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- PDB-6hc0: Bdellovibrio bacteriovorus DgcB FHA domain, tail complex -

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Basic information

Entry
Database: PDB / ID: 6hc0
TitleBdellovibrio bacteriovorus DgcB FHA domain, tail complex
Components
  • DgcB N-terminus
  • GGDEF domain protein
KeywordsSIGNALING PROTEIN / GGDEF / FHA / c-di-GMP / diguanylate cyclase
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / nucleotide binding / plasma membrane
Similarity search - Function
: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Nucleotide cyclase ...: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Nucleotide cyclase / SMAD/FHA domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
FORMIC ACID / diguanylate cyclase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
Bdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsLovering, A.L. / Meek, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for activation of a diguanylate cyclase required for bacterial predation in Bdellovibrio.
Authors: Meek, R.W. / Cadby, I.T. / Moynihan, P.J. / Lovering, A.L.
History
DepositionAug 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DgcB N-terminus
B: GGDEF domain protein
C: GGDEF domain protein
D: GGDEF domain protein
E: GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4596
Polymers45,4135
Non-polymers461
Water5,116284
1
A: DgcB N-terminus


  • defined by author&software
  • Evidence: gel filtration
  • 706 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7061
Polymers7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GGDEF domain protein


Theoretical massNumber of molelcules
Total (without water)11,1771
Polymers11,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2232
Polymers11,1771
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GGDEF domain protein


Theoretical massNumber of molelcules
Total (without water)11,1771
Polymers11,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: GGDEF domain protein


Theoretical massNumber of molelcules
Total (without water)11,1771
Polymers11,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.350, 69.370, 128.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22D
13B
23E
14C
24D
15C
25E
16D
26E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYBB32 - 1331 - 102
21GLYGLYCC32 - 1331 - 102
12LYSLYSBB32 - 1321 - 101
22LYSLYSDD32 - 1321 - 101
13GLYGLYBB32 - 1331 - 102
23GLYGLYEE32 - 1331 - 102
14LYSLYSCC32 - 1321 - 101
24LYSLYSDD32 - 1321 - 101
15SERSERCC32 - 1341 - 103
25SERSEREE32 - 1341 - 103
16LYSLYSDD32 - 1321 - 101
26LYSLYSEE32 - 1321 - 101

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein/peptide DgcB N-terminus


Mass: 705.821 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd0742 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6MPU8*PLUS
#2: Protein
GGDEF domain protein


Mass: 11176.827 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Gene: Bd0742 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6MPU8
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 3.41 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2M ammonium formate, 10% polyvinylpyrrolidone, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→64.46 Å / Num. obs: 52209 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.023 / Rrim(I) all: 0.085 / Net I/σ(I): 19.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.87-1.9212.61.92237870.6170.5582.003100
8.36-36.5310.80.0336820.9990.010.03599.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.29data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→64.46 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.047 / SU ML: 0.087 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.103
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 2569 4.9 %RANDOM
Rwork0.1766 ---
obs0.178 49572 99.96 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 114.65 Å2 / Biso mean: 42.449 Å2 / Biso min: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.87→64.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 3 284 3422
Biso mean--37.92 48.01 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193205
X-RAY DIFFRACTIONr_bond_other_d0.0020.023137
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9854358
X-RAY DIFFRACTIONr_angle_other_deg0.98337325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6995421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6125.963109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99315557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.717158
X-RAY DIFFRACTIONr_chiral_restr0.110.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B59780.1
12C59780.1
21B59320.11
22D59320.11
31B60720.09
32E60720.09
41C59600.09
42D59600.09
51C59460.09
52E59460.09
61D57980.11
62E57980.11
LS refinement shellResolution: 1.87→1.919 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 182 -
Rwork0.283 3599 -
all-3781 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71971.5065-3.41925.2985-2.899539.18230.013-0.03670.18310.0842-0.28730.0694-0.8744-0.15910.27420.15470.0022-0.07410.2003-0.02170.3474-23.64126.5481.032
22.92750.64781.09633.77610.81783.6870.05760.2654-0.1839-0.1538-0.0534-0.16750.17810.2585-0.00410.04720.0378-0.01420.0492-0.0270.0618-17.8237.086-17.106
32.0978-1.3834-0.19423.7320.35474.11170.0207-0.08610.0029-0.1295-0.0110.1983-0.0484-0.2029-0.00970.08910.0002-0.03560.0161-0.00440.0332-38.79217.391-33.598
44.1051-1.751-1.88183.96640.69033.28870.0084-0.2119-0.22-0.10020.08810.02950.0090.2624-0.09660.025-0.00360.00840.0237-0.00060.0431-37.27114.4680.964
52.1010.6673-0.36484.8839-0.94015.5344-0.1191-0.06840.01990.4018-0.0450.3916-0.3018-0.1920.16410.22290.06740.05770.04140.02190.0915-43.63136.951-15.173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13
2X-RAY DIFFRACTION2B32 - 136
3X-RAY DIFFRACTION3C32 - 134
4X-RAY DIFFRACTION4D32 - 133
5X-RAY DIFFRACTION5E32 - 134

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