[English] 日本語
Yorodumi
- PDB-3trb: Structure of an addiction module antidote protein of a HigA (higA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3trb
TitleStructure of an addiction module antidote protein of a HigA (higA) family from Coxiella burnetii
ComponentsVirulence-associated protein I
KeywordsDNA BINDING PROTEIN / Mobile and extrachromosomal element functions
Function / homology
Function and homology information


Toxin-antitoxin system, antidote protein, HigA / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Virulence-associated protein I
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Virulence-associated protein I
B: Virulence-associated protein I


Theoretical massNumber of molelcules
Total (without water)23,3502
Polymers23,3502
Non-polymers00
Water2,486138
1
A: Virulence-associated protein I
B: Virulence-associated protein I

A: Virulence-associated protein I
B: Virulence-associated protein I


Theoretical massNumber of molelcules
Total (without water)46,6994
Polymers46,6994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7930 Å2
ΔGint-46 kcal/mol
Surface area18770 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-17 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.669, 44.669, 221.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Virulence-associated protein I


Mass: 11674.853 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_1490, higA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83BL4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 7.5
Details: 0.2M calcium chloride 20% PEG 3350, pH 7.5, sitting drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 1, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 16259 / Num. obs: 15412 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.035 / Χ2: 1.022 / Net I/σ(I): 20.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.032.40.2097040.647188
2.03-2.073.10.1916920.678190.6
2.07-2.114.10.1667260.68190.3
2.11-2.154.10.1347080.698191.5
2.15-2.24.20.1297130.685192.8
2.2-2.254.10.1067470.708192.6
2.25-2.314.10.0977210.732192.1
2.31-2.374.10.0877530.732193.9
2.37-2.444.10.0747520.765194.5
2.44-2.524.10.0637540.789195
2.52-2.614.20.0597600.833195.5
2.61-2.714.10.0497590.818195.2
2.71-2.844.20.0427730.828195.8
2.84-2.994.20.0417950.93196.5
2.99-3.174.40.0388081.198199.8
3.17-3.424.70.0338151.254199.8
3.42-3.764.70.038201.311199.4
3.76-4.3150.0278301.353198.9
4.31-5.436.30.0278621.309198.6
5.43-508.40.0319201.535194.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CEC

3cec


Resolution: 2.001→34.777 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8664 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 778 5.06 %RANDOM
Rwork0.199 ---
all0.2011 16984 --
obs0.2011 15371 95.08 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.4 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 111.34 Å2 / Biso mean: 34.1258 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.6931 Å20 Å2-0 Å2
2--2.6931 Å2-0 Å2
3----5.3862 Å2
Refinement stepCycle: LAST / Resolution: 2.001→34.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 138 1582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021502
X-RAY DIFFRACTIONf_angle_d0.52032
X-RAY DIFFRACTIONf_chiral_restr0.032232
X-RAY DIFFRACTIONf_plane_restr0.002259
X-RAY DIFFRACTIONf_dihedral_angle_d10.797572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0009-2.12620.28231350.22032238237390
2.1262-2.29030.22681250.19392257238292
2.2903-2.52080.20761230.20282390251394
2.5208-2.88540.29111250.20092415254096
2.8854-3.63470.23341440.20832540268499
3.6347-34.78230.24011260.18952753287998
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)
11.60870.5742-0.86660.2834-0.27961.87390.5930.20090.9775-0.0403-0.50590.1015-0.70310.3615-0.05210.28360.00790.0420.21980.03650.460521.233729.162323.0414
21.0074-0.0581-0.20440.9220.19630.1280.0095-0.17420.05890.0920.07530.0473-0.9495-0.217-0.05990.41340.05470.03630.2747-0.01440.1859.288229.743528.2145
30.6892-0.01850.10150.42550.17950.33990.1258-0.33010.14430.7401-0.68581.11350.1064-0.85110.11510.39660.07390.12490.2993-0.11160.26031.309924.393334.1222
43.39750.1517-1.31921.5482-1.7173.0638-0.0936-0.4114-0.75890.5742-0.1351-0.1396-0.06480.36770.18640.36810.04510.07630.21920.01120.22918.638416.76132.6318
51.5524-0.0433-0.38460.2451-0.04760.1046-0.2623-0.0089-0.09950.16840.17710.1125-0.42390.7650.19680.33620.0111-0.04130.3477-0.00380.183714.946416.766527.8292
60.7858-0.2029-0.01241.1121-0.8091.0813-0.0042-0.0002-0.03190.1913-0.0232-0.1522-0.1362-0.154-0.00270.22770.02140.04620.2262-0.04950.22882.203120.132421.7177
71.26130.008-0.57640.47370.22230.6468-0.23660.3580.4845-0.11590.2513-0.1322-0.21280.2775-0.12750.2005-0.06830.06090.3291-0.06340.218324.358520.606714.3558
80.18150.27390.63672.2719-0.60493.5939-0.1175-0.0110.0583-0.015-0.05370.35310.2635-0.63760.19190.2147-0.0253-0.00150.2535-0.04010.292715.86578.76820.1256
91.6353-0.00681.81345.12940.11222.24420.31920.3495-0.4361-0.71140.32790.2960.90041.1226-0.6540.50130.0219-0.04880.487-0.01620.348728.29485.6951-6.1412
101.6174-0.2207-0.80110.52830.75351.12790.3397-0.2994-0.15090.1943-0.2079-0.07130.71110.4711-0.04590.29590.1120.01940.29140.01040.280428.6825.09296.3522
112.27720.0490.13153.32840.97441.54610.2239-0.21950.24080.1255-0.51340.4310.44530.00930.2850.2726-0.03410.02970.23820.01630.213919.12846.278811.5224
120.3556-0.0791-0.14910.13960.49091.49190.0387-0.03660.4482-0.0093-0.0849-0.41450.12340.0094-0.00420.15750.03730.01310.20660.04470.198326.255316.91546.1427
131.0078-0.5190.02640.5556-0.50040.6146-0.12490.2205-0.2055-0.167-0.11560.15720.2386-0.23330.19450.2199-0.03990.04780.1986-0.08330.23726.593112.799113.8833
140.8444-0.0937-0.78710.00660.0810.7156-0.4194-0.24560.50970.1238-0.43160.091-0.5292-0.3958-0.188-0.77550.99810.4798-0.2602-0.36390.5978-5.435524.426526.2719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:10)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 11:21)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 22:34)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 35:45)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 46:52)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 53:66)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 67:97)A0
8X-RAY DIFFRACTION8chain 'B' and (resseq 7:21)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 22:26)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 27:45)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 46:52)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 53:66)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 67:93)B0
14X-RAY DIFFRACTION14chain 'B' and (resseq 94:98)B0

+
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