370 )

+
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