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- PDB-5zbk: Crystal structure of type-I LOG from Pseudomonas aeruginosa PAO1 ... -

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Basic information

Entry
Database: PDB / ID: 5zbk
TitleCrystal structure of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP
ComponentsPutative cytokinin riboside 5'-monophosphate phosphoribohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / hydrolase activity, hydrolyzing N-glycosyl compounds / AMP nucleosidase / AMP nucleosidase activity / cytokinin biosynthetic process / cytosol
Similarity search - Function
Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeo, H. / Kim, K.-J.
CitationJournal: Environ. Microbiol. / Year: 2018
Title: Structural insight into molecular mechanism of cytokinin activating protein from Pseudomonas aeruginosa PAO1.
Authors: Seo, H. / Kim, K.J.
History
DepositionFeb 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.3Sep 16, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3525
Polymers21,7591
Non-polymers5934
Water18010
1
A: Putative cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules

A: Putative cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,70510
Polymers43,5182
Non-polymers1,1878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5980 Å2
ΔGint-36 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.844, 97.524, 71.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative cytokinin riboside 5'-monophosphate phosphoribohydrolase


Mass: 21758.934 Da / Num. of mol.: 1 / Mutation: E115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4923 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P48636, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: ammonium phosphate dibasic, citrate pH 5.5, sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 23, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→54 Å / Num. obs: 10160 / % possible obs: 97.3 % / Redundancy: 4.3 % / CC1/2: 0.912 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.063 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.349 / Num. unique obs: 493 / CC1/2: 0.713 / Rpim(I) all: 0.162

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ITS

5its


Resolution: 2.3→54 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.463 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.214
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 505 5 %RANDOM
Rwork0.182 ---
obs0.1847 9646 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.94 Å2 / Biso mean: 16.208 Å2 / Biso min: 3.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0 Å2
2--0.87 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 2.3→54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 39 10 1399
Biso mean--29.97 11.2 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191417
X-RAY DIFFRACTIONr_bond_other_d0.0020.021343
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9981924
X-RAY DIFFRACTIONr_angle_other_deg1.04733087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8545181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39122.90955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20915210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5511510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 43 -
Rwork0.227 656 -
all-699 -
obs--91.37 %

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