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- PDB-5x9i: Unique Choloylglycine Hydrolase(CGH) member Mutant (C1S) from She... -

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Basic information

Entry
Database: PDB / ID: 5x9i
TitleUnique Choloylglycine Hydrolase(CGH) member Mutant (C1S) from Shewanella loihica PV-4
ComponentsPenicillin V acylase-like protein
KeywordsHYDROLASE / Choloylglycine Hydrolase / BSH / PVA like / AHL activity / C1S mutant
Function / homology: / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / hydrolase activity / 3-OXOOCTANOIC ACID / Penicillin V acylase-like protein
Function and homology information
Biological speciesShewanella loihica PV-4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRamasamy, S. / Philem, P. / Yadav, Y.
CitationJournal: To Be Published
Title: Unique Choloylglycine Hydrolase(CGH) member from Shewanella loihica PV-4
Authors: Philem, P. / Yadav, Y. / Prabune, A.A. / Ramasamy, S.
History
DepositionMar 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: Penicillin V acylase-like protein
B: Penicillin V acylase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3576
Polymers75,8572
Non-polymers5014
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-2 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.788, 52.420, 99.205
Angle α, β, γ (deg.)90.00, 115.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Penicillin V acylase-like protein / Choloylglycine hydrolase


Mass: 37928.387 Da / Num. of mol.: 2 / Fragment: UNP residues 27-359 / Mutation: C1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica PV-4 (bacteria) / Strain: PV-4 / Gene: Shew_0681 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: A3QAQ5, choloylglycine hydrolase
#2: Chemical ChemComp-OOA / 3-OXOOCTANOIC ACID


Mass: 158.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.38 Å3/Da / Density % sol: 48.39 % / Description: elongated needle crystal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 3350, sodium sulphate, 2-Methyl-2, 4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97855 Å
DetectorType: RAYONIX MX-225 / Detector: FLAT PANEL / Date: Feb 28, 2016
RadiationMonochromator: Si(111) single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 105996 / % possible obs: 100 % / Redundancy: 4.9 % / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBC

3hbc


Resolution: 1.5→35.891 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20767 5588 5 %RANDOM
Rwork0.18458 ---
obs0.18574 105996 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.563 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20.07 Å2
2--0.14 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.5→35.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 34 175 5531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195469
X-RAY DIFFRACTIONr_bond_other_d00.024928
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.9467412
X-RAY DIFFRACTIONr_angle_other_deg3.724311526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54625.118254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69815960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1251522
X-RAY DIFFRACTIONr_chiral_restr0.1350.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026130
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021076
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6111.8642702
X-RAY DIFFRACTIONr_mcbond_other1.6051.8632701
X-RAY DIFFRACTIONr_mcangle_it2.1272.7943382
X-RAY DIFFRACTIONr_mcangle_other2.1272.7953383
X-RAY DIFFRACTIONr_scbond_it2.9122.1312767
X-RAY DIFFRACTIONr_scbond_other2.9122.1312767
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3063.0834011
X-RAY DIFFRACTIONr_long_range_B_refined4.68122.0256051
X-RAY DIFFRACTIONr_long_range_B_other4.68122.036052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 399 -
Rwork0.275 7748 -
obs--98.48 %

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