[English] 日本語
Yorodumi
- PDB-2fmy: CO-dependent transcription factor CooA from Carboxydothermus hydr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fmy
TitleCO-dependent transcription factor CooA from Carboxydothermus hydrogenoformans (Imidazole-bound form)
Componentscarbon monoxide oxidation system transcription regulator CooA-1
KeywordsDNA BINDING PROTEIN / DNA transcription regulator
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / : / Carbon monoxide oxidation system transcription regulator CooA-1
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsHiguchi, Y. / Komori, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of CO-sensing Transcription Activator CooA Bound to Exogenous Ligand Imidazole
Authors: Komori, H. / Inagaki, S. / Yoshioka, S. / Aono, S. / Higuchi, Y.
History
DepositionJan 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: carbon monoxide oxidation system transcription regulator CooA-1
B: carbon monoxide oxidation system transcription regulator CooA-1
C: carbon monoxide oxidation system transcription regulator CooA-1
D: carbon monoxide oxidation system transcription regulator CooA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,10712
Polymers100,3654
Non-polymers2,7428
Water4,576254
1
A: carbon monoxide oxidation system transcription regulator CooA-1
B: carbon monoxide oxidation system transcription regulator CooA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5546
Polymers50,1822
Non-polymers1,3714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-65 kcal/mol
Surface area20920 Å2
MethodPISA
2
C: carbon monoxide oxidation system transcription regulator CooA-1
D: carbon monoxide oxidation system transcription regulator CooA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5546
Polymers50,1822
Non-polymers1,3714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-63 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.654, 93.930, 91.901
Angle α, β, γ (deg.)90.00, 104.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
carbon monoxide oxidation system transcription regulator CooA-1 / CooA


Mass: 25091.197 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 77996136, UniProt: Q3AB29*PLUS
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 280 K / Method: vapor diffusion / pH: 6
Details: 100mM Bis-Tris buffer, 30% polyethyleneglycol 3000, 5% Dioxane, 4.5% Glycerol, pH 6.0, VAPOR DIFFUSION, temperature 280K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→32.365 Å / Num. all: 51329 / Num. obs: 51245 / Observed criterion σ(I): 1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→32.33 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.805 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24732 2563 5 %RANDOM
Rwork0.2072 ---
obs0.2092 48681 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.895 Å2
Baniso -1Baniso -2Baniso -3
1--2.96 Å20 Å21.89 Å2
2---1.61 Å20 Å2
3---5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7000 0 192 254 7446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1492.0649904
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1265868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00324.375320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.907151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4491552
X-RAY DIFFRACTIONr_chiral_restr0.070.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025312
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.23073
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.25025
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2312
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4541.54505
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74627020
X-RAY DIFFRACTIONr_scbond_it1.11333168
X-RAY DIFFRACTIONr_scangle_it1.7734.52876
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 189 -
Rwork0.227 3470 -
obs--100 %
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)
14.2045-1.89460.83872.4-1.22211.9696-0.1209-0.23110.05050.26140.10720.0228-0.0723-0.13030.0137-0.1505-0.01910.027-0.17440.0132-0.1584.155137.18353.0671
24.96721.0221-2.21735.3693-2.42464.07050.02520.13320.56080.01470.0485-0.0665-0.191-0.0466-0.0737-0.20660.0204-0.0172-0.1480.0007-0.0744-27.696940.729646.365
32.9121-0.7601-0.48823.32971.67463.85760.0810.5886-0.3749-0.2041-0.048-0.08790.44590.1901-0.033-0.0618-0.0149-0.02760.0352-0.0041-0.1127-1.498632.138630.9142
47.01231.5564-1.26036.0568-0.57512.2742-0.16490.4595-0.6367-0.60790.21070.21080.2281-0.1407-0.0458-0.0789-0.0195-0.0493-0.1551-0.0151-0.11115.777362.303133.7001
56.2574-3.1881.61152.5959-1.46881.7888-0.3084-0.7897-0.55290.31950.42850.2707-0.0273-0.2386-0.1201-0.12960.01250.0481-0.05020.115-0.0392-7.25732.887996.3359
66.37931.2721-2.6565.5524-2.63184.9548-0.0730.18290.5007-0.00990.13250.1025-0.2086-0.1679-0.0594-0.17760.0115-0.0717-0.15560.0103-0.1544-38.959335.933889.6472
73.2694-1.2327-0.11015.22641.88513.10440.06560.5611-0.7244-0.32730.0875-0.15820.37560.0706-0.1531-0.0122-0.07420.01030.0007-0.07470.0807-12.714926.527974.6281
85.43520.458-0.75128.86840.78612.9527-0.28260.4989-0.5185-0.66280.2739-0.08260.1109-0.10330.0087-0.0847-0.0760.0107-0.1361-0.0595-0.1132-6.202358.391677.0165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1371 - 136
2X-RAY DIFFRACTION2AA138 - 219137 - 218
3X-RAY DIFFRACTION3BB1002 - 11371 - 136
4X-RAY DIFFRACTION4BB1138 - 1219137 - 218
5X-RAY DIFFRACTION5CC2002 - 21371 - 136
6X-RAY DIFFRACTION6CC2138 - 2219137 - 218
7X-RAY DIFFRACTION7DD3002 - 31371 - 136
8X-RAY DIFFRACTION8DD3138 - 3219137 - 218
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3hem.paramhem.top

+
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://pdbjlvh1.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