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- PDB-9lmh: Crystal structure of LooH in complex with FAD -

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Basic information

Entry
Database: PDB / ID: 9lmh
TitleCrystal structure of LooH in complex with FAD
ComponentsLooH
KeywordsBIOSYNTHETIC PROTEIN / halogenase / flavin-dependent / tryptophan / two-component
Function / homologyFlavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / : / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / LooH
Function and homology information
Biological speciesNocardiopsis flavescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsZhang, F. / Li, Y.C. / Zhu, Y. / Wang, K. / Chang, C.Y. / Xu, Z.
Funding support Taiwan, China, 2items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
National Natural Science Foundation of China (NSFC)22107008, 81973197, and 81991525 China
CitationJournal: To Be Published
Title: Crystal structure of LooH in complex with FAD
Authors: Zhang, F. / Li, Y.C. / Zhu, Y. / Wang, K. / Chang, C.Y. / Xu, Z.
History
DepositionJan 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LooH
B: LooH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1214
Polymers124,5502
Non-polymers1,5712
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-36 kcal/mol
Surface area38270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.296, 101.622, 125.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LooH


Mass: 62274.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardiopsis flavescens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6M5K9A4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium formate, 0.1 M BICINE, 20% w/v polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→30 Å / Num. obs: 44717 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Rsym value: 0.04 / Net I/σ(I): 44.47
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 21.14 / Num. unique obs: 4378 / CC1/2: 0.994 / Rpim(I) all: 0.036 / Rsym value: 0.089 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→28.39 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.816 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26714 2245 5 %RANDOM
Rwork0.20575 ---
obs0.20885 42398 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2---0.03 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.44→28.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8428 0 106 150 8684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138774
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177898
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.64611922
X-RAY DIFFRACTIONr_angle_other_deg1.1841.57718148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94651052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78121.489524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.423151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2731572
X-RAY DIFFRACTIONr_chiral_restr0.0560.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022206
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_it1.9173.6144214
X-RAY DIFFRACTIONr_mcbond_other1.9173.6134212
X-RAY DIFFRACTIONr_mcangle_it3.2175.4185264
X-RAY DIFFRACTIONr_mcangle_other3.2175.4185264
X-RAY DIFFRACTIONr_scbond_it1.9553.8684560
X-RAY DIFFRACTIONr_scbond_other1.9543.8674557
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3065.7116659
X-RAY DIFFRACTIONr_long_range_B_refined5.44240.2239580
X-RAY DIFFRACTIONr_long_range_B_other5.44340.2339574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.5 Å
RfactorNum. reflection% reflection
Rfree0.335 141 -
Rwork0.243 2994 -
obs--96.73 %

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