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- PDB-1s66: Crystal structure of heme domain of direct oxygen sensor from E. coli -

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Basic information

Entry
Database: PDB / ID: 1s66
TitleCrystal structure of heme domain of direct oxygen sensor from E. coli
ComponentsHypothetical protein yddUHypothesis
KeywordsOXYGEN STORAGE/TRANSPORT / PAS / oxygen sensor / DOS / Heme protein / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / cyclic-guanylate-specific phosphodiesterase activity / response to oxygen levels / oxygen sensor activity / heme binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Diguanylate cyclase/phosphodiesterase / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain ...Diguanylate cyclase/phosphodiesterase / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Nucleotide cyclase / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Oxygen sensor protein DosP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsPark, H.J. / Suquet, C. / Satterlee, J.D. / Kang, C.H.
CitationJournal: Biochemistry / Year: 2004
Title: Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH)
Authors: Park, H.J. / Suquet, C. / Satterlee, J.D. / Kang, C.H.
History
DepositionJan 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
L: Hypothetical protein yddU
U: Hypothetical protein yddU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4145
Polymers27,1492
Non-polymers1,2653
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-58 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.189, 68.310, 82.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein yddU / Hypothesis


Mass: 13574.491 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YDDU, B1489 / Production host: Escherichia coli (E. coli) / References: UniProt: P76129
#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: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG, Na Tartarate, Na acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.738,1.741,1.033
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2001
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7381
21.7411
31.0331
ReflectionResolution: 1.8→50 Å / Num. all: 23838 / Num. obs: 23111 / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.055

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Processing

Software
NameClassification
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1116 5 %random
Rwork0.189 ---
all0.247 23838 --
obs0.234 21995 --
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 88 164 2132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_angle_deg1.69

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