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- PDB-7v4m: Unique non-heme hydroxylase in biosynthesis of nucleoside antibio... -

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Basic information

Entry
Database: PDB / ID: 7v4m
TitleUnique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction
ComponentsBeta-hydroxylase
KeywordsANTIBIOTIC / caprazamycin / MraY / beta-hydroxylase
Function / homology
Function and homology information


B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / PHOSPHATE ION / Beta-hydroxylase
Similarity search - Component
Biological speciesStreptomyces sp. MK730-62F2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4836
Polymers21,0911
Non-polymers3925
Water2,432135
1
B: Beta-hydroxylase
hetero molecules

B: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,96512
Polymers42,1822
Non-polymers78410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3280 Å2
ΔGint-83 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.184, 77.568, 68.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-302-

K

21B-532-

HOH

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Beta-hydroxylase


Mass: 21090.766 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Calcium acetate 0.1M MES pH 6.4 9% V/V PEG 4K 10 mg

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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: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→19.86 Å / Num. obs: 16089 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.78 / Net I/σ(I): 23.6
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 1596 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V4F

7v4f


Resolution: 1.9→19.86 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1557 10.08 %
Rwork0.1865 --
obs0.1911 15444 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 18 135 1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071422
X-RAY DIFFRACTIONf_angle_d0.9191930
X-RAY DIFFRACTIONf_dihedral_angle_d12.756845
X-RAY DIFFRACTIONf_chiral_restr0.056208
X-RAY DIFFRACTIONf_plane_restr0.006254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95950.24161100.2382972X-RAY DIFFRACTION75
1.9595-2.02950.26941330.20731107X-RAY DIFFRACTION85
2.0295-2.11070.23671370.19751238X-RAY DIFFRACTION96
2.1107-2.20660.26961420.19871300X-RAY DIFFRACTION99
2.2066-2.32280.28581480.20031285X-RAY DIFFRACTION100
2.3228-2.46810.25481390.20261310X-RAY DIFFRACTION100
2.4681-2.65820.26411430.20331306X-RAY DIFFRACTION100
2.6582-2.9250.22141520.18941306X-RAY DIFFRACTION100
2.925-3.34650.21941450.18571333X-RAY DIFFRACTION100
3.3465-4.20960.18971500.15561335X-RAY DIFFRACTION100

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