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- PDB-5j9r: Structure of Penicillin V acylase from Agrobacterium tumefaciens -

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Basic information

Entry
Database: PDB / ID: 5j9r
TitleStructure of Penicillin V acylase from Agrobacterium tumefaciens
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / Ntn hydrolase / Penicillin V / quorum quenching / cholylglcine hydrolase
Function / homology
Function and homology information


choloylglycine hydrolase activity / choloylglycine hydrolase
Similarity search - Function
Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Choloylglycine hydrolase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRamasamy, S. / Avinash, V.S. / Pundle, A.V.
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2017
Title: Penicillin V acylases from gram-negative bacteria degrade N-acylhomoserine lactones and attenuate virulence in Pseudomonas aeruginosa.
Authors: Sunder, A.V. / Utari, P.D. / Ramasamy, S. / van Merkerk, R. / Quax, W. / Pundle, A.
History
DepositionApr 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
D: Choloylglycine hydrolase
C: Choloylglycine hydrolase


Theoretical massNumber of molelcules
Total (without water)144,4984
Polymers144,4984
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-62 kcal/mol
Surface area45980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.660, 134.771, 215.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23C
14B
24D
15B
25C
16D
26C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 326 / Label seq-ID: 1 - 326

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22DC
13AA
23CD
14BB
24DC
15BB
25CD
16DC
26CD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Choloylglycine hydrolase


Mass: 36124.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_4548 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: A0A083ZJN8, choloylglycine hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES pH 7.5, 12% (w/v) PEG 3350, PEG Rx crystallization screen

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2014
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.8→39.55 Å / Num. obs: 37299 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WL2

4wl2


Resolution: 2.8→38.067 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24505 2000 5.4 %RANDOM
Rwork0.20843 ---
obs0.21037 35236 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å20 Å2
2---0.15 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.8→38.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10180 0 0 33 10213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910140
X-RAY DIFFRACTIONr_bond_other_d00.029460
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.93813796
X-RAY DIFFRACTIONr_angle_other_deg3.679321744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06151260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4324.196448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.661151636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2471552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21540
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111532
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022368
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_it2.6273.7345064
X-RAY DIFFRACTIONr_mcbond_other2.6263.7345063
X-RAY DIFFRACTIONr_mcangle_it4.2765.5966316
X-RAY DIFFRACTIONr_mcangle_other4.2765.5966317
X-RAY DIFFRACTIONr_scbond_it3.2764.0085076
X-RAY DIFFRACTIONr_scbond_other3.2764.0085077
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9085.8857481
X-RAY DIFFRACTIONr_long_range_B_refined8.09330.03911313
X-RAY DIFFRACTIONr_long_range_B_other8.09330.04111314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A182350.13
12B182350.13
21A180780.13
22D180780.13
31A184630.13
32C184630.13
41B180350.13
42D180350.13
51B179620.14
52C179620.14
61D180990.14
62C180990.14
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 144 -
Rwork0.314 2547 -
obs--99.7 %

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