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- PDB-6i2z: Isolated globin domain of the Bordetella pertussis globin-coupled... -

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Basic information

Entry
Database: PDB / ID: 6i2z
TitleIsolated globin domain of the Bordetella pertussis globin-coupled sensor
ComponentsUncharacterized protein
KeywordsTRANSFERASE / heme-based sensor / oxygen affinity / c-di-GMP and enzyme specificity / biofilm formation.
Function / homology
Function and homology information


diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / oxygen binding / nucleotide binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Diguanylate cyclase DosC, globin sensor domain / : / DosC CZB-like middle domain / Globin-sensor domain / Protoglobin / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain ...Diguanylate cyclase DosC, globin sensor domain / : / DosC CZB-like middle domain / Globin-sensor domain / Protoglobin / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Diguanylate cyclase DosC
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGermani, F. / De Schutter, A. / Cuypers, B. / Berghmans, H. / Van Hauwaert, M.-L. / Bruno, S. / Mozzarelli, A. / Moens, L. / Van Doorslaer, S. / Bolognesi, M. ...Germani, F. / De Schutter, A. / Cuypers, B. / Berghmans, H. / Van Hauwaert, M.-L. / Bruno, S. / Mozzarelli, A. / Moens, L. / Van Doorslaer, S. / Bolognesi, M. / Pesce, A. / Dewilde, S.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - FlandersG.0247.09N Belgium
CitationJournal: Antioxid.Redox Signal. / Year: 2020
Title: Structural and Functional Characterization of the Globin-Coupled Sensors ofAzotobacter vinelandiiandBordetella pertussis.
Authors: Germani, F. / Nardini, M. / De Schutter, A. / Cuypers, B. / Berghmans, H. / Van Hauwaert, M.L. / Bruno, S. / Mozzarelli, A. / Moens, L. / Van Doorslaer, S. / Bolognesi, M. / Pesce, A. / Dewilde, S.
History
DepositionNov 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Sep 23, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1644
Polymers39,9312
Non-polymers1,2332
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-50 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.960, 86.720, 41.820
Angle α, β, γ (deg.)90.00, 93.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein


Mass: 19965.529 Da / Num. of mol.: 2 / Mutation: C16S, C45S, C114S, C154S
Source method: isolated from a genetically manipulated source
Details: HEM: PROTOPORPHYRIN IX CONTAINING FE HEME
Source: (gene. exp.) Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q7VTL8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M magnesium sulphate and 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→66.81 Å / Num. obs: 6186 / % possible obs: 99.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.246 / Net I/σ(I): 3.4
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Num. unique obs: 897 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uiq

4uiq


Resolution: 3.2→66.81 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.853 / SU B: 23.86 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23983 610 9.9 %RANDOM
Rwork0.20946 ---
obs0.21235 5575 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.077 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å2-1.76 Å2
2--0.29 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: 1 / Resolution: 3.2→66.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 86 30 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192549
X-RAY DIFFRACTIONr_bond_other_d0.0020.022306
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9813503
X-RAY DIFFRACTIONr_angle_other_deg2.08935290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27722.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98415381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3661519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022865
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02566
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1233.9161223
X-RAY DIFFRACTIONr_mcbond_other2.1233.9161222
X-RAY DIFFRACTIONr_mcangle_it3.6285.8621524
X-RAY DIFFRACTIONr_mcangle_other3.6275.8621525
X-RAY DIFFRACTIONr_scbond_it1.9964.2561326
X-RAY DIFFRACTIONr_scbond_other1.9964.2531324
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3976.3051978
X-RAY DIFFRACTIONr_long_range_B_refined6.79747.113030
X-RAY DIFFRACTIONr_long_range_B_other6.79647.1283031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 47 -
Rwork0.274 402 -
obs--99.34 %

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