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- PDB-8cxl: Structure of NapH3, a vanadium-dependent haloperoxidase homolog c... -

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Basic information

Entry
Database: PDB / ID: 8cxl
TitleStructure of NapH3, a vanadium-dependent haloperoxidase homolog catalyzing the stereospecific alpha-hydroxyketone rearrangement reaction in napyradiomycin biosynthesis
ComponentsNapH3
KeywordsBIOSYNTHETIC PROTEIN / Vanadium-dependent haloperoxidase / VHPO / alpha-hydroxyketone rearrangement / napyradiomycin
Biological speciesStreptomyces sp. CNQ-525 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsChen, P.Y.-T. / Chekan, J.R. / Moore, B.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI047818 United States
CitationJournal: Biochemistry / Year: 2022
Title: Structural Basis of Stereospecific Vanadium-Dependent Haloperoxidase Family Enzymes in Napyradiomycin Biosynthesis.
Authors: Chen, P.Y. / Adak, S. / Chekan, J.R. / Liscombe, D.K. / Miyanaga, A. / Bernhardt, P. / Diethelm, S. / Fielding, E.N. / George, J.H. / Miles, Z.D. / Murray, L.A.M. / Steele, T.S. / Winter, J. ...Authors: Chen, P.Y. / Adak, S. / Chekan, J.R. / Liscombe, D.K. / Miyanaga, A. / Bernhardt, P. / Diethelm, S. / Fielding, E.N. / George, J.H. / Miles, Z.D. / Murray, L.A.M. / Steele, T.S. / Winter, J.M. / Noel, J.P. / Moore, B.S.
History
DepositionMay 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NapH3
B: NapH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6105
Polymers103,5262
Non-polymers843
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-27 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.447, 96.095, 72.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 11 through 26 or resid 29...
d_2ens_1(chain "B" and (resid 11 through 48 or resid 50...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROTHRA7 - 22
d_12ens_1GLYTRPA25 - 44
d_13ens_1THRGLYA48 - 163
d_14ens_1PROTYRA167 - 174
d_15ens_1PROTYRA178 - 230
d_16ens_1ASPALAA232 - 292
d_17ens_1ALAVALA296 - 338
d_18ens_1HISVALA342 - 482
d_21ens_1PROTRPB1 - 36
d_22ens_1THRGLYB40 - 155
d_23ens_1PROTYRB159 - 166
d_24ens_1PROTYRB168 - 220
d_25ens_1ASPALAB224 - 284
d_26ens_1ALAVALB288 - 330
d_27ens_1HISVALB334 - 474

NCS oper: (Code: givenMatrix: (-0.78868324926, 0.567624344346, -0.2361807275), (0.567478778047, 0.524322176392, -0.63486541236), (-0.236530270374, -0.634735266902, -0.735638887055)Vector: -46. ...NCS oper: (Code: given
Matrix: (-0.78868324926, 0.567624344346, -0.2361807275), (0.567478778047, 0.524322176392, -0.63486541236), (-0.236530270374, -0.634735266902, -0.735638887055)
Vector: -46.0964248139, 13.4344949177, -9.12987406766)

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Components

#1: Protein NapH3


Mass: 51762.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CNQ-525 (bacteria) / Gene: napH3 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (Bis-Tris) pH 6.5, 0.2 M magnesium chloride , 17% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999912 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 75852 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 28.55 Å2 / Rsym value: 0.096 / Net I/σ(I): 14.8
Reflection shellResolution: 1.98→2.1 Å / Num. unique obs: 12034 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3w36

3w36


Resolution: 1.98→29.64 Å / SU ML: 0.1973 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 19.1463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 3793 5 %
Rwork0.1826 72049 -
obs0.1835 75842 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.55 Å2
Refinement stepCycle: LAST / Resolution: 1.98→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7171 0 3 514 7688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00337454
X-RAY DIFFRACTIONf_angle_d0.645410205
X-RAY DIFFRACTIONf_chiral_restr0.04291084
X-RAY DIFFRACTIONf_plane_restr0.00471378
X-RAY DIFFRACTIONf_dihedral_angle_d20.69632644
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.482251324203 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.010.34241380.29442617X-RAY DIFFRACTION97.42
2.01-2.030.25441360.24852599X-RAY DIFFRACTION100
2.03-2.060.2681400.23292651X-RAY DIFFRACTION100
2.06-2.090.24521390.22042624X-RAY DIFFRACTION99.96
2.09-2.120.2151390.21292645X-RAY DIFFRACTION99.96
2.12-2.150.27521370.21032617X-RAY DIFFRACTION100
2.15-2.190.22381410.19992686X-RAY DIFFRACTION100
2.19-2.230.23471390.20862628X-RAY DIFFRACTION100
2.23-2.270.25581380.20592633X-RAY DIFFRACTION100
2.27-2.310.21091420.19532672X-RAY DIFFRACTION100
2.31-2.360.22451370.19752623X-RAY DIFFRACTION99.96
2.36-2.410.22541410.19772662X-RAY DIFFRACTION99.96
2.41-2.470.21261390.1942639X-RAY DIFFRACTION99.96
2.47-2.530.21271390.19232644X-RAY DIFFRACTION99.96
2.53-2.60.19181390.19032661X-RAY DIFFRACTION100
2.6-2.670.23971420.19322675X-RAY DIFFRACTION99.96
2.67-2.760.21861390.19692650X-RAY DIFFRACTION100
2.76-2.860.22331400.19462654X-RAY DIFFRACTION100
2.86-2.970.21671390.20312655X-RAY DIFFRACTION99.96
2.97-3.110.20941430.20622703X-RAY DIFFRACTION99.96
3.11-3.270.23091400.20552666X-RAY DIFFRACTION100
3.27-3.470.20711420.19492689X-RAY DIFFRACTION100
3.47-3.740.20981420.17872695X-RAY DIFFRACTION99.96
3.74-4.120.15931400.15022694X-RAY DIFFRACTION99.82
4.12-4.710.14481450.13952731X-RAY DIFFRACTION99.9
4.71-5.930.15731450.14572762X-RAY DIFFRACTION99.83
5.93-29.640.14931520.14592874X-RAY DIFFRACTION99.47

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