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- PDB-7v4n: Unique non-heme hydroxylase in biosynthesis of nucleoside antibio... -

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Basic information

Entry
Database: PDB / ID: 7v4n
TitleUnique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction
ComponentsBeta-hydroxylase
KeywordsANTIBIOTIC / caprazamycin / MraY / beta-hydroxylase
Function / homologyB-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / : / Beta-hydroxylase
Function and homology information
Biological speciesStreptomyces sp. MK730-62F2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, T.L. / Saeid, M.Z.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)108-2113-M-001-021-MY3 Taiwan
CitationJournal: Commun Chem / Year: 2022
Title: beta-Hydroxylation of alpha-amino-beta-hydroxylbutanoyl-glycyluridine catalyzed by a nonheme hydroxylase ensures the maturation of caprazamycin
Authors: Zadeh, S.M. / Chen, M.H. / Wang, Z.C. / Astani, E.K. / Lo, I.W. / Lin, K.H. / Hsu, N.S. / Adhikari, K. / Lyu, S.Y. / Tsai, H.Y. / Terasawa, Y. / Yabe, M. / Yamamoto, K. / Ichikawa, S. / Li, T.L.
History
DepositionAug 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-hydroxylase
B: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2934
Polymers42,1822
Non-polymers1122
Water79344
1
A: Beta-hydroxylase
hetero molecules

B: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2934
Polymers42,1822
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1620 Å2
ΔGint-14 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.243, 82.243, 104.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-201-

FE

21B-315-

HOH

31B-316-

HOH

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Components

#1: Protein Beta-hydroxylase


Mass: 21090.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. MK730-62F2 (bacteria) / Gene: cpz10
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1 (others)
References: UniProt: C4NCJ7
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.2M Sodium chloride 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→29.83 Å / Num. obs: 18830 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.874 / Net I/σ(I): 24.9
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 18812 / CC1/2: 0.874

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p7x

4p7x


Resolution: 2.2→29.83 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 1876 10 %
Rwork0.1868 --
obs0.1932 18757 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 2 44 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152888
X-RAY DIFFRACTIONf_angle_d1.7573929
X-RAY DIFFRACTIONf_dihedral_angle_d21.441395
X-RAY DIFFRACTIONf_chiral_restr0.076422
X-RAY DIFFRACTIONf_plane_restr0.01520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.29661410.22311272X-RAY DIFFRACTION100
2.26-2.330.30651420.22611271X-RAY DIFFRACTION100
2.33-2.40.30631400.2271266X-RAY DIFFRACTION100
2.4-2.490.30181430.22331282X-RAY DIFFRACTION100
2.49-2.590.31031400.21671265X-RAY DIFFRACTION100
2.59-2.70.26771430.22761288X-RAY DIFFRACTION100
2.7-2.850.32041420.21781278X-RAY DIFFRACTION100
2.85-3.020.29811440.2271292X-RAY DIFFRACTION100
3.03-3.260.27751430.21081294X-RAY DIFFRACTION100
3.26-3.590.26641450.18671302X-RAY DIFFRACTION100
3.59-4.10.22251460.16041309X-RAY DIFFRACTION100
4.1-5.160.17981490.13411340X-RAY DIFFRACTION100

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