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- PDB-6hq5: Structure of EAL Enzyme Bd1971 - cAMP and cyclic-di-GMP bound form -

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Basic information

Entry
Database: PDB / ID: 6hq5
TitleStructure of EAL Enzyme Bd1971 - cAMP and cyclic-di-GMP bound form
ComponentsEAL Enzyme Bd1971
KeywordsSIGNALING PROTEIN / EAL / cyclic-di-GMP / cAMP / Bdellovibrio
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Signal transduction protein
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsLovering, A.L. / Cadby, I.T.
CitationJournal: Embo J. / Year: 2019
Title: Nucleotide signaling pathway convergence in a cAMP-sensing bacterial c-di-GMP phosphodiesterase.
Authors: Cadby, I.T. / Basford, S.M. / Nottingham, R. / Meek, R. / Lowry, R. / Lambert, C. / Tridgett, M. / Till, R. / Ahmad, R. / Fung, R. / Hobley, L. / Hughes, W.S. / Moynihan, P.J. / Sockett, R.E. / Lovering, A.L.
History
DepositionSep 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_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: EAL Enzyme Bd1971
B: EAL Enzyme Bd1971
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,95910
Polymers89,7592
Non-polymers2,2008
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-81 kcal/mol
Surface area33910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.857, 83.857, 138.454
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 6 - 401 / Label seq-ID: 2 - 397

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein EAL Enzyme Bd1971


Mass: 44879.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Gene: Bd1971 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MLN6
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2mM cAMP 10mM CaCl2 0.1M MES pH 6.5 0.2M Na Acetate 15% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.83→64.31 Å / Num. obs: 25916 / % possible obs: 99.7 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.037 / Rrim(I) all: 0.074 / Net I/σ(I): 9.3 / Num. measured all: 103343 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Redundancy: 4 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.83-3.060.53853760.7770.3060.6299.6
7.49-64.310.03614000.9970.0210.04299.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.1data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: used full length model

Resolution: 2.83→64.31 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 41.72 / SU ML: 0.382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 6.603 / ESU R Free: 0.386
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1181 4.6 %RANDOM
Rwork0.2227 ---
obs0.2248 24618 99.24 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 180.41 Å2 / Biso mean: 103.979 Å2 / Biso min: 59.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.78 Å20 Å2
2--1.55 Å20 Å2
3----5.04 Å2
Refinement stepCycle: final / Resolution: 2.83→64.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5998 0 140 2 6140
Biso mean--80.85 68.82 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196258
X-RAY DIFFRACTIONr_bond_other_d0.0030.026137
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9998429
X-RAY DIFFRACTIONr_angle_other_deg0.9523.00814097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.085748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90724.792288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.134151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7191540
X-RAY DIFFRACTIONr_chiral_restr0.0630.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026896
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021394
Refine LS restraints NCS

Ens-ID: 1 / Number: 20626 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.83→2.903 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 77 -
Rwork0.415 1830 -
all-1907 -
obs--97.25 %
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)
10.5612-0.3486-0.16932.0017-1.44171.43970.1458-0.14890.07620.1560.21060.23-0.2203-0.0399-0.35640.1085-0.0250.030.1776-0.02520.6158100.685-5.117-18.952
23.4219-0.9975-0.24440.5162-0.0290.1558-0.04930.1395-0.41590.0937-0.0339-0.06550.01290.07570.08320.09320.05380.00510.23830.05090.555683.996-16.809-15.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 402
2X-RAY DIFFRACTION2B6 - 401

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