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- PDB-4bvj: Structure of Y105A mutant of PhaZ7 PHB depolymerase -

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Basic information

Entry
Database: PDB / ID: 4bvj
TitleStructure of Y105A mutant of PhaZ7 PHB depolymerase
ComponentsPHB DEPOLYMERASE PHAZ7
KeywordsHYDROLASE / CATALYTIC TRIAD / BIOPOLYMER BINDING
Function / homology
Function and homology information


lipase activity / lipid catabolic process
Similarity search - Function
Lipase EstA/Esterase EstB / Lipase (class 2) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPAUCIMONAS LEMOIGNEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsHermawan, S. / Subedi, B. / Papageorgiou, A.C. / Jendrossek, D.
Citation
Journal: Mol.Microbiol. / Year: 2013
Title: Biochemical Analysis and Structure Determination of Paucimonas Lemoignei Poly(3-Hydroxybutyrate) (Phb) Depolymerase Phaz7 Muteins Reveal the Phb Binding Site and Details of Substrate-Enzyme Interactions.
Authors: Jendrossek, D. / Hermawan, S. / Subedi, B. / Papageorgiou, A.C.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Structural Basis of Poly(3-Hydroxybutyrate) Hydrolysis by Phaz7 Depolymerase from Paucimonas Lemoignei.
Authors: Papageorgiou, A.C. / Hermawan, S. / Singh, C.B. / Jendrossek, D.
History
DepositionJun 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHB DEPOLYMERASE PHAZ7
B: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5875
Polymers72,5182
Non-polymers693
Water22,1581230
1
A: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3053
Polymers36,2591
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2822
Polymers36,2591
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.370, 200.050, 44.180
Angle α, β, γ (deg.)90.00, 114.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHB DEPOLYMERASE PHAZ7


Mass: 36259.012 Da / Num. of mol.: 2 / Fragment: RESIDUES 39-380 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PAUCIMONAS LEMOIGNEI (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): WB800
References: UniProt: Q939Q9, poly(3-hydroxybutyrate) depolymerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1230 / 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: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: VAPOUR DIFFUSION HANGING DROP, PROTEIN CONCENTRATION 10 MG/ML, 0.1 M NAOAC (PH 5.0), 0.2 M NH4CL, 20% W/V PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 84896 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BRS

4brs


Resolution: 1.599→20.005 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 4245 5 %
Rwork0.1553 --
obs0.1569 84894 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.599→20.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5072 0 3 1230 6305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085251
X-RAY DIFFRACTIONf_angle_d1.0827136
X-RAY DIFFRACTIONf_dihedral_angle_d12.4911774
X-RAY DIFFRACTIONf_chiral_restr0.074755
X-RAY DIFFRACTIONf_plane_restr0.005929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5991-1.61720.31421290.25812453X-RAY DIFFRACTION92
1.6172-1.63620.2931430.25182711X-RAY DIFFRACTION99
1.6362-1.65620.26811430.23032720X-RAY DIFFRACTION99
1.6562-1.67710.25011380.21612632X-RAY DIFFRACTION99
1.6771-1.69920.25941430.21612710X-RAY DIFFRACTION99
1.6992-1.72250.2411430.20232727X-RAY DIFFRACTION99
1.7225-1.74710.23331390.20142625X-RAY DIFFRACTION99
1.7471-1.77310.23221430.19462721X-RAY DIFFRACTION99
1.7731-1.80080.24741420.19812697X-RAY DIFFRACTION99
1.8008-1.83030.22731400.19252664X-RAY DIFFRACTION99
1.8303-1.86180.19651440.18012734X-RAY DIFFRACTION100
1.8618-1.89570.23021410.17552677X-RAY DIFFRACTION99
1.8957-1.93210.22941430.1692726X-RAY DIFFRACTION99
1.9321-1.97150.20581410.16032676X-RAY DIFFRACTION99
1.9715-2.01430.21011430.15792724X-RAY DIFFRACTION100
2.0143-2.06120.21551420.15782687X-RAY DIFFRACTION100
2.0612-2.11260.18671440.15512739X-RAY DIFFRACTION99
2.1126-2.16970.18791410.14472671X-RAY DIFFRACTION100
2.1697-2.23350.16031410.13952696X-RAY DIFFRACTION100
2.2335-2.30550.18751450.14542739X-RAY DIFFRACTION99
2.3055-2.38770.17781380.14642633X-RAY DIFFRACTION99
2.3877-2.48320.18391430.14832723X-RAY DIFFRACTION99
2.4832-2.59590.19561450.1482743X-RAY DIFFRACTION99
2.5959-2.73250.16051410.14782689X-RAY DIFFRACTION99
2.7325-2.90320.15961420.14482685X-RAY DIFFRACTION99
2.9032-3.12660.17511420.14342700X-RAY DIFFRACTION99
3.1266-3.43980.17361420.13412697X-RAY DIFFRACTION99
3.4398-3.93430.14751400.12132670X-RAY DIFFRACTION98
3.9343-4.94440.13641420.11912692X-RAY DIFFRACTION99
4.9444-20.00660.17181420.14872688X-RAY DIFFRACTION98

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