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- PDB-6jjs: Crystal structure of an enzyme from Penicillium herquei in condition2 -

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Basic information

Entry
Database: PDB / ID: 6jjs
TitleCrystal structure of an enzyme from Penicillium herquei in condition2
ComponentsPhnH
KeywordsTRANSFERASE / prenyltransferase
Function / homologyProtein of unknown function (DUF3237) / Lyases / lyase activity / ACETATE ION / Hydroalkoxylation enzyme phnH
Function and homology information
Biological speciesPenicillium herquei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsFen, Y. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure and proposed mechanism of an enantioselective hydroalkoxylation enzyme from Penicillium herquei.
Authors: Feng, Y. / Yu, X. / Huang, J.W. / Liu, W. / Li, Q. / Hu, Y. / Yang, Y. / Chen, Y. / Jin, J. / Li, H. / Chen, C.C. / Guo, R.T.
History
DepositionFeb 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: PhnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2825
Polymers16,0461
Non-polymers2364
Water3,135174
1
A: PhnH
hetero molecules

A: PhnH
hetero molecules

A: PhnH
hetero molecules

A: PhnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,12820
Polymers64,1844
Non-polymers94516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_664-y+1,-x+1,-z-1/31
Buried area12850 Å2
ΔGint-62 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.617, 74.617, 108.926
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein PhnH / Prenylcyclase


Mass: 16045.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium herquei (fungus) / Gene: phnH / Plasmid: pET-46EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S6PUA4
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.73 Å3/Da / Density % sol: 54.91 % / Mosaicity: 0.431 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG4000, 0.1 M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 26, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→25 Å / Num. obs: 23321 / % possible obs: 99.2 % / Redundancy: 20 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.011 / Rrim(I) all: 0.05 / Χ2: 1.124 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.6820.80.46322860.9910.1030.4741.19100
1.68-1.7520.90.30722970.9960.0680.3151.158100
1.75-1.8221.30.20522900.9980.0450.211.107100
1.82-1.9221.40.15823140.9990.0350.1621.117100
1.92-2.0421.50.10223050.9990.0220.1041.21499.9
2.04-2.221.50.07623270.9990.0170.0780.94599.9
2.2-2.4221.40.06723390.9990.0150.0691.004100
2.42-2.7721.30.07423570.9980.0160.0761.39199.9
2.77-3.4920.80.045238210.010.0461.06999.3
3.491-2518.20.03424240.9990.0080.0351.03394

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5O

3c5o


Resolution: 1.62→24.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.565 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20229 1116 4.8 %RANDOM
Rwork0.18543 ---
obs0.18627 22115 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.539 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20.57 Å2-0 Å2
2--1.15 Å20 Å2
3----3.72 Å2
Refinement stepCycle: 1 / Resolution: 1.62→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 16 174 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131034
X-RAY DIFFRACTIONr_bond_other_d00.017918
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6461415
X-RAY DIFFRACTIONr_angle_other_deg1.4581.5632130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.265129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5624.4949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17515146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.926153
X-RAY DIFFRACTIONr_chiral_restr0.1120.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021184
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02205
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8593.311523
X-RAY DIFFRACTIONr_mcbond_other2.5613.292518
X-RAY DIFFRACTIONr_mcangle_it3.7884.933647
X-RAY DIFFRACTIONr_mcangle_other3.8114.935648
X-RAY DIFFRACTIONr_scbond_it4.8013.82511
X-RAY DIFFRACTIONr_scbond_other4.8023.822512
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5355.554769
X-RAY DIFFRACTIONr_long_range_B_refined7.27166.4184267
X-RAY DIFFRACTIONr_long_range_B_other7.19465.3944110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 69 -
Rwork0.246 1616 -
obs--99.94 %

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