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- PDB-7fco: ChlB4 Halogenase -

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Basic information

Entry
Database: PDB / ID: 7fco
TitleChlB4 Halogenase
ComponentsChlB4
KeywordsFLAVOPROTEIN / Halogenase / Flavin reduction
Function / homology: / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / ChlB4
Function and homology information
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsSaeed, A.U. / Zheng, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070040 China
Other government2020YFA0907900 China
CitationJournal: To Be Published
Title: Crystal insight of FAD-dependent bifunctional halogenase ChlB4 in the biosynthesis of Chlorothricin
Authors: Saeed, A.U. / Zheng, J.
History
DepositionJul 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: ChlB4
B: ChlB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2556
Polymers101,6132
Non-polymers1,6424
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-52 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.651, 53.076, 83.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ChlB4


Mass: 50806.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q0R4P7
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Cl
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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 26 % PEG mono-ethyl ether 2000, 0.1M bis Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 28085 / % possible obs: 97.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.076 / Rrim(I) all: 0.166 / Χ2: 0.878 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.593.80.78613040.6520.450.910.85294.9
2.59-2.643.90.80413420.5770.4520.9260.86393.3
2.64-2.6940.83113430.680.4630.9550.85994.7
2.69-2.754.10.76213120.6210.4240.8760.89294.3
2.75-2.813.90.69914000.630.3940.8060.85595.7
2.81-2.874.30.66813620.7270.3620.7630.85897.2
2.87-2.944.50.66613810.7540.350.7560.86996.3
2.94-3.024.70.53413990.840.2740.6030.88298
3.02-3.114.80.46313870.8420.2350.5210.89796.3
3.11-3.214.70.3814060.8910.1940.4280.84498.2
3.21-3.334.60.29613940.9120.1530.3340.87296.6
3.33-3.464.60.2213770.9480.1140.2490.84898.1
3.46-3.624.30.1814170.9630.0970.2050.90897.9
3.62-3.814.30.13914230.970.0740.1580.90197.2
3.81-4.054.70.10414170.9840.0520.1170.87998.3
4.05-4.364.70.08214290.9870.040.0910.97798.8
4.36-4.84.60.06314540.9890.0320.0710.95698.9
4.8-5.494.30.05614660.9910.030.0640.8699.3
5.49-6.924.60.05614940.9910.0280.0620.77599.3
6.92-504.20.03915780.9950.0210.0440.88997.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5buk

5buk


Resolution: 2.51→46.91 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.872 / SU B: 13.34 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 1338 5.1 %RANDOM
Rwork0.2306 ---
obs0.2333 24836 88.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.88 Å2 / Biso mean: 33.39 Å2 / Biso min: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.51→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 108 0 6688
Biso mean--25.28 --
Num. residues----862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196879
X-RAY DIFFRACTIONr_bond_other_d0.0040.026156
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9579397
X-RAY DIFFRACTIONr_angle_other_deg1.057314039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86123310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19815943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0881546
X-RAY DIFFRACTIONr_chiral_restr0.0780.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217873
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021671
LS refinement shellResolution: 2.51→2.571 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.343 48 -
Rwork0.283 901 -
obs--44.49 %

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