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- PDB-6fxd: Crystal structure of MupZ from Pseudomonas fluorescens -

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Basic information

Entry
Database: PDB / ID: 6fxd
TitleCrystal structure of MupZ from Pseudomonas fluorescens
ComponentsMupZ
KeywordsBIOSYNTHETIC PROTEIN / epoxide hydrolase
Function / homologyDimeric alpha-beta barrel / MupZ
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWang, L. / Parnell, A. / Williams, C. / Bakar, N.A. / van der Kamp, M.W. / Simpson, T.J. / Race, P.R. / Crump, M.P. / Willis, C.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L01386X/1 United Kingdom
CitationJournal: Nat Catal / Year: 2018
Title: A Rieske oxygenase/epoxide hydrolase-catalysed reaction cascade creates oxygen heterocycles in mupirocin biosynthesis
Authors: Wang, L. / Parnell, A. / Williams, C. / Bakar, N.A. / van der Kamp, M.W. / Simpson, T.J. / Race, P.R. / Crump, M.P. / Willis, C.L.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MupZ
B: MupZ


Theoretical massNumber of molelcules
Total (without water)32,3572
Polymers32,3572
Non-polymers00
Water2,360131
1
A: MupZ
B: MupZ

A: MupZ
B: MupZ


Theoretical massNumber of molelcules
Total (without water)64,7144
Polymers64,7144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_858-x+3,y,-z+31
Buried area9430 Å2
ΔGint-43 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.330, 80.090, 78.820
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-255-

HOH

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Components

#1: Protein MupZ


Mass: 16178.448 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: mupZ / Production host: Escherichia coli (E. coli) / References: UniProt: H7CRF0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM amino acids II, 0.1 M MOPSO, Bis-Tris pH 6.5 and 25% w/v PEG 4000, 40% w/v 1,2,6-hexanetriol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→31.233 Å / Num. all: 147200 / Num. obs: 45031 / % possible obs: 98.63 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.04094 / Rpim(I) all: 0.02652 / Rrim(I) all: 0.04894 / Net I/σ(I): 13.21
Reflection shellResolution: 1.45→1.502 Å

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Processing

Software
NameClassification
GDAdata collection
PDB_EXTRACTdata extraction
PHENIXmodel building
PHENIXrefinement
MOLREPphasing
PHASERphasing
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dpo

4dpo


Resolution: 1.45→31.233 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.1947 2279 5.06 %
Rwork0.1607 --
obs0.1624 45018 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→31.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 0 131 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062069
X-RAY DIFFRACTIONf_angle_d0.7812795
X-RAY DIFFRACTIONf_dihedral_angle_d3.0681014
X-RAY DIFFRACTIONf_chiral_restr0.078287
X-RAY DIFFRACTIONf_plane_restr0.004370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4501-1.48160.26021350.23472652X-RAY DIFFRACTION98
1.4816-1.5160.30691400.2332672X-RAY DIFFRACTION98
1.516-1.5540.27161470.21292647X-RAY DIFFRACTION98
1.554-1.5960.2391410.19672599X-RAY DIFFRACTION97
1.596-1.64290.23841500.1992628X-RAY DIFFRACTION98
1.6429-1.6960.23711500.18292678X-RAY DIFFRACTION99
1.696-1.75660.22081560.17232671X-RAY DIFFRACTION99
1.7566-1.82690.1981330.15262696X-RAY DIFFRACTION100
1.8269-1.910.16561410.14782702X-RAY DIFFRACTION100
1.91-2.01070.19631420.14442697X-RAY DIFFRACTION100
2.0107-2.13670.18361760.14572653X-RAY DIFFRACTION99
2.1367-2.30160.20441420.14632693X-RAY DIFFRACTION99
2.3016-2.53310.2044960.15862749X-RAY DIFFRACTION100
2.5331-2.89940.19051410.16222671X-RAY DIFFRACTION98
2.8994-3.65210.17751410.15372664X-RAY DIFFRACTION98
3.6521-31.23980.18751480.16262667X-RAY DIFFRACTION96

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