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

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Basic information

Entry
Database: PDB / ID: 5zbj
TitleCrystal structure of type-I LOG from Pseudomonas aeruginosa PAO1
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
IMIDAZOLE / PHOSPHATE ION / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 1.2Sep 16, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 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)22,3197
Polymers21,8171
Non-polymers5026
Water1,802100
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)44,63914
Polymers43,6342
Non-polymers1,00512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5610 Å2
ΔGint-41 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.931, 97.917, 71.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21816.969 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 106 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: ammonium phosphate dibasic, imidazole pH 8.0

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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: Feb 28, 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: 1.89→54.11 Å / Num. obs: 18128 / % possible obs: 98.1 % / Redundancy: 5 % / CC1/2: 0.804 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.036 / Net I/σ(I): 4.5
Reflection shellResolution: 1.89→1.93 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 845 / CC1/2: 0.944 / Rpim(I) all: 0.158

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ITS

5its


Resolution: 1.89→54.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.718 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.118
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 900 5 %RANDOM
Rwork0.1516 ---
obs0.1541 17219 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.68 Å2 / Biso mean: 22.512 Å2 / Biso min: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0 Å2
2--1.7 Å20 Å2
3----1.56 Å2
Refinement stepCycle: final / Resolution: 1.89→54.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 32 100 1504
Biso mean--27.75 34.79 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191455
X-RAY DIFFRACTIONr_bond_other_d0.0020.021384
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.9861977
X-RAY DIFFRACTIONr_angle_other_deg1.04933185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32723.15857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84115221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.271510
X-RAY DIFFRACTIONr_chiral_restr0.120.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
LS refinement shellResolution: 1.894→1.943 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 57 -
Rwork0.221 1147 -
all-1204 -
obs--90.59 %

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