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- PDB-6zxm: Diguanylate cyclase DgcR in complex with c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 6zxm
TitleDiguanylate cyclase DgcR in complex with c-di-GMP
ComponentsPutative GGDEF/response regulator receiver domain protein
KeywordsSIGNALING PROTEIN / GGDEF domain / receiver domain / Rec / c-di-GMP / Leptospira
Function / homology
Function and homology information


phosphorelay signal transduction system
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
Chem-C2E / Putative GGDEF/response regulator receiver domain protein
Similarity search - Component
Biological speciesLeptospira biflexa serovar Patoc strain 'Patoc 1 '
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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
E: Putative GGDEF/response regulator receiver domain protein
F: Putative GGDEF/response regulator receiver domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,97724
Polymers216,5476
Non-polymers8,43118
Water0
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)74,9928
Polymers72,1822
Non-polymers2,8106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)74,9928
Polymers72,1822
Non-polymers2,8106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Putative GGDEF/response regulator receiver domain protein
F: Putative GGDEF/response regulator receiver domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9928
Polymers72,1822
Non-polymers2,8106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.603, 72.917, 125.729
Angle α, β, γ (deg.)90.000, 118.200, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 6 - 298 / Label seq-ID: 26 - 318

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(-0.617158594349, -0.127358896514, -0.776463122692), (0.028079783246, -0.989749816698, 0.140024376875), (-0.786337583481, 0.0646143314232, 0.614408815839)-102.750811454, 16.9702022784, -51.5885276343
2given(-0.260155190792, 0.377615444054, 0.888665208679), (-0.125982092902, -0.925763205469, 0.356498246373), (0.957312795784, -0.019211033577, 0.288414887301)74.3270476237, 22.0905359503, 19.5837799678
3given(-0.498826588395, -0.158827114604, 0.852024637189), (-0.238353396079, 0.970298732116, 0.0413283078806), (-0.833282481088, -0.182467306993, -0.521867788421)63.9846226678, -10.374314488, -89.9685647153
4given(0.982447782092, -0.185455031529, -0.0200695476688), (-0.183590743272, -0.980362806944, 0.0719944841373), (-0.0330271774122, -0.0670462380898, -0.997203092409)1.39306274777, 1.27651345965, -53.7501981614
5given(-0.591413969835, 0.0786547227567, -0.802522866261), (0.15675643381, 0.987459476713, -0.0187403924235), (0.790984789198, -0.136883952446, -0.596326963016)-101.012029412, -2.09913596968, -0.453965074195

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Components

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


Mass: 36091.098 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' (bacteria)
Strain: Paris / Gene: LEPBI_p0053 / Production host: Escherichia coli (E. coli) / References: UniProt: B0SUI1
#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 / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Mg
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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Potassium thiocyanate; 0.1 M Tris pH 7.5; 25% PEG 2000 MME

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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: Feb 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→48 Å / Num. obs: 28038 / % possible obs: 99 % / Redundancy: 3.78 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.75
Reflection shellResolution: 3.3→3.4 Å / Rmerge(I) obs: 0.682 / Num. unique obs: 1877 / % possible all: 91.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V0N

2v0n


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.861 / SU B: 98.502 / SU ML: 0.684 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.728 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1503 5.1 %RANDOM
Rwork0.225 ---
obs0.228 28038 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 219.75 Å2 / Biso mean: 90.38 Å2 / Biso min: 44.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å20 Å20.99 Å2
2---0.13 Å20 Å2
3----2.49 Å2
Refinement stepCycle: final / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14070 0 558 0 14628
Biso mean--79.54 --
Num. residues----1758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01314921
X-RAY DIFFRACTIONr_bond_other_d0.0020.01714163
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.64320211
X-RAY DIFFRACTIONr_angle_other_deg1.2251.58632676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.60351751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52322.197792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.542152754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.32615114
X-RAY DIFFRACTIONr_chiral_restr0.0780.22070
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023264
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A93020.09
12B93020.09
21A93580.09
22C93580.09
31A92240.09
32D92240.09
41A92770.09
42E92770.09
51A93460.09
52F93460.09
61B93360.09
62C93360.09
71B93810.08
72D93810.08
81B94210.08
82E94210.08
91B93250.1
92F93250.1
101C93220.09
102D93220.09
111C93870.08
112E93870.08
121C94020.09
122F94020.09
131D94260.08
132E94260.08
141D92610.1
142F92610.1
151E93580.09
152F93580.09
LS refinement shellResolution: 3.3→3.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 100 -
Rwork0.309 1877 -
all-1977 -
obs--91.78 %
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)
14.1292-3.59360.52753.95420.07091.8719-0.31050.2519-0.1952-0.0935-0.25710.65020.1087-0.33310.56760.64-0.08020.15791.2203-0.12060.5579-50.98113.597-50.152
22.1213-1.5868-1.32366.4417-0.60581.7001-0.344-0.1461-0.07771.17210.1423-0.45290.4346-0.00390.20170.9258-0.0870.02981.04430.04110.3718-35.658-4.278-39.996
34.8389-0.5179-1.35964.30952.16093.7773-0.32280.5530.0653-0.70650.3766-0.0443-0.1009-0.393-0.05390.5824-0.04240.17271.178-0.0230.42545.415-1.907-44.78
44.3530.4930.18536.19840.67221.36130.1962-0.73360.80491.09290.1242-0.6749-0.63480.2664-0.32041.0098-0.11050.32181.3348-0.14540.725448.45113.573-25.161
53.9571.6365-0.48661.3301-0.03580.17550.1608-0.01470.74360.3096-0.20911.13950.1699-0.33920.04831.3022-0.1398-0.08991.4257-0.16171.3518-51.06-5.822-4.761
60.93112.2466-0.30097.0289-0.89970.1776-0.27060.23460.1591-1.29880.35230.00640.25230.1643-0.08171.1664-0.0111-0.11741.071-0.00360.5705-29.2953.956-12.776
75.85280.736-0.71930.50680.0461.2850.20210.081-0.0835-0.0064-0.11450.0916-0.3066-0.1819-0.08760.28780.0809-0.02570.7278-0.00150.1258-40.354-0.357-84.464
84.7418-0.39070.36560.8048-0.26134.15870.1084-0.3986-0.06320.1264-0.07590.0429-0.06370.0858-0.03250.1815-0.00710.12790.70990.01430.0997-11.3044.09-72.778
92.88611.2335-2.27323.6082-2.05765.4486-0.00150.2020.0028-0.26590.1513-0.13170.19430.1097-0.14980.3490.12510.02880.70560.00510.038911.581-2.562-42.937
103.19520.34730.88591.6259-0.49225.11940.1714-0.11420.38820.15130.00710.07960.0070.1797-0.17850.30480.09870.12310.6396-0.07240.11019.596-5.253-11.387
115.1601-0.28290.2870.9291-0.39113.53190.079-0.14650.0499-0.2-0.0144-0.03410.2612-0.2197-0.06460.189-0.06040.08650.72570.03350.0593-35.8462.76332.914
121.817-0.08120.20170.58061.50255.76320.04040.052-0.148-0.1010.00380.02820.37370.0464-0.04430.31870.04170.05450.63350.07570.1244-9.653-7.05318.069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 130
2X-RAY DIFFRACTION1A303
3X-RAY DIFFRACTION2B6 - 130
4X-RAY DIFFRACTION2B303
5X-RAY DIFFRACTION3C6 - 130
6X-RAY DIFFRACTION3C303
7X-RAY DIFFRACTION4D6 - 130
8X-RAY DIFFRACTION4D303
9X-RAY DIFFRACTION5E6 - 130
10X-RAY DIFFRACTION5E303
11X-RAY DIFFRACTION6F6 - 130
12X-RAY DIFFRACTION6F303
13X-RAY DIFFRACTION7A131 - 298
14X-RAY DIFFRACTION7A301
15X-RAY DIFFRACTION8B131 - 298
16X-RAY DIFFRACTION8B301
17X-RAY DIFFRACTION9C131 - 298
18X-RAY DIFFRACTION9C301
19X-RAY DIFFRACTION10D131 - 298
20X-RAY DIFFRACTION10D301
21X-RAY DIFFRACTION11E131 - 298
22X-RAY DIFFRACTION11E301
23X-RAY DIFFRACTION12F131 - 298
24X-RAY DIFFRACTION12F301

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