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- PDB-6zxc: Diguanylate cyclase DgcR (I-site mutant) in activated state -

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Basic information

Entry
Database: PDB / ID: 6zxc
TitleDiguanylate cyclase DgcR (I-site mutant) in activated state
ComponentsPutative GGDEF/response regulator receiver domain protein
KeywordsSIGNALING PROTEIN / GGDEF domain / receiver domain / Rec / c-di-GMP / Leptospira / Beryllium Fluoride
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / phosphorelay signal transduction system / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE / Putative GGDEF/response regulator receiver domain protein
Similarity search - Component
Biological speciesLeptospira biflexa serovar Patoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTeixeira, R.D. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-166652 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase.
Authors: Teixeira, R.D. / Holzschuh, F. / Schirmer, T.
History
DepositionJul 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: 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 1.2Jan 31, 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: Putative GGDEF/response regulator receiver domain protein
B: Putative GGDEF/response regulator receiver domain protein
C: Putative GGDEF/response regulator receiver domain protein
D: Putative GGDEF/response regulator receiver domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,42420
Polymers144,1044
Non-polymers2,32016
Water59433
1
A: Putative GGDEF/response regulator receiver domain protein
B: Putative GGDEF/response regulator receiver domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,21210
Polymers72,0522
Non-polymers1,1608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-74 kcal/mol
Surface area28320 Å2
MethodPISA
2
C: Putative GGDEF/response regulator receiver domain protein
D: Putative GGDEF/response regulator receiver domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,21210
Polymers72,0522
Non-polymers1,1608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-78 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.812, 247.368, 41.539
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 6 - 298 / Label seq-ID: 26 - 318

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative GGDEF/response regulator receiver domain protein


Mass: 36025.973 Da / Num. of mol.: 4 / Mutation: R206A, D209A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris) (bacteria)
Strain: Patoc 1 / ATCC 23582 / Paris / Gene: LEPBI_p0053 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0SUI1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GH3 / 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE


Type: RNA linking / Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.06 M Divalents, 0.1M Buffer System 1 pH 6.5, 50%v/v Precipitant Mix 2 (Morpheus I A2). Divalents: 0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate. Buffer System 1: 1. ...Details: 0.06 M Divalents, 0.1M Buffer System 1 pH 6.5, 50%v/v Precipitant Mix 2 (Morpheus I A2). Divalents: 0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate. Buffer System 1: 1.0M Imidazole; MES monohydrate (acid), pH 6.5. Precipitant Mix 2: EDO_P8K, 40% v/v Ethylene glycol, 20 % w/v PEG 8000.

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.26 Å / Num. obs: 36666 / % possible obs: 95.6 % / Redundancy: 4.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.101 / Rrim(I) all: 0.177 / Net I/σ(I): 6.3
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.901 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 19016 / CC1/2: 0.513 / Rpim(I) all: 0.649 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZXB

6zxb


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 19.693 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28813 1599 4.9 %RANDOM
Rwork0.23658 ---
obs0.2282 35759 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.76 Å2 / Biso mean: 66.792 Å2 / Biso min: 25.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å2-0 Å2-0.43 Å2
2---3.1 Å2-0 Å2
3---1.5 Å2
Refinement stepCycle: final / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9360 0 136 33 9529
Biso mean--65.63 72.58 -
Num. residues----1172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139632
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179316
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.6613012
X-RAY DIFFRACTIONr_angle_other_deg1.2711.59221464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92751168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44222.266512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.721151816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9741572
X-RAY DIFFRACTIONr_chiral_restr0.1290.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022136
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89170.12
12B89170.12
21A87930.12
22C87930.12
31A87390.14
32D87390.14
41B87900.13
42C87900.13
51B86540.14
52D86540.14
61C86260.15
62D86260.15
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 111 -
Rwork0.297 2294 -
all-2405 -
obs--97.29 %
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)
11.6981-1.38950.597531.21453.78430.06440.18830.0741-0.2028-0.0869-0.0485-0.0590.09690.02260.1761-0.0171-0.01110.35120.01170.046842.124302.3145.743
21.578-0.5503-0.66514.3958-0.25722.99780.0593-0.1424-0.01090.2242-0.1041-0.13020.11780.15170.04480.2029-0.052-0.02610.3502-0.00650.008549.65282.98860.859
33.1404-1.3665-0.27824.6186-2.66384.9941-0.2896-0.09090.350.3205-0.1209-0.3072-0.7096-0.17550.41050.39590.0417-0.25880.3478-0.0640.286934.48220.87251.275
45.17930.9124-1.21234.97882.31155.7641-0.01840.13380.3203-0.36660.17080.2156-0.1595-0.3015-0.15240.3343-0.0109-0.1210.51240.07440.299810.088223.343.438
52.16341.59920.70372.81920.26253.17910.03220.2557-0.0174-0.16810.10490.1161-0.0409-0.1507-0.13710.14230.03140.09090.42830.01450.141677.808323.73748.531
64.08740.9025-1.46992.2539-0.36573.2392-0.011-0.5211-0.17610.0736-0.00590.15060.02460.00840.01690.19010.0009-0.01730.4135-0.00620.108487.151296.28566.006
71.45150.6693-0.09634.2283-2.19034.39160.2271-0.1592-0.12970.0253-0.0313-0.00440.55530.0556-0.19580.41630.0147-0.0520.3331-0.00890.088150.509253.96448.2
80.9876-0.23480.31073.09261.90833.30960.25530.08060.0195-0.9112-0.0074-0.07990.38880.1421-0.24791.08280.1001-0.13220.39730.04070.052920.37264.3133.399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 125
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B6 - 125
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C6 - 125
6X-RAY DIFFRACTION3C406
7X-RAY DIFFRACTION4D6 - 125
8X-RAY DIFFRACTION5A139 - 298
9X-RAY DIFFRACTION5A300 - 301
10X-RAY DIFFRACTION5A403 - 413
11X-RAY DIFFRACTION6B139 - 298
12X-RAY DIFFRACTION6B402 - 404
13X-RAY DIFFRACTION7C139 - 298
14X-RAY DIFFRACTION8D139 - 298

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