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- PDB-4urs: Crystal Structure of GGDEF domain from T.maritima -

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Basic information

Entry
Database: PDB / ID: 4urs
TitleCrystal Structure of GGDEF domain from T.maritima
ComponentsDIGUANYLATE CYCLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / GGDEF domain-containing protein
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDeepthi, A. / Liew, C.W. / Liang, Z.X. / Swaminathan, K. / Lescar, J.
CitationJournal: Plos One / Year: 2014
Title: Structure of a Diguanylate Cyclase from Thermotoga Maritima: Insights Into Activation, Feedback Inhibition and Thermostability
Authors: Deepthi, A. / Liew, C.W. / Liang, Z.X. / Kunchithapadam, S. / Lescar, J.
History
DepositionJul 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIGUANYLATE CYCLASE
B: DIGUANYLATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,91510
Polymers43,6822
Non-polymers3,2338
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-2.2 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.150, 37.140, 62.280
Angle α, β, γ (deg.)95.48, 100.23, 107.78
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.30715, 0.95165, -0.00389), (0.95159, 0.30717, 0.01094), (0.0116, -0.00034, -0.99993)
Vector: 18.4061, -13.23409, -28.17164)

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Components

#1: Protein DIGUANYLATE CYCLASE


Mass: 21841.121 Da / Num. of mol.: 2 / Fragment: GGDEF DOMAIN, RESIDUES 82-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q9X2A8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: 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.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MONOBASIC SODIUM PHOSPHATE MONOHYDRATE, 0.1 M MONOBASIC POTASSIUM PHOSPHATE, 0.1 M MES MONOHYDRATE (PH 6.5), 2 M NACL

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→34.83 Å / Num. obs: 13630 / % possible obs: 99.6 % / Observed criterion σ(I): 2.6 / Redundancy: 4.6 % / Biso Wilson estimate: 39.85 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.5
Reflection shellResolution: 2.27→2.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ICL

3icl


Resolution: 2.27→32.58 Å / Cor.coef. Fo:Fc: 0.9144 / Cor.coef. Fo:Fc free: 0.8888 / SU R Cruickshank DPI: 0.662 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.588 / SU Rfree Blow DPI: 0.279 / SU Rfree Cruickshank DPI: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.268 682 5.01 %RANDOM
Rwork0.218 ---
obs0.2204 13625 95.63 %-
Displacement parametersBiso mean: 39.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.3776 Å2-0.8383 Å20.0472 Å2
2---1.2635 Å2-1.0992 Å2
3---1.6411 Å2
Refine analyzeLuzzati coordinate error obs: 0.294 Å
Refinement stepCycle: LAST / Resolution: 2.27→32.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 214 93 2965
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012963HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.24030HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1020SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes406HARMONIC5
X-RAY DIFFRACTIONt_it2963HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion19.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion360SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3503SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.45 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2713 129 5.46 %
Rwork0.195 2234 -
all0.1993 2363 -
obs--95.63 %

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