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- PDB-8zop: Structure of FasV in complex with FAD -

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Basic information

Entry
Database: PDB / ID: 8zop
TitleStructure of FasV in complex with FAD
ComponentsHalogenase
KeywordsBIOSYNTHETIC PROTEIN / Naphthacemycins / Flavin-dependent halogenases / FasV
Function / homologyFlavin-dependent halogenase / Tryptophan halogenase / : / NAD(P)-binding Rossmann-like domain / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Halogenase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMa, X.Y. / Chen, Q.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Functional Characterization and Molecular Basis of a Multi-Site Halogenase in Naphthacemycin Biosynthesis.
Authors: Hu, Y. / Peng, S.Y. / Ma, X. / Chen, H. / Nie, Q.Y. / He, J.B. / Chen, Q. / Zhou, Q. / Lu, X.H. / Hua, Q. / Yang, D. / Liang, Y. / Ma, M. / Tang, G.L.
History
DepositionMay 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7163
Polymers45,8951
Non-polymers8212
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-19 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.607, 117.607, 63.829
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-821-

HOH

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Components

#1: Protein Halogenase


Mass: 45895.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Streptomyces sp. (1931) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID G3EGL7.
Source: (gene. exp.) Streptomyces sp. (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G3EGL7
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Ammonium citrate tribasic, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→58.8 Å / Num. obs: 81400 / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.8
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.412 / Num. unique obs: 4045

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.778 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17145 1994 2.5 %RANDOM
Rwork0.14791 ---
obs0.14848 79329 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å2-0 Å2
2---0.09 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 54 312 3579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133344
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153072
X-RAY DIFFRACTIONr_angle_refined_deg2.0641.6454542
X-RAY DIFFRACTIONr_angle_other_deg1.6111.5827045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.09420.722194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11715530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231532
X-RAY DIFFRACTIONr_chiral_restr0.1170.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02819
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4141.2351630
X-RAY DIFFRACTIONr_mcbond_other1.4131.2341629
X-RAY DIFFRACTIONr_mcangle_it2.0751.8512034
X-RAY DIFFRACTIONr_mcangle_other2.0741.8522035
X-RAY DIFFRACTIONr_scbond_it2.8831.5041714
X-RAY DIFFRACTIONr_scbond_other2.8861.5061711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2892.142509
X-RAY DIFFRACTIONr_long_range_B_refined4.85215.0493853
X-RAY DIFFRACTIONr_long_range_B_other4.81314.7433801
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 145 -
Rwork0.159 5846 -
obs--99.98 %

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