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- PDB-5x8z: Unique Choloylglycine Hydrolase(CGH) member from Shewanella loihi... -

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Basic information

Entry
Database: PDB / ID: 5x8z
TitleUnique Choloylglycine Hydrolase(CGH) member from Shewanella loihica PV-4
ComponentsPenicillin V acylase-like protein
KeywordsHYDROLASE / Choloylglycine Hydrolase / BSH / PVA like / AHL activity
Function / homology: / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / hydrolase activity / 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.D. / Yadav, Y.
CitationJournal: To Be Published
Title: Unique Choloylglycine Hydrolase(CGH) member from Shewanella loihica PV-4
Authors: Philem, P.D. / Yadav, Y. / Prabune, A.A. / Ramasamy, S.
History
DepositionMar 3, 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


Theoretical massNumber of molelcules
Total (without water)75,8892
Polymers75,8892
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MALDI-MS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.397, 52.337, 140.068
Angle α, β, γ (deg.)90.00, 103.81, 90.00
Int Tables number5
Space group name H-MI121

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Components

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


Mass: 37944.449 Da / Num. of mol.: 2 / Fragment: UNP residues 27-359
Source method: isolated from a genetically manipulated source
Details: Marine bacteria / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.33 Å3/Da / Density % sol: 48.58 % / Description: Elongated needles
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: ELETTRA / Beamline: 5.2R / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 15, 2015
RadiationMonochromator: Double crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.5→89.43 Å / Num. obs: 109332 / % possible obs: 97.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8

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Processing

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

3hbc


Resolution: 1.5→89.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.275 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21616 5491 5 %RANDOM
Rwork0.19004 ---
obs0.19135 103814 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→89.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 0 172 5494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0195318
X-RAY DIFFRACTIONr_bond_other_d0.0060.024742
X-RAY DIFFRACTIONr_angle_refined_deg2.241.9387194
X-RAY DIFFRACTIONr_angle_other_deg1.146311060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07325.04250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85215910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8811522
X-RAY DIFFRACTIONr_chiral_restr0.1520.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025966
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021056
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_it1.4391.322662
X-RAY DIFFRACTIONr_mcbond_other1.4271.3192661
X-RAY DIFFRACTIONr_mcangle_it1.9721.9833324
X-RAY DIFFRACTIONr_mcangle_other1.9731.9843325
X-RAY DIFFRACTIONr_scbond_it2.7391.582656
X-RAY DIFFRACTIONr_scbond_other2.7381.582657
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9022.2623871
X-RAY DIFFRACTIONr_long_range_B_refined4.41915.855794
X-RAY DIFFRACTIONr_long_range_B_other4.4215.8085776
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
Rfree0.255 405 -
Rwork0.211 7551 -
obs--95.69 %

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