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- PDB-1v9z: Crystal Structure of the heme PAS sensor domain of Ec DOS (Ferrou... -

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Basic information

Entry
Database: PDB / ID: 1v9z
TitleCrystal Structure of the heme PAS sensor domain of Ec DOS (Ferrous Form)
ComponentsHeme pas sensor protein
KeywordsSIGNALING PROTEIN / HEME / PAS / SENSOR
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 sensor protein DosP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKurokawa, H. / Lee, D.S. / Watanabe, M. / Sagami, I. / Mikami, B. / Raman, C.S. / Shimizu, T.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor.
Authors: Kurokawa, H. / Lee, D.S. / Watanabe, M. / Sagami, I. / Mikami, B. / Raman, C.S. / Shimizu, T.
History
DepositionFeb 4, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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_ref_seq_dif.details / _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: Heme pas sensor protein
B: Heme pas sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2804
Polymers38,0472
Non-polymers1,2332
Water3,531196
1
A: Heme pas sensor protein
B: Heme pas sensor protein
hetero molecules

A: Heme pas sensor protein
B: Heme pas sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5618
Polymers76,0954
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)46.400, 69.180, 82.450
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 Heme pas sensor protein


Mass: 19023.660 Da / Num. of mol.: 2 / Fragment: heme pas domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: DOS / Plasmid: pET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 16129448, UniProt: P76129*PLUS
#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.: 196 / 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: 2.24 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→46.6 Å / Num. obs: 19009 / % possible obs: 89.3 %
Reflection shellResolution: 1.9→2 Å / % possible all: 88.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→14.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 120007.4 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1751 9.9 %RANDOM
Rwork0.244 ---
obs-17698 82.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.1259 Å2 / ksol: 0.402096 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→14.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 86 196 2114
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.941.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it3.72
X-RAY DIFFRACTIONc_scangle_it3.982.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 237 9.1 %
Rwork0.309 2360 -
obs--73.4 %

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