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- PDB-6ui5: Tmn9 in complex with cofactor FAD -

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Basic information

Entry
Database: PDB / ID: 6ui5
TitleTmn9 in complex with cofactor FAD
Components2-polyprenyl-6-methoxyphenol hydroxylase-like FAD-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Complex / cyclase / UNKNOWN FUNCTION
Function / homologyFAD-binding domain / FAD binding domain / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / 2-polyprenyl-6-methoxyphenol hydroxylase-like FAD-dependent oxidoreductase / Putative FAD-dependent monooxygenase
Function and homology information
Biological speciesStreptomyces sp. NRRL 11266 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPaiva, F.C.R. / Little, R. / Leadlay, P. / Dias, M.V.B.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/003511 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)141090/2016-2 Brazil
CitationJournal: To Be Published
Title: Tmn9 in complex with cofactor FAD
Authors: Paiva, F.C.R. / Little, R. / Leadlay, P. / Dias, M.V.B.
History
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-polyprenyl-6-methoxyphenol hydroxylase-like FAD-dependent oxidoreductase
B: 2-polyprenyl-6-methoxyphenol hydroxylase-like FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2404
Polymers108,6692
Non-polymers1,5712
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-47 kcal/mol
Surface area38920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.205, 85.605, 207.683
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 2-polyprenyl-6-methoxyphenol hydroxylase-like FAD-dependent oxidoreductase


Mass: 54334.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NRRL 11266 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2M8ZYZ6, UniProt: Q1MX79*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 30% w/v PEG 8000, 100 mM sodium cacodylate pH 6,5, 200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976255 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976255 Å / Relative weight: 1
ReflectionResolution: 2.26→49.79 Å / Num. obs: 52087 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 57.47 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Net I/σ(I): 12 / Num. measured all: 328949 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.26-2.3361.3382563843070.5240.5891.4661.396.6
9.31-49.795.40.03346038600.9920.0150.03636.498.9

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XGV

5xgv


Resolution: 2.4→49.788 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.75
RfactorNum. reflection% reflection
Rfree0.2487 2156 4.96 %
Rwork0.2027 --
obs0.205 43485 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 222.85 Å2 / Biso mean: 83.9249 Å2 / Biso min: 32.1 Å2
Refinement stepCycle: final / Resolution: 2.4→49.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7584 0 106 38 7728
Biso mean--94.1 56.41 -
Num. residues----994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017860
X-RAY DIFFRACTIONf_angle_d1.24410718
X-RAY DIFFRACTIONf_chiral_restr0.0631182
X-RAY DIFFRACTIONf_plane_restr0.011412
X-RAY DIFFRACTIONf_dihedral_angle_d19.2964618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.45580.40081410.3303271799
2.4558-2.51720.39461220.31942738100
2.5172-2.58530.35481440.29952690100
2.5853-2.66140.37641550.29672707100
2.6614-2.74730.35651380.2952710100
2.7473-2.84540.33761550.28932736100
2.8454-2.95940.33911350.26822712100
2.9594-3.0940.33711550.24582738100
3.094-3.25710.30681390.24312745100
3.2571-3.46110.31191400.23052742100
3.4611-3.72830.24811260.20232769100
3.7283-4.10330.20321450.17372780100
4.1033-4.69670.20851470.1542789100
4.6967-5.91580.20241520.1753279899
5.9158-49.7880.18921620.1636295899
Refinement TLS params.Method: refined / Origin x: 35.2767 Å / Origin y: -11.2119 Å / Origin z: 233.1232 Å
111213212223313233
T0.3886 Å2-0.0148 Å20.0144 Å2-0.3467 Å20.1253 Å2--0.4724 Å2
L0.8966 °2-0.229 °20.3735 °2-0.5009 °2-0.5815 °2--1.7457 °2
S0.0327 Å °-0.1601 Å °-0.1102 Å °0.0555 Å °0.1517 Å °0.2459 Å °0.0858 Å °-0.161 Å °-0.1288 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 499
2X-RAY DIFFRACTION1allB3 - 499
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 50
5X-RAY DIFFRACTION1allS70 - 100

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