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- PDB-7v4f: Unique non-heme hydroxylase in biosynthesis of nucleoside antibio... -

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Basic information

Entry
Database: PDB / ID: 7v4f
TitleUnique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction
ComponentsBeta-hydroxylase
KeywordsANTIBIOTIC / caprazamycin / MraY / beta-hydroxylase
Function / homologyAspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / Isopenicillin N synthase-like superfamily / metal ion binding / Chem-5KC / CARBON DIOXIDE / : / SUCCINIC ACID / Beta-hydroxylase
Function and homology information
Biological speciesStreptomyces sp. MK730-62F2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLi, T.L. / Saeid, M.Z.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) 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)42,87710
Polymers42,1822
Non-polymers6968
Water3,081171
1
B: Beta-hydroxylase
hetero molecules

B: Beta-hydroxylase
hetero molecules

A: Beta-hydroxylase
hetero molecules

A: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,75520
Polymers84,3634
Non-polymers1,39116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation2_555-x,-y,z+1/21
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area6210 Å2
ΔGint-89 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.049, 82.049, 103.893
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
11B-205-

FE

21B-343-

HOH

31A-349-

HOH

41A-355-

HOH

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Components

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Protein , 1 types, 2 molecules BA

#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

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-5KC / (2S,3S)-2-azanyl-4-(2-hydroxy-2-oxoethylamino)-3-oxidanyl-butanoic acid


Mass: 192.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium sulfate 12% V/V PEG 8K 10 mg

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.97→26.48 Å / Num. obs: 25823 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.905 / Net I/σ(I): 33.5
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 2497 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P7X

4p7x


Resolution: 1.98→26.46 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 3041 7.89 %
Rwork0.1911 --
obs0.1959 25285 81.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→26.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 4 171 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082852
X-RAY DIFFRACTIONf_angle_d1.133869
X-RAY DIFFRACTIONf_dihedral_angle_d26.342391
X-RAY DIFFRACTIONf_chiral_restr0.065419
X-RAY DIFFRACTIONf_plane_restr0.007511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.010.3263880.26231024X-RAY DIFFRACTION51
2.01-2.040.2832880.25181019X-RAY DIFFRACTION52
2.04-2.080.3445890.25041044X-RAY DIFFRACTION53
2.08-2.120.2888890.23931048X-RAY DIFFRACTION53
2.12-2.160.3223950.22981066X-RAY DIFFRACTION54
2.16-2.20.2584910.23191080X-RAY DIFFRACTION55
2.2-2.250.2859970.22881128X-RAY DIFFRACTION57
2.25-2.30.26971040.22151272X-RAY DIFFRACTION64
2.3-2.360.3341240.20871505X-RAY DIFFRACTION75
2.36-2.420.28961540.21981720X-RAY DIFFRACTION88
2.42-2.490.30751630.21981918X-RAY DIFFRACTION97
2.49-2.580.28181650.21811955X-RAY DIFFRACTION99
2.58-2.670.30941740.22511976X-RAY DIFFRACTION100
2.67-2.770.30861660.19881975X-RAY DIFFRACTION100
2.77-2.90.30731710.21631975X-RAY DIFFRACTION100
2.9-3.050.29071720.20891987X-RAY DIFFRACTION100
3.05-3.240.29961700.21011964X-RAY DIFFRACTION100
3.24-3.490.21341660.17951954X-RAY DIFFRACTION100
3.49-3.840.25081720.16521967X-RAY DIFFRACTION100
3.84-4.40.18371710.14721983X-RAY DIFFRACTION100
4.4-5.530.16931700.15091988X-RAY DIFFRACTION100
5.53-26.460.21841620.181948X-RAY DIFFRACTION99

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