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- PDB-2d81: PHB depolymerase (S39A) complexed with R3HB trimer -

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Basic information

Entry
Database: PDB / ID: 2d81
TitlePHB depolymerase (S39A) complexed with R3HB trimer
ComponentsPHB depolymerase
KeywordsHYDROLASE / alpha/beta hydrolase fold / circular permutation
Function / homologypoly(3-hydroxybutyrate) depolymerase / Esterase, PHB depolymerase / Esterase PHB depolymerase / carboxylic ester hydrolase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / Chem-RB3 / Polyhydroxybutyrate depolymerase
Function and homology information
Biological speciesPenicillium funiculosum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsHisano, T. / Kasuya, K. / Saito, T. / Iwata, T. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of Polyhydroxybutyrate Depolymerase from Penicillium funiculosum Provides Insights into the Recognition and Degradation of Biopolyesters
Authors: Hisano, T. / Kasuya, K. / Tezuka, Y. / Ishii, N. / Kobayashi, T. / Shiraki, M. / Oroudjev, E. / Hansma, H. / Iwata, T. / Doi, Y. / Saito, T. / Miki, K.
History
DepositionNov 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: PHB depolymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0213
Polymers33,5101
Non-polymers5122
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.934, 48.863, 64.198
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PHB depolymerase


Mass: 33509.969 Da / Num. of mol.: 1 / Mutation: S39A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium funiculosum (fungus) / Strain: IFO 6345 / Gene: phaZ / Plasmid: pPICZaB / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H
References: UniProt: B2NHN2*PLUS, poly(3-hydroxybutyrate) depolymerase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-RB3 / (1R)-3-{[(1R)-3-METHOXY-1-METHYL-3-OXOPROPYL]OXY}-1-METHYL-3-OXOPROPYL (3R)-3-HYDROXYBUTANOATE / METHYL (3R)-3-{[(3R)-3-{[(3R)-3-HYDROXYBUTANOYL]OXY}BUTANOYL]OXY}BUTANOATE


Mass: 290.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.91 Å3/Da / Density % sol: 35.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.0M sodium chloride, 0.1M acetate-NaOH, 5% 1,4-dioxane, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2005 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→40.84 Å / Num. obs: 29362 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.9
Reflection shellResolution: 1.66→1.72 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 0.262 / % possible all: 89.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2D80

2d80


Resolution: 1.66→40.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1501929.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2930 10 %RANDOM
Rwork0.176 ---
obs0.176 29362 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.1321 Å2 / ksol: 0.385146 e/Å3
Displacement parametersBiso mean: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å23.68 Å2
2---1.61 Å20 Å2
3---3.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.66→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 33 237 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.422
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shellResolution: 1.66→1.76 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 461 10.5 %
Rwork0.207 3916 -
obs-4377 87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param_dihprotein.top_dih
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4r3hbtri2_prodrg.param_dihr3hbtri2_prodrg.top

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