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- PDB-8wkc: Crystal structure of OgBVMO(Oceanicola granulosus) -

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Basic information

Entry
Database: PDB / ID: 8wkc
TitleCrystal structure of OgBVMO(Oceanicola granulosus)
ComponentsPutative monooxygenase
KeywordsOXIDOREDUCTASE / Baeyer-Villiger monooxygenases
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative monooxygenase
Similarity search - Component
Biological speciesOceanicola granulosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDu, Y. / Wang, Y.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystal structure of OgBVMO(Oceanicola granulosus)
Authors: Du, Y. / Wang, Y.H.
History
DepositionSep 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9014
Polymers60,2801
Non-polymers1,6213
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-9 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.640, 47.450, 98.550
Angle α, β, γ (deg.)90.000, 99.340, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1334-

HOH

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Components

#1: Protein Putative monooxygenase


Mass: 60279.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanicola granulosus (strain ATCC BAA-861 / DSM 15982 / KCTC 12143 / HTCC2516) (bacteria)
Gene: OG2516_16079 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2CGV0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200 mM sodium chloride,100 mM imidazole hydrochloric acid pH 8.0, and 30% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.48→31.16 Å / Num. obs: 92990 / % possible obs: 97.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.39 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 1.48→1.52 Å / Num. unique obs: 92990 / CC1/2: 0.575

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→31.15 Å / SU ML: 0.1463 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.5332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1867 1354 2.15 %
Rwork0.1603 61691 -
obs0.1609 63045 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 107 635 4926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624407
X-RAY DIFFRACTIONf_angle_d0.97125997
X-RAY DIFFRACTIONf_chiral_restr0.0571630
X-RAY DIFFRACTIONf_plane_restr0.0065768
X-RAY DIFFRACTIONf_dihedral_angle_d16.88361574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.19131340.16836097X-RAY DIFFRACTION98.9
1.76-1.830.20761330.16456080X-RAY DIFFRACTION99.09
1.83-1.910.19661340.1696099X-RAY DIFFRACTION99.16
1.91-2.020.24151350.16266130X-RAY DIFFRACTION99.35
2.02-2.140.16531340.166154X-RAY DIFFRACTION99.51
2.14-2.310.18631360.16356160X-RAY DIFFRACTION99.57
2.31-2.540.20961360.16836183X-RAY DIFFRACTION99.81
2.54-2.910.22111360.17046208X-RAY DIFFRACTION99.8
2.91-3.660.18411380.15686237X-RAY DIFFRACTION99.7
3.66-31.150.15141380.15016343X-RAY DIFFRACTION99.22
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.724489114180.2658147690820.2529660025340.6322566196950.1703789926170.4446255960080.01586951214650.2643316628510.158904804083-0.0925171541978-0.03463985475880.0251530334896-0.0335806780417-0.001228054235680.01507866673580.1449198986140.01645858691930.000867321827110.148823958680.02619957719650.121627436262-7.2150385149910.080669930217.1430320921
21.212222563370.3155162769390.7188777206160.1091315774630.1264893496090.502682929166-0.0181255008103-0.1889488222540.2136782314390.0397677652071-0.08726138092670.0712854369834-0.0369742457482-0.1586272541450.05934335073510.1503258754340.01003889481680.005844324378860.147384132477-0.03366895386020.151537094025-1.2494695410511.337461446536.351008446
30.759818030117-0.1183079608770.1290674030820.4832454193250.1104148363870.3895292891630.03568625802230.23858545559-0.0348287793472-0.0850796278553-0.0643192908993-0.0171589782054-0.02338770510510.04495231805310.04150767524090.1285899693840.01297188571830.0165969363980.1678252853260.004267060985940.11944735632114.8056971274-6.4647259202522.4448925715
40.8371780966250.3626737981030.186798715171.044119174750.2233184379360.404605392940.050089285152-0.146467564361-0.008589533858160.198309340567-0.0587126708823-0.06271813835040.0365734671871-0.05294271077210.01049442164430.150359447997-0.0139260218668-0.005851284924040.1274931983820.01299089263160.085212409922213.4325181619-0.24197411805642.8976862097
51.32396928494-0.523081418283-0.1948451763550.854483019432-0.01622323470320.9632153545280.03740287073930.126033236372-0.210631929523-0.0910787480944-0.02697514802580.113497397870.101049604999-0.0885275132741-0.001532153480880.13896707508-0.00325147688403-0.0117139318390.153324198522-0.03499183223720.163840030777-15.1950277392-6.3876420808221.3226758815
61.059178663430.2163015956840.2233479237640.7794432510640.07474181012930.6768734213030.04896942452260.00311574639177-0.213332845876-0.0299485921859-0.07134563547730.03232315077840.0982455319321-0.08260035697570.04323409182850.1327864962070.02357205920750.01826449126540.136897200039-0.03515250264180.169553441092-6.61452940183-11.963988297223.918169934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 133 )7 - 1331 - 127
22chain 'A' and (resid 134 through 203 )134 - 203128 - 197
33chain 'A' and (resid 204 through 298 )204 - 298198 - 292
44chain 'A' and (resid 299 through 391 )299 - 391293 - 385
55chain 'A' and (resid 392 through 486 )392 - 486386 - 480
66chain 'A' and (resid 487 through 536 )487 - 536481 - 530

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