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- PDB-7v4o: Unique non-heme hydroxylase in biosynthesis of nucleoside antibio... -

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Basic information

Entry
Database: PDB / ID: 7v4o
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 / 3,6,9,12,15-PENTAOXAHEPTADECANE / Beta-hydroxylase
Function and homology information
Biological speciesStreptomyces sp. MK730-62F2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
B: Beta-hydroxylase
A: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5104
Polymers42,0092
Non-polymers5012
Water7,584421
1
A: Beta-hydroxylase
hetero molecules

B: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5104
Polymers42,0092
Non-polymers5012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3080 Å2
ΔGint-14 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.839, 39.035, 76.591
Angle α, β, γ (deg.)90.00, 119.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-hydroxylase


Mass: 21004.650 Da / Num. of mol.: 2 / Mutation: R170A
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-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Lithium sulfate monohydrate 0.1M ADA pH 6.5 12% PEG 4K 2% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→25.03 Å / Num. obs: 46721 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.99 / Net I/σ(I): 32.3
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 4689 / CC1/2: 0.99

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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: 1.65→25.03 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 1999 4.28 %
Rwork0.1803 --
obs0.1817 46715 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→25.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 34 421 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063002
X-RAY DIFFRACTIONf_angle_d1.034064
X-RAY DIFFRACTIONf_dihedral_angle_d22.852430
X-RAY DIFFRACTIONf_chiral_restr0.063438
X-RAY DIFFRACTIONf_plane_restr0.006530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.22711300.19893060X-RAY DIFFRACTION94
1.69-1.740.24321490.19663167X-RAY DIFFRACTION100
1.74-1.790.23091420.19363216X-RAY DIFFRACTION100
1.79-1.840.21451440.19043214X-RAY DIFFRACTION100
1.84-1.910.21711460.18643200X-RAY DIFFRACTION99
1.91-1.990.20921440.18933210X-RAY DIFFRACTION100
1.99-2.080.23091410.19333198X-RAY DIFFRACTION99
2.08-2.190.22351450.18563196X-RAY DIFFRACTION99
2.19-2.320.21621430.18643244X-RAY DIFFRACTION100
2.32-2.50.24721470.18673215X-RAY DIFFRACTION100
2.5-2.750.23361440.18773262X-RAY DIFFRACTION100
2.75-3.150.19891450.1833244X-RAY DIFFRACTION100
3.15-3.970.18661390.16383240X-RAY DIFFRACTION98

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