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- PDB-5mly: Closed loop conformation of PhaZ7 Y105E mutant -

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Basic information

Entry
Database: PDB / ID: 5mly
TitleClosed loop conformation of PhaZ7 Y105E mutant
ComponentsPHB depolymerase PhaZ7
KeywordsHYDROLASE / depolymerase / conformational change / biopolymer degradation
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 / FOURIER SYNTHESIS / Resolution: 1.598 Å
AuthorsKellici, T. / Mavromoustakos, T. / Jendrossek, D. / Papageorgiou, A.C.
Citation
Journal: Proteins / Year: 2017
Title: Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.
Authors: Kellici, T.F. / Mavromoustakos, T. / Jendrossek, D. / Papageorgiou, A.C.
#1: 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.
#2: 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
DepositionDec 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 17, 2024Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHB depolymerase PhaZ7
B: PHB depolymerase PhaZ7


Theoretical massNumber of molelcules
Total (without water)74,5482
Polymers74,5482
Non-polymers00
Water21,6541202
1
A: PHB depolymerase PhaZ7


Theoretical massNumber of molelcules
Total (without water)37,2741
Polymers37,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHB depolymerase PhaZ7


Theoretical massNumber of molelcules
Total (without water)37,2741
Polymers37,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.410, 199.760, 43.960
Angle α, β, γ (deg.)90.00, 114.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHB depolymerase PhaZ7


Mass: 37274.086 Da / Num. of mol.: 2 / Mutation: Y105E
Source method: isolated from a genetically manipulated source
Details: No electron density for the last C-ter residues / Source: (gene. exp.) Paucimonas lemoignei (bacteria) / Gene: phaZ7 / Production host: Bacillus subtilis (bacteria) / Variant (production host): WB800 / References: UniProt: Q939Q9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1202 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M NaCl, 0.1 M MES, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.598→19.4 Å / Num. obs: 78330 / % possible obs: 91.3 % / Redundancy: 1.8 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.999 / Rsym value: 0.03 / Net I/σ(I): 25.8
Reflection shellResolution: 1.598→1.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.8 / CC1/2: 0.938 / % possible all: 77.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4brs

4brs


Resolution: 1.598→19.4 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 14.23
RfactorNum. reflection% reflection
Rfree0.1566 3909 4.99 %
Rwork0.1281 --
obs0.1295 78327 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.598→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 0 1202 6292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085253
X-RAY DIFFRACTIONf_angle_d0.8787154
X-RAY DIFFRACTIONf_dihedral_angle_d11.9082996
X-RAY DIFFRACTIONf_chiral_restr0.07751
X-RAY DIFFRACTIONf_plane_restr0.006928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5984-1.61790.21291040.18031915X-RAY DIFFRACTION67
1.6179-1.63840.22031320.17162555X-RAY DIFFRACTION88
1.6384-1.65990.18851280.16032579X-RAY DIFFRACTION88
1.6599-1.68260.19181280.15452554X-RAY DIFFRACTION89
1.6826-1.70670.19211390.15742631X-RAY DIFFRACTION90
1.7067-1.73210.21931340.15082611X-RAY DIFFRACTION90
1.7321-1.75920.22221380.14912619X-RAY DIFFRACTION91
1.7592-1.7880.18031430.152666X-RAY DIFFRACTION91
1.788-1.81880.19181340.14852657X-RAY DIFFRACTION93
1.8188-1.85190.18141430.14492664X-RAY DIFFRACTION92
1.8519-1.88740.18791450.14662722X-RAY DIFFRACTION93
1.8874-1.92590.17941440.14142676X-RAY DIFFRACTION93
1.9259-1.96780.1821400.13512715X-RAY DIFFRACTION94
1.9678-2.01350.15041370.13422733X-RAY DIFFRACTION94
2.0135-2.06380.16881420.13092757X-RAY DIFFRACTION94
2.0638-2.11950.15981450.12882740X-RAY DIFFRACTION95
2.1195-2.18180.13881570.12072771X-RAY DIFFRACTION95
2.1818-2.25210.16941350.11722708X-RAY DIFFRACTION95
2.2521-2.33250.16551500.12062774X-RAY DIFFRACTION95
2.3325-2.42570.1371440.11862801X-RAY DIFFRACTION96
2.4257-2.53590.16171390.12062712X-RAY DIFFRACTION95
2.5359-2.66930.16041440.12032740X-RAY DIFFRACTION95
2.6693-2.83610.1321500.11822745X-RAY DIFFRACTION94
2.8361-3.05430.13771350.12122740X-RAY DIFFRACTION94
3.0543-3.36020.14411490.11892759X-RAY DIFFRACTION94
3.3602-3.84310.14731430.11272656X-RAY DIFFRACTION91
3.8431-4.82960.10931430.10082588X-RAY DIFFRACTION89
4.8296-19.42140.14351440.14362630X-RAY DIFFRACTION90

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