[English] 日本語
Yorodumi
- PDB-2f7b: CatM effector binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f7b
TitleCatM effector binding domain
ComponentsHTH-type transcriptional regulator catM
KeywordsGENE REGULATION / LTTR / lysR-type transcriptional regulator / inducer binding domain / effector binding domain
Function / homology
Function and homology information


aromatic compound catabolic process / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
LysR substrate binding domain / LysR, substrate-binding / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator CatM
Similarity search - Component
Biological speciesAcinetobacter baylyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsClark, T. / Haddad, S. / Ezezika, O. / Neidle, E. / Momany, C.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation by BenM, a LysR-type Regulator.
Authors: Ezezika, O.C. / Haddad, S. / Clark, T.J. / Neidle, E.L. / Momany, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of the effector-binding domains of BenM and CatM, LysR-type transcriptional regulators from Acinetobacter sp. ADP1.
Authors: Clark, T. / Haddad, S. / Neidle, E. / Momany, C.
History
DepositionNov 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6326
Polymers26,2131
Non-polymers4205
Water6,467359
1
A: HTH-type transcriptional regulator catM
hetero molecules

A: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,26512
Polymers52,4252
Non-polymers83910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+11
Buried area4170 Å2
ΔGint-134 kcal/mol
Surface area18790 Å2
MethodPISA
2
A: HTH-type transcriptional regulator catM
hetero molecules

A: HTH-type transcriptional regulator catM
hetero molecules

A: HTH-type transcriptional regulator catM
hetero molecules

A: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,52924
Polymers104,8514
Non-polymers1,67920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area11770 Å2
ΔGint-358 kcal/mol
Surface area34910 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)66.184, 75.529, 102.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1004-

SO4

DetailsThe biological unit (effector binding domain) is a dimer generated from the monomer in the asymmetric unit by the operation, 1-x, y, -z

-
Components

#1: Protein HTH-type transcriptional regulator catM / Cat operon transcriptional regulator


Mass: 26212.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Strain: ADP1 / Gene: catM, catR / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07774
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 288 K / Method: microbatch under oil
Details: PEG 4000, ammonium sulfate, sodium acetate, NaCl, tris, glycerol, imidazole, microbatch under oil, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.00727 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00727 Å / Relative weight: 1
ReflectionResolution: 1.8→60.746 Å / Num. all: 22581 / Num. obs: 22581 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 20.47029 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 29.7
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 88.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 7.5 / Num. measured obs: 2107 / Num. unique all: 2107 / Χ2: 1.44 / % possible all: 88.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2F6G
Resolution: 1.9→60.746 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.186 / SU B: 7.879 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: 14 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.159 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1007 5.186 %Random
Rwork0.1718 ---
all0.175 18410 --
obs0.175 18410 94.441 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.847 Å2
Baniso -1Baniso -2Baniso -3
1-0.296 Å20 Å20 Å2
2--0.682 Å20 Å2
3----0.978 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 21 359 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221754
X-RAY DIFFRACTIONr_bond_other_d0.0010.021781
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9942387
X-RAY DIFFRACTIONr_angle_other_deg0.7273.0014067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3915217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54324.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19115314
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg16.097153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.931158
X-RAY DIFFRACTIONr_chiral_restr0.0590.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined0.1830.2311
X-RAY DIFFRACTIONr_nbd_other0.1570.21862
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2801
X-RAY DIFFRACTIONr_nbtor_other0.0770.21074
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.227
X-RAY DIFFRACTIONr_mcbond_it0.77821403
X-RAY DIFFRACTIONr_mcbond_other0.0812432
X-RAY DIFFRACTIONr_mcangle_it1.1751755
X-RAY DIFFRACTIONr_mcangle_other0.49951468
X-RAY DIFFRACTIONr_scbond_it2.3627755
X-RAY DIFFRACTIONr_scbond_other0.7471538
X-RAY DIFFRACTIONr_scangle_it3.16110630
X-RAY DIFFRACTIONr_scangle_other1.312102599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.9-1.9490.278630.20913710.212147197.485
1.949-2.0030.233790.19213590.195147397.624
2.003-2.0610.254690.18613100.189141197.732
2.061-2.1240.293740.17812670.184137797.386
2.124-2.1940.496380.3545010.365134939.956
2.194-2.270.263570.17812140.182129997.844
2.27-2.3560.195600.1811630.181124997.918
2.356-2.4520.215700.17611390.178122898.453
2.452-2.5610.225500.17510930.177115798.79
2.561-2.6860.215660.16910210.172110298.639
2.686-2.8310.258500.1799960.182106098.679
2.831-3.0020.249530.1679570.171101899.214
3.002-3.2090.179520.1628690.16293298.82
3.209-3.4650.211490.1518420.15490099
3.465-3.7940.224490.1467640.1581999.267
3.794-4.240.257350.1397080.14474699.598
4.24-4.8920.204290.1296260.13265999.393
4.892-5.9820.214250.1675490.16957699.653
5.982-8.4190.206220.1894310.1945799.125
8.419-60.7460.318170.2472300.25127789.17
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.9727-0.4633-0.18633.07861.40612.868-0.06110.0458-0.0361-0.0047-0.00380.1243-0.1851-0.09890.065-0.04160.00310.0170.0340.0244-0.048450.79617.88355.696
27.21833.4069-2.065817.3811-4.47338.6557-0.42140.33470.3727-1.01850.4110.2282-0.23760.03040.0105-0.0773-0.0002-0.05960.20670.0190.075640.0917.19950.73
34.8257-0.2011-1.28021.46050.71961.9671-0.0287-0.01610.42740.06060.0315-0.0434-0.32420.002-0.00280.01190.01320.0073-0.03540.0225-0.015352.9627.64461.733
411.80364.43218.04175.5541.4578.6977-0.212-0.2231-0.030.37620.0608-0.2257-0.49740.26750.15120.02060.00830.04580.0204-0.0098-0.025650.89427.06572.291
516.9209-10.5499-6.72546.76834.81214.6831-0.3005-0.2932-0.10590.33190.2356-0.2159-0.28420.1250.06490.0023-0.00420.0360.01530.03450.010255.5713.48769.363
65.9591-1.2712-2.92614.97410.70563.80410.1611-0.1486-0.05470.06510.1045-0.48520.09820.294-0.2656-0.03550.0118-0.06740.0158-0.01770.001178.9377.77362.274
73.09212.82660.759514.75125.87542.9319-0.12130.0659-0.03090.07150.1679-0.3020.01540.3875-0.0466-0.0097-0.0081-0.06870.007-0.0122-0.02878.98.98271.497
817.0563-5.74031.50527.2752-1.76692.357-0.268-0.08770.01410.49520.0736-0.1626-0.39940.06730.19440.0091-0.0708-0.02810.00770.0003-0.080374.58223.06563.186
94.6898-1.99692.69581.0235-2.0726.4807-0.1678-0.29090.28010.19780.0181-0.0855-0.5668-0.02370.14970.0291-0.031-0.06170.0134-0.0460.022672.83722.84371.58
101.38950.38781.23995.2489-0.16641.15740.02040.0570.1087-0.1198-0.0458-0.0946-0.21010.07910.02540.0012-0.01770.00330.0514-0.0016-0.025374.15620.41156.481
116.52272.96292.20723.1940.58182.7306-0.09050.08640.1025-0.15270.14650.01350.13110.104-0.056-0.00760.00020.00110.02890.01710.003170.61912.89660.437
120.4466-0.0589-1.63971.06120.40628.6489-0.1062-0.0096-0.02170.1431-0.1361-0.00080.2055-0.28220.2422-0.0378-0.024-0.00130.0331-0.025-0.00171.7878.93464.237
132.1528-1.57421.82654.4081-0.02562.0766-0.1283-0.3363-0.17730.2095-0.06640.3179-0.159-0.30510.1947-0.05530.04430.07050.08490.0164-0.014744.19420.83764.908
146.2677-0.71684.86563.8434-1.5644.0470.0627-0.28170.19960.4102-0.02510.4071-0.1308-0.4761-0.0375-0.0193-0.00560.05860.02630.01560.048148.8386.23765.78
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1190 - 11210 - 32
22113 - 12033 - 40
33121 - 14841 - 68
44149 - 15669 - 76
55157 - 16377 - 83
66164 - 17584 - 95
77176 - 18896 - 108
88189 - 199109 - 119
99200 - 220120 - 140
1010221 - 237141 - 157
1111238 - 250158 - 170
1212251 - 266171 - 186
1313267 - 289187 - 209
1414290 - 303210 - 223

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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