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- PDB-9lmj: Crystal structure of LooH in complex with I-Trp -

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Basic information

Entry
Database: PDB / ID: 9lmj
TitleCrystal structure of LooH in complex with I-Trp
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 / : / LooH
Function and homology information
Biological speciesNocardiopsis flavescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 I-Trp
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)125,2104
Polymers124,5502
Non-polymers6602
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-11 kcal/mol
Surface area39240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.201, 123.744, 82.039
Angle α, β, γ (deg.)90.00, 97.79, 90.00
Int Tables number4
Space group name H-MP1211

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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 (bacteria) / References: UniProt: A0A6M5K9A4
#2: Chemical ChemComp-A1L7E / (2~{S})-2-azanyl-3-(7-iodanyl-1~{H}-indol-3-yl)propanoic acid


Type: L-peptide linking / Mass: 330.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11IN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→30 Å / Num. obs: 86662 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.033 / Net I/σ(I): 19.94
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.748 / Num. unique obs: 11486 / CC1/2: 0.638 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
SCALAdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21387 4543 5 %RANDOM
Rwork0.17989 ---
obs0.18158 86662 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.01 Å2
2---0.02 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.8→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8440 0 32 749 9221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0128714
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167882
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.8211824
X-RAY DIFFRACTIONr_angle_other_deg0.7791.76518109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41451056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.892572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.028101372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1770.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210627
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022205
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_it0.8911.5824233
X-RAY DIFFRACTIONr_mcbond_other0.8911.5824233
X-RAY DIFFRACTIONr_mcangle_it1.4992.855286
X-RAY DIFFRACTIONr_mcangle_other1.4992.855287
X-RAY DIFFRACTIONr_scbond_it1.2561.7434481
X-RAY DIFFRACTIONr_scbond_other1.2561.7434482
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.13.1286539
X-RAY DIFFRACTIONr_long_range_B_refined3.40517.019851
X-RAY DIFFRACTIONr_long_range_B_other3.405179852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 315 -
Rwork0.234 5973 -
obs--91.34 %

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