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- PDB-4zvf: Crystal structure of GGDEF domain of the E. coli DosC - form II (... -

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Basic information

Entry
Database: PDB / ID: 4zvf
TitleCrystal structure of GGDEF domain of the E. coli DosC - form II (GTP-alpha-S-bound)
ComponentsDiguanylate cyclase DosC
KeywordsSIGNALING PROTEIN / oxygen sensing / diguanylate cyclase / cyclic-di-GMP
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / carbon monoxide binding / response to oxygen levels / cell adhesion involved in single-species biofilm formation / response to stress / oxygen binding / heme binding / GTP binding ...negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / carbon monoxide binding / response to oxygen levels / cell adhesion involved in single-species biofilm formation / response to stress / oxygen binding / heme binding / GTP binding / protein homodimerization activity / 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 / Reverse transcriptase/Diguanylate cyclase domain / Globin/Protoglobin / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE / Diguanylate cyclase DosC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsTarnawski, M. / Barends, T.R.M. / Schlichting, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural analysis of an oxygen-regulated diguanylate cyclase.
Authors: Tarnawski, M. / Barends, T.R. / Schlichting, I.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diguanylate cyclase DosC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6446
Polymers19,9011
Non-polymers7445
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-19 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.500, 52.530, 50.930
Angle α, β, γ (deg.)90.00, 106.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Diguanylate cyclase DosC / DGC / Direct oxygen-sensing cyclase


Mass: 19900.594 Da / Num. of mol.: 1 / Fragment: UNP residues 297-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dosC, yddV, b1490, JW5241 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA89, diguanylate cyclase
#2: Chemical ChemComp-GAV / GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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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: 33.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M imidazole pH 8.0, 0.2M calcium acetate, 22% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97627 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 48048 / % possible obs: 93.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.07
Reflection shellResolution: 1.15→1.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.14 / % possible all: 72.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZVE

4zve


Resolution: 1.15→35.806 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1648 2403 5 %
Rwork0.138 --
obs0.1393 48043 93.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→35.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 42 172 1540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061449
X-RAY DIFFRACTIONf_angle_d1.1771978
X-RAY DIFFRACTIONf_dihedral_angle_d12.589554
X-RAY DIFFRACTIONf_chiral_restr0.073226
X-RAY DIFFRACTIONf_plane_restr0.004249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1501-1.17350.30631030.22881945X-RAY DIFFRACTION68
1.1735-1.1990.28991160.21592215X-RAY DIFFRACTION77
1.199-1.22690.22391290.19732452X-RAY DIFFRACTION86
1.2269-1.25760.22351390.17492629X-RAY DIFFRACTION93
1.2576-1.29160.23711420.1592704X-RAY DIFFRACTION94
1.2916-1.32960.18241440.13682727X-RAY DIFFRACTION95
1.3296-1.37260.19891430.12662715X-RAY DIFFRACTION95
1.3726-1.42160.1481450.11052765X-RAY DIFFRACTION97
1.4216-1.47850.14721460.10782764X-RAY DIFFRACTION98
1.4785-1.54580.12751490.10152832X-RAY DIFFRACTION98
1.5458-1.62730.14381480.10042827X-RAY DIFFRACTION99
1.6273-1.72930.13791490.10392826X-RAY DIFFRACTION99
1.7293-1.86280.14771510.11982870X-RAY DIFFRACTION100
1.8628-2.05020.1381480.11952815X-RAY DIFFRACTION98
2.0502-2.34690.16051490.12692821X-RAY DIFFRACTION99
2.3469-2.95660.1621490.15122829X-RAY DIFFRACTION98
2.9566-35.82370.17131530.15332904X-RAY DIFFRACTION99

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