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- PDB-7v4p: Unique non-heme hydroxylase in biosynthesis of nucleoside antibio... -

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Basic information

Entry
Database: PDB / ID: 7v4p
TitleUnique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction
ComponentsBeta-hydroxylase
KeywordsANTIBIOTIC / caprazamycin / MraY / beta-hydroxylase
Function / homologyIsopenicillin N synthase-like superfamily / metal ion binding / : / Beta-hydroxylase
Function and homology information
Biological speciesStreptomyces sp. MK730-62F2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)45,5474
Polymers45,4352
Non-polymers1122
Water2,018112
1
A: Beta-hydroxylase
hetero molecules

B: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5474
Polymers45,4352
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1610 Å2
ΔGint-15 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.083, 82.083, 104.172
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-346-

HOH

31B-351-

HOH

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Components

#1: Protein Beta-hydroxylase


Mass: 22717.574 Da / Num. of mol.: 2 / Mutation: D117A
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.: 112 / 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: 2.08 Å3/Da / Density % sol: 36.3 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium acetate 0.1M Bis Tris propane pH 6.5 20 % W/V PEG 3350

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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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→26.46 Å / Num. obs: 26710 / % possible obs: 100 % / Redundancy: 15.7 % / CC1/2: 0.939 / Net I/σ(I): 36.9
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 26733 / CC1/2: 0.939

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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: 1.95→26.46 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 3013 7.53 %
Rwork0.1877 --
obs0.1917 26621 80.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→26.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 2 112 2854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112881
X-RAY DIFFRACTIONf_angle_d1.273917
X-RAY DIFFRACTIONf_dihedral_angle_d24.842394
X-RAY DIFFRACTIONf_chiral_restr0.066420
X-RAY DIFFRACTIONf_plane_restr0.007519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.3093850.27051058X-RAY DIFFRACTION51
1.98-2.010.2699910.24121105X-RAY DIFFRACTION53
2.01-2.050.3045880.23811092X-RAY DIFFRACTION53
2.05-2.080.2472900.23251096X-RAY DIFFRACTION53
2.08-2.120.2999880.23871091X-RAY DIFFRACTION53
2.12-2.170.3116910.23621122X-RAY DIFFRACTION53
2.17-2.210.2839920.22351146X-RAY DIFFRACTION55
2.21-2.260.286990.23571237X-RAY DIFFRACTION59
2.27-2.320.29161120.21611420X-RAY DIFFRACTION68
2.32-2.380.25881370.21911665X-RAY DIFFRACTION80
2.38-2.450.2711640.20342002X-RAY DIFFRACTION96
2.45-2.530.27191690.19782071X-RAY DIFFRACTION100
2.53-2.620.25781760.19912095X-RAY DIFFRACTION100
2.62-2.730.28891690.19752099X-RAY DIFFRACTION100
2.73-2.850.26111730.21172084X-RAY DIFFRACTION100
2.85-30.23961700.20542077X-RAY DIFFRACTION100
3-3.190.27871640.2082097X-RAY DIFFRACTION100
3.19-3.440.28491730.18992083X-RAY DIFFRACTION100
3.44-3.780.20191730.16932088X-RAY DIFFRACTION100
3.78-4.330.18071670.14362098X-RAY DIFFRACTION100
4.33-5.440.17451750.1342078X-RAY DIFFRACTION100

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