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- PDB-6hq3: Structure of EAL Enzyme Bd1971 - halfsite-occupied form -

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Basic information

Entry
Database: PDB / ID: 6hq3
TitleStructure of EAL Enzyme Bd1971 - halfsite-occupied 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
: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / 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
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Signal transduction protein
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: EAL Enzyme Bd1971
B: EAL Enzyme Bd1971
C: EAL Enzyme Bd1971
D: EAL Enzyme Bd1971
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7536
Polymers50,0944
Non-polymers6582
Water00
1
A: EAL Enzyme Bd1971
D: EAL Enzyme Bd1971
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3763
Polymers25,0472
Non-polymers3291
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-25 kcal/mol
Surface area12050 Å2
MethodPISA
2
B: EAL Enzyme Bd1971
C: EAL Enzyme Bd1971
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3763
Polymers25,0472
Non-polymers3291
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-25 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.580, 120.750, 56.300
Angle α, β, γ (deg.)90.000, 116.800, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGAA5 - 1102 - 107
21ALAALAARGARGBB5 - 1102 - 107
12GLNGLNASNASNAA6 - 1133 - 110
22GLNGLNASNASNCC6 - 1133 - 110
13ALAALAARGARGAA5 - 1102 - 107
23ALAALAARGARGDD5 - 1102 - 107
14GLNGLNARGARGBB6 - 1103 - 107
24GLNGLNARGARGCC6 - 1103 - 107
15ALAALAARGARGBB5 - 1112 - 108
25ALAALAARGARGDD5 - 1112 - 108
16GLNGLNARGARGCC6 - 1103 - 107
26GLNGLNARGARGDD6 - 1103 - 107

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
EAL Enzyme Bd1971


Mass: 12523.563 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: Bd1971 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MLN6
#2: 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

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.2M K Nitrate pH 6.9 2.5mM cAMP 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→36.33 Å / Num. obs: 13884 / % possible obs: 98.5 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.058 / Rrim(I) all: 0.105 / Net I/σ(I): 8.3 / Num. measured all: 44245
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.79-2.862.70.90110310.5180.6741.13199.3
12.48-36.333.10.0361590.9980.0250.04494.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.11data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: full length protein

Resolution: 2.79→36.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 42.322 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.379
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 665 4.8 %RANDOM
Rwork0.2122 ---
obs0.2143 13219 98.5 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 166.54 Å2 / Biso mean: 103.471 Å2 / Biso min: 77.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å2-0 Å22.15 Å2
2---2.6 Å20 Å2
3----1.42 Å2
Refinement stepCycle: final / Resolution: 2.79→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 44 0 3478
Biso mean--92.45 --
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193504
X-RAY DIFFRACTIONr_bond_other_d0.0020.023612
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.0074716
X-RAY DIFFRACTIONr_angle_other_deg1.01538274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67524.177158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94915710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8731536
X-RAY DIFFRACTIONr_chiral_restr0.10.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61040.13
12B61040.13
21A64200.11
22C64200.11
31A60600.13
32D60600.13
41B60960.13
42C60960.13
51B63760.1
52D63760.1
61C61180.13
62D61180.13
LS refinement shellResolution: 2.79→2.862 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 57 -
Rwork0.379 973 -
all-1030 -
obs--99.04 %
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)
12.0756-0.433-0.02986.54681.76092.7969-0.1541-0.3549-0.01330.38850.19040.56610.2051-0.1413-0.03630.4453-0.03940.14720.12920.03570.1205-36.352-14.78213.442
25.21281.8001-0.24743.92450.5231.7421-0.1427-0.14330.2096-0.05780.19960.13350.2250.0175-0.05690.54690.01970.13750.02440.00630.0563-15.092.8043.704
32.50730.6143-0.22346.80051.1622.6252-0.07280.52910.1366-0.97640.0465-0.1369-0.0625-0.01560.02620.7558-0.11740.14740.23340.01950.0401-22.99-16.401-12.851
43.6998-1.75850.98383.1194-1.03983.1526-0.2507-0.0678-0.04640.1130.3559-0.40930.21690.2313-0.10520.714-0.02940.13010.0935-0.09880.1884-17.964-33.22110.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 114
2X-RAY DIFFRACTION2B5 - 111
3X-RAY DIFFRACTION3C6 - 114
4X-RAY DIFFRACTION4D5 - 111

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