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- PDB-5mlx: Open loop conformation of PhaZ7 Y105E mutant -

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Basic information

Entry
Database: PDB / ID: 5mlx
TitleOpen 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: 1.6 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7349
Polymers74,5482
Non-polymers1867
Water20,4291134
1
A: PHB depolymerase PhaZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4146
Polymers37,2741
Non-polymers1405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHB depolymerase PhaZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3203
Polymers37,2741
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.300, 199.500, 44.400
Angle α, β, γ (deg.)90.00, 114.20, 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
Source method: isolated from a genetically manipulated source
Details: No electron density for the last C-terminal residues
Source: (gene. exp.) Paucimonas lemoignei (bacteria) / Gene: phaZ7 / Production host: Bacillus subtilis (bacteria) / Variant (production host): WB800 / References: UniProt: Q939Q9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1134 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M NH4Cl, O.1 M sodium acetate, 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: 1.6→23.1 Å / Num. obs: 77568 / % possible obs: 89.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 9.4 Å2 / CC1/2: 0.998 / Rsym value: 0.04 / Net I/σ(I): 18.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7.1 / CC1/2: 0.959 / % possible all: 91.2

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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: 1.6→23.082 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 12.55
RfactorNum. reflection% reflection
Rfree0.152 3836 5 %
Rwork0.126 --
obs0.1273 76716 88.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4993 0 7 1134 6134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085189
X-RAY DIFFRACTIONf_angle_d0.8827072
X-RAY DIFFRACTIONf_dihedral_angle_d12.3032981
X-RAY DIFFRACTIONf_chiral_restr0.14749
X-RAY DIFFRACTIONf_plane_restr0.006915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5968-1.6170.18441150.16082169X-RAY DIFFRACTION72
1.617-1.63830.17591480.14772828X-RAY DIFFRACTION93
1.6383-1.66070.17541480.1412809X-RAY DIFFRACTION92
1.6607-1.68440.18571460.13482766X-RAY DIFFRACTION93
1.6844-1.70950.15691500.13332864X-RAY DIFFRACTION93
1.7095-1.73620.16841480.1322795X-RAY DIFFRACTION92
1.7362-1.76470.17141460.13482777X-RAY DIFFRACTION92
1.7647-1.79510.17471490.13162842X-RAY DIFFRACTION92
1.7951-1.82770.16831430.13522702X-RAY DIFFRACTION92
1.8277-1.86290.17451490.13232837X-RAY DIFFRACTION92
1.8629-1.90090.14881430.12892725X-RAY DIFFRACTION91
1.9009-1.94220.16281500.12642835X-RAY DIFFRACTION92
1.9422-1.98740.14761420.12332703X-RAY DIFFRACTION91
1.9874-2.0370.1551470.12242796X-RAY DIFFRACTION91
2.037-2.09210.15491420.12052704X-RAY DIFFRACTION90
2.0921-2.15360.15281440.11882724X-RAY DIFFRACTION90
2.1536-2.22310.16641450.11862772X-RAY DIFFRACTION90
2.2231-2.30240.13611430.11542706X-RAY DIFFRACTION89
2.3024-2.39450.13921400.11962667X-RAY DIFFRACTION88
2.3945-2.50340.12591410.11572671X-RAY DIFFRACTION88
2.5034-2.63520.15641420.11392690X-RAY DIFFRACTION88
2.6352-2.80.12961390.12152648X-RAY DIFFRACTION87
2.8-3.01580.16991380.12362616X-RAY DIFFRACTION86
3.0158-3.31850.16681370.12372613X-RAY DIFFRACTION86
3.3185-3.79690.13141370.12272601X-RAY DIFFRACTION85
3.7969-4.77670.12741330.1182531X-RAY DIFFRACTION83
4.7767-23.08450.15081310.15442489X-RAY DIFFRACTION81

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