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- PDB-5w10: Lcd1 GAF domain in complex with cAMP ligand -

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Basic information

Entry
Database: PDB / ID: 5w10
TitleLcd1 GAF domain in complex with cAMP ligand
ComponentscGMP-specific phosphodiesterase
KeywordsHYDROLASE / GAF domain / cAMP binding domain / Effector domain / Regulates the DGC activity of the GGDEF domain
Function / homology
Function and homology information


Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cGMP-specific phosphodiesterase
Similarity search - Component
Biological speciesLeptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsGuzzo, C.R. / Maciel, N.K. / Barbosa, A.S. / Farah, C.S.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/084147 Brazil
Sao Paulo Research Foundation (FAPESP)2013/18664-2 Brazil
Sao Paulo Research Foundation (FAPESP)2013/06650-7 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474907/2013-9 Brazil
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural and Enzymatic Characterization of a cAMP-Dependent Diguanylate Cyclase from Pathogenic Leptospira Species.
Authors: da Costa Vasconcelos, F.N. / Maciel, N.K. / Favaro, D.C. / de Oliveira, L.C. / Barbosa, A.S. / Salinas, R.K. / de Souza, R.F. / Farah, C.S. / Guzzo, C.R.
History
DepositionJun 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cGMP-specific phosphodiesterase
B: cGMP-specific phosphodiesterase
C: cGMP-specific phosphodiesterase
D: cGMP-specific phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2678
Polymers88,9504
Non-polymers1,3174
Water6,233346
1
A: cGMP-specific phosphodiesterase
D: cGMP-specific phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1334
Polymers44,4752
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-24 kcal/mol
Surface area16060 Å2
MethodPISA
2
B: cGMP-specific phosphodiesterase
C: cGMP-specific phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1334
Polymers44,4752
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-24 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.190, 119.995, 62.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 174
2010B4 - 174
1020A3 - 174
2020C3 - 174
1030A3 - 174
2030D3 - 174
1040B4 - 173
2040C4 - 173
1050B4 - 174
2050D4 - 174
1060C1 - 174
2060D1 - 174

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
cGMP-specific phosphodiesterase


Mass: 22237.525 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130) (bacteria)
Strain: Fiocruz L1-130 / Gene: LIC_13137 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: Q72MQ6
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium citrate and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2014
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 93522 / % possible obs: 99.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→29.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.944 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22519 2498 5.1 %RANDOM
Rwork0.19463 ---
obs0.19617 46800 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.894 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2--0.13 Å20 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 2.15→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5479 0 88 346 5913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195814
X-RAY DIFFRACTIONr_bond_other_d0.0070.025640
X-RAY DIFFRACTIONr_angle_refined_deg1.54727881
X-RAY DIFFRACTIONr_angle_other_deg1.4313063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91724.521261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.429151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5951534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026406
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021292
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_mcbond_it3.0573.9032780
X-RAY DIFFRACTIONr_mcbond_other3.0513.9022779
X-RAY DIFFRACTIONr_mcangle_it4.6165.8283475
X-RAY DIFFRACTIONr_mcangle_other4.6155.833476
X-RAY DIFFRACTIONr_scbond_it3.8064.3583034
X-RAY DIFFRACTIONr_scbond_other3.8054.3583035
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9396.3364386
X-RAY DIFFRACTIONr_long_range_B_refined8.00631.2156854
X-RAY DIFFRACTIONr_long_range_B_other7.97231.0566721
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)
11A105840.09
12B105840.09
21A95720.16
22C95720.16
31A95200.16
32D95200.16
41B95840.16
42C95840.16
51B94700.16
52D94700.16
61C103300.1
62D103300.1
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 185 -
Rwork0.329 3315 -
obs--97.52 %

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