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- PDB-2p7j: Crystal structure of the domain of putative sensory box/GGDEF fam... -

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Basic information

Entry
Database: PDB / ID: 2p7j
TitleCrystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus
ComponentsPutative sensory box/GGDEF family protein
KeywordsTRANSCRIPTION / Sensory box/GGDEF family protein / Structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


protein histidine kinase activity
Similarity search - Function
: / Bacterial histidine kinase, sensor domain / Periplasmic sensor-like domain superfamily / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal ...: / Bacterial histidine kinase, sensor domain / Periplasmic sensor-like domain superfamily / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Putative sensory box/GGDEF family protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsWu, R. / James, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus
Authors: Wu, R. / James, A. / Joachimiak, A.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS A DIMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sensory box/GGDEF family protein
B: Putative sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8896
Polymers66,6142
Non-polymers2754
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.980, 81.596, 121.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein exists as a dimer

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Components

#1: Protein Putative sensory box/GGDEF family protein


Mass: 33306.918 Da / Num. of mol.: 2 / Fragment: Residues 27-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: 223926 / Gene: VP0354 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87SR8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M LiSO4, 25% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2007
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 34928 / Num. obs: 33442 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 32.2
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3.96 / Num. unique all: 3433 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→38.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.175 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.264 / ESU R Free: 0.21
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23863 1746 5 %RANDOM
Rwork0.19346 ---
all0.19577 33090 --
obs0.19577 33090 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.187 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2--0.81 Å20 Å2
3----2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 15 321 4727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224619
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9636275
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.555562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48724.5240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41515813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2391531
X-RAY DIFFRACTIONr_chiral_restr0.1150.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023581
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.22048
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23179
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7091.52771
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37824502
X-RAY DIFFRACTIONr_scbond_it2.15431911
X-RAY DIFFRACTIONr_scangle_it3.4844.51773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 110 -
Rwork0.209 2173 -
obs-2173 89.32 %
Refinement TLS params.Method: refined / Origin x: 43.3463 Å / Origin y: 28.0199 Å / Origin z: 9.8719 Å
111213212223313233
T-0.0815 Å2-0.0376 Å20.0194 Å2--0.0562 Å2-0.019 Å2---0.0792 Å2
L0.332 °2-0.0627 °20.1315 °2-0.5334 °2-0.1556 °2--0.6171 °2
S-0.0217 Å °0.0485 Å °-0.0119 Å °-0.0377 Å °0.0122 Å °-0.0057 Å °0.0506 Å °-0.0055 Å °0.0094 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 6010 - 61
2X-RAY DIFFRACTION1AA61 - 12062 - 121
3X-RAY DIFFRACTION1AA121 - 180122 - 181
4X-RAY DIFFRACTION1AA181 - 240182 - 241
5X-RAY DIFFRACTION1AA241 - 273242 - 274
6X-RAY DIFFRACTION1BB8 - 609 - 61
7X-RAY DIFFRACTION1BB61 - 12062 - 121
8X-RAY DIFFRACTION1BB121 - 180122 - 181
9X-RAY DIFFRACTION1BB181 - 240182 - 241
10X-RAY DIFFRACTION1BB241 - 281242 - 282

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