[English] 日本語
Yorodumi
- PDB-3eqx: CRYSTAL STRUCTURE OF A FIC FAMILY PROTEIN (SO_4266) FROM SHEWANEL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eqx
TitleCRYSTAL STRUCTURE OF A FIC FAMILY PROTEIN (SO_4266) FROM SHEWANELLA ONEIDENSIS AT 1.6 A RESOLUTION
ComponentsFIC DOMAIN CONTAINING TRANSCRIPTIONAL REGULATOR
KeywordsDNA BINDING PROTEIN / FIC FAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


AMPylase activity / protein adenylyltransferase / protein adenylylation / 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 / Fido domain / Fic/DOC family / Fido domain profile.
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Protein adenylyltransferase SoFic
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution.
Authors: Das, D. / Krishna, S.S. / McMullan, D. / Miller, M.D. / Xu, Q. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M.C. ...Authors: Das, D. / Krishna, S.S. / McMullan, D. / Miller, M.D. / Xu, Q. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elias, Y. / Elsliger, M.A. / Ernst, D. / Feuerhelm, J. / Grzechnik, A. / Grzechnik, S.K. / Hale, J. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Kumar, A. / Marciano, D. / Morse, A.T. / Murphy, K.D. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H. / Trame, C.B. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionOct 14, 2008ID: 2QC0
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: FIC DOMAIN CONTAINING TRANSCRIPTIONAL REGULATOR
B: FIC DOMAIN CONTAINING TRANSCRIPTIONAL REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4523
Polymers85,3022
Non-polymers1501
Water14,664814
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.210, 80.300, 141.000
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
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6 / Auth seq-ID: 11 - 370 / Label seq-ID: 11 - 370

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein FIC DOMAIN CONTAINING TRANSCRIPTIONAL REGULATOR


Mass: 42650.926 Da / Num. of mol.: 2 / Mutation: G109C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: NP_719793.1, SO_4266 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8E9K5
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS A CYSTEINE AT POSITION 109 INSTEAD OF A GLYCINE. THE CYSTEINE AT POSITION 109 IS SUPPORTED BY THE ELECTRON DENSITY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.2M NaF, 20.0% PEG-3350, No Buffer pH 7.1, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97905,0.97935
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979051
30.979351
ReflectionResolution: 1.6→29.553 Å / Num. obs: 106471 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.465 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.660.52423752521263198.7
1.66-1.720.4152.43314418630199.7
1.72-1.80.3273.13761121027199.6
1.8-1.90.2344.33891221626199.7
1.9-2.020.1586.33719520547199.5
2.02-2.170.1029.43593319785199.7
2.17-2.390.06613.93790820659199.3
2.39-2.730.043203747620049198.7
2.73-3.440.02629.63882620295197.7
3.44-29.5530.01548.83857219736194.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→29.553 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.098 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.083
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. MODELING EXPERIMENTS SUGGEST THAT THE ELECTRON DENSITY NEAR THE HPFXXGNG MOTIF (PRESENT IN FIC PROTEINS) STARTING AT HIS198 IN CHAIN A IS LIKELY TO BE A PORTION (B1-B4) OF THE PARTIALLY MISSING N-TERMINUS OF CHAIN B FROM A SYMMETRY RELATED MOLECULE. B1(MSE) IS SUPPORTED BY A SIGNIGICANT PEAK IN THE ANOMALOUS DIFFERENCE FOURIER MAP CALCULATED FOR THIS SELENOMETHIONINE DERIVATIZED PROTEIN CRYSTAL. 5. PGE HAS BEEN MODELED BASED ON CRYSTALLIZATION CONDITIONS. 6. RESIDUES A344-A345 IN CHAIN A AND B5-B10 ARE DISORDERED AND HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 5304 5 %RANDOM
Rwork0.168 ---
obs0.17 106418 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.52 Å2 / Biso mean: 23.39 Å2 / Biso min: 10.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---0.94 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5810 0 10 814 6634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226177
X-RAY DIFFRACTIONr_bond_other_d0.0010.024109
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.978474
X-RAY DIFFRACTIONr_angle_other_deg1.035310159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8895805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87824.982281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.687151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2611531
X-RAY DIFFRACTIONr_chiral_restr0.1080.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021164
X-RAY DIFFRACTIONr_nbd_refined0.2250.21450
X-RAY DIFFRACTIONr_nbd_other0.1890.24356
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23101
X-RAY DIFFRACTIONr_nbtor_other0.0880.22896
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2616
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.241
X-RAY DIFFRACTIONr_mcbond_it2.24634192
X-RAY DIFFRACTIONr_mcbond_other0.57531487
X-RAY DIFFRACTIONr_mcangle_it2.80356203
X-RAY DIFFRACTIONr_scbond_it4.88982612
X-RAY DIFFRACTIONr_scangle_it6.642112232
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4510 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.55
LOOSE THERMAL3.6510
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 400 -
Rwork0.224 7337 -
all-7737 -
obs--98.75 %
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)
10.69270.1875-0.1321.1745-0.19130.783-0.02970.0571-0.1512-0.08740.01580.00990.021-0.02120.0139-0.0709-0.00570.0038-0.0518-0.0147-0.01917.968311.8622-75.3204
20.32810.01310.060.91250.12580.8867-0.01910.0280.0557-0.0473-0.00480.00740.0004-0.06410.0238-0.06990.01170.0098-0.04970.0093-0.044718.191449.689-84.8692
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 370
2X-RAY DIFFRACTION2B11 - 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