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- PDB-4n9x: Crystal Structure of the OCTAPRENYL-METHYL-METHOXY-BENZQ MOLECULE... -

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Basic information

Entry
Database: PDB / ID: 4n9x
TitleCrystal Structure of the OCTAPRENYL-METHYL-METHOXY-BENZQ MOLECULE from Erwina carotovora subsp. atroseptica strain SCRI 1043 / ATCC BAA-672, Northeast Structural Genomics Consortium (NESG) Target EwR161
ComponentsPutative monooxygenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) Target EwR161
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / ubiquinone biosynthetic process / Oxidoreductases / FAD binding
Similarity search - Function
Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6, conserved site / ubiH/COQ6 monooxygenase family signature. / Ubiquinone biosynthesis hydroxylase UbiH/COQ6 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Putative monooxygenase
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsKuzin, A. / Chen, Y. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Chen, Y. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the OCTAPRENYL-METHYL-METHOXY-BENZQ MOLECULE from Erwina carotovora subsp. atroseptica strain SCRI 1043 / ATCC BAA-672, Northeast Structural Genomics Consortium (NESG) Target EwR161
Authors: Kuzin, A. / Chen, Y. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural ...Authors: Kuzin, A. / Chen, Y. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative monooxygenase


Theoretical massNumber of molelcules
Total (without water)46,2041
Polymers46,2041
Non-polymers00
Water1448
1
A: Putative monooxygenase
x 6


Theoretical massNumber of molelcules
Total (without water)277,2246
Polymers277,2246
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area19630 Å2
ΔGint-117 kcal/mol
Surface area80260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.098, 120.098, 149.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Putative monooxygenase


Mass: 46203.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Strain: SCRI 1043 / ATCC BAA-672 / Gene: visC, ECA0457 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DA06, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 0.1M Ammonium phosphate-dibasic, 0.1M TAPS, 20% (w/v) PEG4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 26980 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 59.26 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.6

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K22

4k22


Resolution: 2.503→28.811 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.739 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 32.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1310 4.87 %random
Rwork0.225 ---
obs0.227 26903 96.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 256.45 Å2 / Biso mean: 88.641 Å2 / Biso min: 41.17 Å2
Refinement stepCycle: LAST / Resolution: 2.503→28.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2879 0 0 8 2887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112954
X-RAY DIFFRACTIONf_angle_d1.453994
X-RAY DIFFRACTIONf_chiral_restr0.101443
X-RAY DIFFRACTIONf_plane_restr0.006522
X-RAY DIFFRACTIONf_dihedral_angle_d18.9961085
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.503-2.6030.3381380.2782922306099
2.603-2.7210.4011470.28129143061100
2.721-2.8640.3461500.27129573107100
2.864-3.0440.3351650.2472888305399
3.044-3.2780.2871480.252899304798
3.278-3.6080.3851390.2472777291695
3.608-4.1280.271280.2192851297996
4.128-5.1960.2111550.1912816297196
5.196-28.8130.21400.2072569270987
Refinement TLS params.Method: refined / Origin x: -1.2194 Å / Origin y: -22.4295 Å / Origin z: -25.1571 Å
111213212223313233
T0.8355 Å2-0.0274 Å20.2631 Å2-0.5817 Å2-0.1891 Å2--0.6676 Å2
L1.9014 °20.2218 °2-0.0553 °2-1.536 °2-0.0886 °2--1.6818 °2
S-0.3005 Å °0.5698 Å °-0.44 Å °-0.5658 Å °-0.0776 Å °0.0623 Å °0.5051 Å °-0.15 Å °0.3317 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 396
2X-RAY DIFFRACTION1allA1 - 516

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