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- PDB-4urq: Crystal Structure of GGDEF domain (I site mutant) from T.maritima -

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Basic information

Entry
Database: PDB / ID: 4urq
TitleCrystal Structure of GGDEF domain (I site mutant) from T.maritima
ComponentsDIGUANYLATE CYCLASE
KeywordsTRANSFERASE
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
GGDEF domain-containing protein
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDeepthi, A. / Liew, C.W. / Liang, Z.X. / Swamianthan, 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 1, 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 / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: DIGUANYLATE CYCLASE
V: DIGUANYLATE CYCLASE
W: DIGUANYLATE CYCLASE
X: DIGUANYLATE CYCLASE
Y: DIGUANYLATE CYCLASE
Z: DIGUANYLATE CYCLASE


Theoretical massNumber of molelcules
Total (without water)116,9256
Polymers116,9256
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-14.8 kcal/mol
Surface area51280 Å2
MethodPQS
Unit cell
Length a, b, c (Å)159.410, 91.980, 87.590
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DIGUANYLATE CYCLASE


Mass: 19487.449 Da / Num. of mol.: 6 / Fragment: GGDEF DOMAIN, RESIDUES 81-248 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X2A8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.82 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 2 M NACL, 10% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→58.97 Å / Num. obs: 43759 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Biso Wilson estimate: 58.14 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3 / % possible all: 100

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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: 2.5→38.37 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9122 / SU R Cruickshank DPI: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.249 / SU Rfree Cruickshank DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 2196 5.02 %RANDOM
Rwork0.222 ---
obs0.2232 43743 99.67 %-
Displacement parametersBiso mean: 53.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.4233 Å20 Å20.1705 Å2
2--0.0119 Å20 Å2
3---0.4115 Å2
Refine analyzeLuzzati coordinate error obs: 0.374 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7526 0 0 127 7653
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017670HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1110306HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2820SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes180HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1109HARMONIC5
X-RAY DIFFRACTIONt_it7670HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion923SEMIHARMONIC5
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_contact8642SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2543 153 4.74 %
Rwork0.2321 3072 -
all0.2331 3225 -
obs--99.67 %

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