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- PDB-3eea: The crystal structure of the GAF domain/HD domain protein from Ge... -

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Basic information

Entry
Database: PDB / ID: 3eea
TitleThe crystal structure of the GAF domain/HD domain protein from Geobacter sulfurreducens
ComponentsGAF domain/HD domain protein
Keywordsstructural genomics / unknown function / GAF domain/HD domain protein / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


phosphatase activity
Similarity search - Function
HD-GYP domain / HD domain / HD-GYP domain profile. / GAF domain / GAF domain / HD domain profile. / HD domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain ...HD-GYP domain / HD domain / HD-GYP domain profile. / GAF domain / GAF domain / HD domain profile. / HD domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PG6 / Sensor cyclic diguanylate phosphodiesterase, GAF and GAF domain-containing
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the GAF domain/HD domain protein from Geobacter sulfurreducens
Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A.
History
DepositionSep 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: GAF domain/HD domain protein
B: GAF domain/HD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4024
Polymers36,8702
Non-polymers5332
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint5 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.453, 79.471, 112.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein may exists as dimer.

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Components

#1: Protein GAF domain/HD domain protein


Mass: 18434.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU1007 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q74EF5
#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M CaCl2, 0.1M Tris, 20%(w/v)PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→64.96 Å / Num. all: 28838 / Num. obs: 28282 / % possible obs: 98.07 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 24.57
Reflection shellResolution: 1.8→1.847 Å / Redundancy: 3 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.12 / Num. unique all: 2228 / % possible all: 90.48

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→64.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.921 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.138 / ESU R Free: 0.134
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24131 1504 5 %RANDOM
Rwork0.19984 ---
obs0.20183 28282 98.07 %-
all-28838 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.627 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.54 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→64.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 36 99 2550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222498
X-RAY DIFFRACTIONr_bond_other_d0.0010.021810
X-RAY DIFFRACTIONr_angle_refined_deg1.7012.0113366
X-RAY DIFFRACTIONr_angle_other_deg0.9634392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.34421.04296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31115456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9681530
X-RAY DIFFRACTIONr_chiral_restr0.10.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02508
X-RAY DIFFRACTIONr_mcbond_it1.0461.51530
X-RAY DIFFRACTIONr_mcbond_other0.3051.5592
X-RAY DIFFRACTIONr_mcangle_it1.93822494
X-RAY DIFFRACTIONr_scbond_it3.0423968
X-RAY DIFFRACTIONr_scangle_it4.7644.5872
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 107 -
Rwork0.274 1909 -
obs-2016 90.48 %
Refinement TLS params.Method: refined / Origin x: -7.268 Å / Origin y: -3.461 Å / Origin z: 11.635 Å
111213212223313233
T0.013 Å20.0054 Å2-0.0095 Å2-0.0241 Å20.0004 Å2--0.0784 Å2
L1.2292 °20.2823 °2-0.4942 °2-0.7808 °2-0.136 °2--0.8383 °2
S-0.0272 Å °-0.0325 Å °-0.0235 Å °-0.0597 Å °-0.0145 Å °-0.0339 Å °0.0398 Å °-0.0005 Å °0.0417 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 506 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 160101 - 160
4X-RAY DIFFRACTION1BB9 - 609 - 60
5X-RAY DIFFRACTION1BB61 - 11061 - 110
6X-RAY DIFFRACTION1BB111 - 162111 - 162

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