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- PDB-5its: Crystal structure of LOG from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5its
TitleCrystal structure of LOG from Corynebacterium glutamicum
ComponentsCytokinin riboside 5'-monophosphate phosphoribohydrolase
KeywordsHYDROLASE / Rossmann fold / nucleotide-binding domain / phosphoribohydrolase
Function / homology
Function and homology information


cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process
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
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.-G. / Kim, K.-J.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for cytokinin production by LOG from Corynebacterium glutamicum
Authors: Seo, H.-G. / Kim, S. / Sagong, H.Y. / Son, H.F. / Jin, K.S. / Kim, I.K. / Kim, K.J.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Derived calculations / Structure summary / Category: pdbx_struct_oper_list / struct
Item: _pdbx_struct_oper_list.symmetry_operation / _struct.title
Revision 1.2Nov 8, 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)91,07012
Polymers90,3284
Non-polymers7438
Water3,675204
1
A: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6277
Polymers45,1642
Non-polymers4635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-40 kcal/mol
Surface area15580 Å2
MethodPISA
2
C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
D: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4435
Polymers45,1642
Non-polymers2793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-37 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.506, 130.501, 140.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#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: Cgl2379 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8NN34, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, DL-malic acid

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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: Oct 28, 2014
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→95.62 Å / Num. obs: 44133 / % possible obs: 95.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.5 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
HKL-2000data processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A33

2a33


Resolution: 2.3→95.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.513 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 2182 4.9 %RANDOM
Rwork0.1749 ---
obs0.1775 41951 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.95 Å2 / Biso mean: 29.687 Å2 / Biso min: 12.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--1.62 Å20 Å2
3----0.84 Å2
Refinement stepCycle: final / Resolution: 2.3→95.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5899 0 46 204 6149
Biso mean--34.16 30.13 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196068
X-RAY DIFFRACTIONr_bond_other_d0.0010.025831
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9718203
X-RAY DIFFRACTIONr_angle_other_deg0.817313442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08924.449254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.863151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.691528
X-RAY DIFFRACTIONr_chiral_restr0.0850.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021333
X-RAY DIFFRACTIONr_mcbond_it2.0842.7263043
X-RAY DIFFRACTIONr_mcbond_other2.0822.7243042
X-RAY DIFFRACTIONr_mcangle_it3.3434.0773798
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 127 -
Rwork0.304 2790 -
all-2917 -
obs--85.74 %

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