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- PDB-1ft9: STRUCTURE OF THE REDUCED (FEII) CO-SENSING PROTEIN FROM R. RUBRUM -

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Basic information

Entry
Database: PDB / ID: 1ft9
TitleSTRUCTURE OF THE REDUCED (FEII) CO-SENSING PROTEIN FROM R. RUBRUM
ComponentsCARBON MONOXIDE OXIDATION SYSTEM TRANSCRIPTION REGULATOR
KeywordsTRANSCRIPTION / carbon monoxide / heme sensor / catabolite gene activator protein
Function / homology
Function and homology information


DNA-templated transcription / 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-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 ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / 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 / CooA protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsLanzilotta, W.N. / Schuller, D.J. / Poulos, T.L. / Thorsteinsson, M.V. / Kirby, B. / Roberts, G.P.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the CO sensing transcription activator CooA.
Authors: Lanzilotta, W.N. / Schuller, D.J. / Thorsteinsson, M.V. / Kerby, R.L. / Roberts, G.P. / Poulos, T.L.
History
DepositionSep 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBON MONOXIDE OXIDATION SYSTEM TRANSCRIPTION REGULATOR
B: CARBON MONOXIDE OXIDATION SYSTEM TRANSCRIPTION REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5614
Polymers49,3282
Non-polymers1,2332
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-71 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.253, 92.253, 143.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: Protein CARBON MONOXIDE OXIDATION SYSTEM TRANSCRIPTION REGULATOR / COOA GENE PRODUCT


Mass: 24663.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P72322
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 292 K / Method: liquid diffusion / pH: 8.5
Details: 0.3 M MgCl2, 0.1 M Tris, 20% PEG 8000, pH 8.5, LIQUID DIFFUSION, temperature 292K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
20.1 MTris-HCl11
30.6 M11MgCl2
420 %(v/v)PEG800011
520 %(v/v)glycerol11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL1-511.74
SYNCHROTRONSSRL BL7-121.02
Detector
TypeIDDetectorDate
ADSC1CCDMay 17, 1999
OTHER2IMAGE PLATESep 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.741
21.021
ReflectionResolution: 2.5→50 Å / Num. all: 22102 / Num. obs: 21881 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.8 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / % possible all: 99.1
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→50 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 985 5.1 %Random
Rwork0.23 ---
all0.25 19517 --
obs0.25 19459 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 86 199 3520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.26

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