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- PDB-4uii: Crystal structure of the Azotobacter vinelandii globin-coupled ox... -

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Basic information

Entry
Database: PDB / ID: 4uii
TitleCrystal structure of the Azotobacter vinelandii globin-coupled oxygen sensor in the aquo-met form
ComponentsGGDEF DOMAIN PROTEIN
KeywordsTRANSFERASE / GLOBIN-COUPLED SENSOR / HEME-BASED SENSOR / OXYGEN AFFINITY / DIGUANYLATE CYCLASE / C-DI-GMP / MODERATE ENZYME EFFICIENCY / SENSOR CRYSTAL STRUCTURE
Function / homology
Function and homology information


diguanylate cyclase / diguanylate cyclase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Diguanylate cyclase DosC, globin sensor domain / Protoglobin / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Globin/Protoglobin / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Diguanylate cyclase DosC
Similarity search - Component
Biological speciesAZOTOBACTER VINELANDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.827 Å
AuthorsGermani, F. / De Schutter, A. / Pesce, A. / Berghmans, H. / Van Hauwaert, M.-L. / Cuypers, B. / Bruno, S. / Mozzarelli, A. / Moens, L. / Van Doorslaer, S. ...Germani, F. / De Schutter, A. / Pesce, A. / Berghmans, H. / Van Hauwaert, M.-L. / Cuypers, B. / Bruno, S. / Mozzarelli, A. / Moens, L. / Van Doorslaer, S. / Bolognesi, M. / Nardini, M. / Dewilde, S.
CitationJournal: To be Published
Title: Azotobacter Vinelandii Globin-Coupled Oxygen Sensor is a Diguanylate Cyclase with a Biphasic Oxygen Dissociation
Authors: Germani, F. / De Schutter, A. / Pesce, A. / Berghmans, H. / Van Hauwaert, M.-L. / Cuypers, B. / Bruno, S. / Mozzarelli, A. / Moens, L. / Van Doorslaer, S. / Bolognesi, M. / Nardini, M. / Dewilde, S.
History
DepositionMar 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
A: GGDEF DOMAIN PROTEIN
B: GGDEF DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9114
Polymers49,6782
Non-polymers1,2332
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-32 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.890, 49.490, 62.770
Angle α, β, γ (deg.)90.00, 91.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GGDEF DOMAIN PROTEIN / GLOBIN-COUPLED SENSOR WITH DIGUANYLATE CYCLASE ACTIVITY


Mass: 24839.133 Da / Num. of mol.: 2 / Fragment: GLOBIN DOMAIN, RESIDUES 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: M9YE33, diguanylate cyclase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GLOBIN DOMAIN CORRESPONDS TO RESIDUES 1-170 OF THE WHOLE MOLECULE. HIS TAG AND RESIDUES FROM ...THE GLOBIN DOMAIN CORRESPONDS TO RESIDUES 1-170 OF THE WHOLE MOLECULE. HIS TAG AND RESIDUES FROM THE PLASMID ARE ALSO PRESENT AT THE N-TERMINAL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33 %
Crystal growDetails: 33% PEG 6000, 10 MM NA-CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.97906
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: BENDABLE FOCUSSING MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.83→30.5 Å / Num. obs: 6845 / % possible obs: 95.8 % / Observed criterion σ(I): 2.5 / Redundancy: 3.3 % / Biso Wilson estimate: 88.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6
Reflection shellResolution: 2.83→2.98 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 2.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UIQ

4uiq


Resolution: 2.827→30.461 Å / SU ML: 0.45 / σ(F): 1.4 / Phase error: 37.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2967 313 4.6 %
Rwork0.2525 --
obs0.2545 6825 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.827→30.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 86 4 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112251
X-RAY DIFFRACTIONf_angle_d1.9713069
X-RAY DIFFRACTIONf_dihedral_angle_d20.782838
X-RAY DIFFRACTIONf_chiral_restr0.126326
X-RAY DIFFRACTIONf_plane_restr0.009386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.827-3.56090.39241580.33233X-RAY DIFFRACTION96
3.5609-30.46230.2691550.23983279X-RAY DIFFRACTION95

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