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- PDB-3lid: Crystal Structure of the extracellular domain of the putative his... -

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Basic information

Entry
Database: PDB / ID: 3lid
TitleCrystal Structure of the extracellular domain of the putative histidine kinase vpHK1S-Z8
ComponentsPutative sensory box/GGDEF family protein
KeywordsSIGNALING PROTEIN / PDC fold
Function / homology
Function and homology information


protein histidine kinase activity / histidine kinase
Similarity search - Function
Periplasmic sensor-like domain superfamily / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / PAS domain / PAC domain profile. / PAS-associated, C-terminal / Nucleotide cyclase ...Periplasmic sensor-like domain superfamily / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / PAS domain / PAC domain profile. / PAS-associated, C-terminal / Nucleotide cyclase / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Histidine kinase
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
AuthorsZhang, Z. / Hendrickson, W.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural characterization of the predominant family of histidine kinase sensor domains.
Authors: Zhang, Z. / Hendrickson, W.A.
History
DepositionJan 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)69,33015
Polymers68,5112
Non-polymers81913
Water10,521584
1
A: Putative sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6968
Polymers34,2551
Non-polymers4417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6347
Polymers34,2551
Non-polymers3796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-29 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.102, 79.444, 123.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative sensory box/GGDEF family protein


Mass: 34255.449 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 28-313)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP0354 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87SR8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: 5% PEG8K, 0.2M NaCl, 0.1M Na/K Phosphate pH6.2, vapor diffusion, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.97924 0.97929 0.96784
SYNCHROTRONNSLS X4A20.97921
DetectorDetector: CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979291
30.967841
40.979211
ReflectionRedundancy: 6.3 % / Av σ(I) over netI: 33.54 / Number: 581055 / Rmerge(I) obs: 0.102 / Χ2: 1.02 / D res high: 2.01 Å / D res low: 50 Å / Num. obs: 92883 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.335098.910.0511.0256.5
3.444.3399.810.0571.0076.5
33.4499.910.0761.0016.5
2.73310010.1111.0276.4
2.532.7399.910.1551.0276.3
2.382.5399.910.1951.0326.2
2.262.3899.810.241.0336.2
2.172.2699.510.3221.166.1
2.082.1799.210.3761.0026.1
2.012.0899.310.4450.9135.9
ReflectionResolution: 1.76→50 Å / Num. obs: 72469 / % possible obs: 99 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.054 / Χ2: 1.004 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.76-1.825.60.25669010.84795.7
1.82-1.95.90.17972430.88599.9
1.9-1.985.90.12872200.978100
1.98-2.0960.09272391.028100
2.09-2.2260.06972691.014100
2.22-2.3960.05372411.026100
2.39-2.6360.04473071.083100
2.63-3.016.20.04373311.0499.9
3.01-3.7912.10.06173351.06599.1
3.79-5011.60.04673830.9996.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.76→37.807 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.961 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3641 5 %RANDOM
Rwork0.182 ---
obs0.184 72414 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.94 Å2 / Biso mean: 24.942 Å2 / Biso min: 11.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.76→37.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 48 584 5161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224687
X-RAY DIFFRACTIONr_angle_refined_deg2.1171.976338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92524.31239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15315831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9041533
X-RAY DIFFRACTIONr_chiral_restr0.1870.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213563
X-RAY DIFFRACTIONr_mcbond_it1.3721.52787
X-RAY DIFFRACTIONr_mcangle_it2.39924525
X-RAY DIFFRACTIONr_scbond_it3.57931900
X-RAY DIFFRACTIONr_scangle_it5.5814.51809
LS refinement shellResolution: 1.756→1.802 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 240 -
Rwork0.236 4725 -
all-4965 -
obs--92.67 %

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