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

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Basic information

Entry
Database: PDB / ID: 3lif
TitleCrystal Structure of the extracellular domain of the putative histidine kinase rpHK1S-Z16
ComponentsPutative diguanylate cyclase (GGDEF) with PAS/PAC domain
KeywordsSIGNALING PROTEIN / PDC fold
Function / homology
Function and homology information


diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / plasma membrane
Similarity search - Function
: / Histidine kinase sensor domain / Cache domain / : / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain ...: / Histidine kinase sensor domain / Cache domain / : / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / diguanylate cyclase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 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
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Putative diguanylate cyclase (GGDEF) with PAS/PAC domain
B: Putative diguanylate cyclase (GGDEF) with PAS/PAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1606
Polymers57,5402
Non-polymers6214
Water1,67593
1
A: Putative diguanylate cyclase (GGDEF) with PAS/PAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0803
Polymers28,7701
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative diguanylate cyclase (GGDEF) with PAS/PAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0803
Polymers28,7701
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.780, 184.780, 184.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Putative diguanylate cyclase (GGDEF) with PAS/PAC domain


Mass: 28769.756 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 40-293)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA3616 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6N3S7
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.57 Å3/Da / Density % sol: 73.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 0.2M NH4Ac, 0.1M citrate pH5.6, 30% MPD, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97918, 0.97935, 0.96788
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979351
30.967881
ReflectionRedundancy: 12.9 % / Av σ(I) over netI: 43.17 / Number: 725323 / Rmerge(I) obs: 0.065 / Χ2: 1 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 56039 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815099.610.0351.0212.7
4.625.8110010.0410.97313
4.034.6210010.0440.95813
3.664.0310010.0551.03613
3.43.6610010.0711.03513
3.23.410010.0981.03113
3.043.210010.1331.03213
2.913.0410010.1870.98412.9
2.82.9110010.2550.95412.9
2.72.810010.3520.93812.9
ReflectionResolution: 2.7→50 Å / Num. obs: 56039 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.065 / Χ2: 0.996 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.812.90.35256060.938100
2.8-2.9112.90.25556050.954100
2.91-3.0412.90.18755940.984100
3.04-3.2130.13355821.032100
3.2-3.4130.09856341.031100
3.4-3.66130.07155891.035100
3.66-4.03130.05555911.036100
4.03-4.62130.04456030.958100
4.62-5.81130.04156240.973100
5.81-5012.70.03556111.0299.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.7→42.39 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.23 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1500 5 %RANDOM
Rwork0.205 ---
obs0.208 30163 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 103.57 Å2 / Biso mean: 41.753 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 42 93 3969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223987
X-RAY DIFFRACTIONr_angle_refined_deg2.4171.9625435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.2955486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52722.623183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.51115626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.51534
X-RAY DIFFRACTIONr_chiral_restr0.1830.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213060
X-RAY DIFFRACTIONr_mcbond_it0.9911.52425
X-RAY DIFFRACTIONr_mcangle_it1.88623935
X-RAY DIFFRACTIONr_scbond_it2.7531562
X-RAY DIFFRACTIONr_scangle_it4.5764.51499
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 106 -
Rwork0.334 2078 -
all-2184 -
obs--100 %

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