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- PDB-3hbc: Crystal Structure of Choloylglycine Hydrolase from Bacteroides th... -

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Basic information

Entry
Database: PDB / ID: 3hbc
TitleCrystal Structure of Choloylglycine Hydrolase from Bacteroides thetaiotaomicron VPI
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / alpha-beta sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / 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 speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.269 Å
AuthorsKim, Y. / Bigelow, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Choloylglycine Hydrolase from Bacteroides thetaiotaomicron VPI
Authors: Kim, Y. / Bigelow, L. / Buck, K. / Joachimiak, A.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9989
Polymers36,3811
Non-polymers6178
Water2,126118
1
A: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,99236
Polymers145,5264
Non-polymers2,46732
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x,-y+1/2,-z+3/21
crystal symmetry operation11_556-x+1/2,y,-z+3/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area15180 Å2
ΔGint2 kcal/mol
Surface area46800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.281, 135.208, 167.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-21-

HOH

21A-367-

HOH

31A-409-

HOH

Detailstetramer, x,y,z -x+1/2,y,-z+3/2 ; translation +1 in z axis x,-y+1/2,-z+3/2 -x+1/2,-y+1/2,z; translation +1 in Z axis

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Components

#1: Protein Choloylglycine hydrolase


Mass: 36381.418 Da / Num. of mol.: 1 / Fragment: CGH 26-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2086 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: Q8A600
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M Magnesium chloride, 0.1 M HEPES 7.5, 30 % v/v Polyethylene glycol monomethyl ether 550, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→42.39 Å / Num. obs: 19843 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 50.22 Å2 / Rsym value: 0.11 / Net I/σ(I): 11.8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 949 / Rsym value: 0.849 / % possible all: 96.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.269→42.39 Å / SU ML: 1.02 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1000 5.14 %random
Rwork0.191 ---
all0.193 19461 --
obs0.193 19461 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.185 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8606 Å2-0 Å20 Å2
2---7.5759 Å2-0 Å2
3---1.7153 Å2
Refinement stepCycle: LAST / Resolution: 2.269→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 40 118 2591
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.195
X-RAY DIFFRACTIONf_dihedral_angle_d18.647
X-RAY DIFFRACTIONfhirality0.076
X-RAY DIFFRACTIONflanarity0.004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2692-2.38880.34551370.28462380251791
2.3888-2.53850.30391510.260726302781100
2.5385-2.73450.29111320.232126622794100
2.7345-3.00960.26071490.215426422791100
3.0096-3.44490.23761340.192426842818100
3.4449-4.33950.18721520.161426902842100
4.3395-42.40230.21141450.1722773291899

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