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- PDB-5zbl: Crystal structure of type-I LOG from Corynebacterium glutamicum i... -

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Basic information

Entry
Database: PDB / ID: 5zbl
TitleCrystal structure of type-I LOG from Corynebacterium glutamicum in complex with AMP
ComponentsCytokinin riboside 5'-monophosphate phosphoribohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process / nucleotide binding / 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 / PHOSPHATE ION / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (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 1.2Sep 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: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
D: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,24320
Polymers90,3284
Non-polymers1,91516
Water1,35175
1
A: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,10413
Polymers45,1642
Non-polymers94111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-88 kcal/mol
Surface area16670 Å2
MethodPISA
2
C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
D: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1387
Polymers45,1642
Non-polymers9755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-39 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.153, 70.714, 190.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytokinin riboside 5'-monophosphate phosphoribohydrolase


Mass: 22581.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cg2612 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8NN34, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 6 types, 91 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ethylene glycol, sodium phosphate dibasic titrated with citric acid to pH 4.2, ammonium sulfate

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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: Jul 21, 2016
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→95.4 Å / Num. obs: 41734 / % possible obs: 96.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.033 / Net I/σ(I): 37.3
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.394 / Num. unique obs: 2002 / CC1/2: 0.671 / Rpim(I) all: 0.157

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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→95.4 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.539 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 2025 4.9 %RANDOM
Rwork0.1962 ---
obs0.1994 39686 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.18 Å2 / Biso mean: 51.467 Å2 / Biso min: 25.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---2.33 Å20 Å2
3---2.31 Å2
Refinement stepCycle: final / Resolution: 2.3→95.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 118 75 5861
Biso mean--68.87 48.24 -
Num. residues----733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195898
X-RAY DIFFRACTIONr_bond_other_d0.0020.025533
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9837970
X-RAY DIFFRACTIONr_angle_other_deg0.996312814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96624.385244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.834151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6571528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216430
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021188
LS refinement shellResolution: 2.299→2.358 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 122 -
Rwork0.315 2709 -
all-2831 -
obs--88.94 %

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