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- PDB-8fhj: Crystal structure of a FAD monooxygenease from Methylocystis sp. ... -

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Basic information

Entry
Database: PDB / ID: 8fhj
TitleCrystal structure of a FAD monooxygenease from Methylocystis sp. Strain SB2
ComponentsMonooxygenase
KeywordsBIOSYNTHETIC PROTEIN / methanobactin
Function / homologyBROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesMethylocystis sp. SB2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsStewart, A.M. / Sawaya, M.R. / Stewart, C.E.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0018059 United States
National Science Foundation (NSF, United States)1912482 United States
Iowa State University (ISU) Bailey Research and Career Development AwardSG0600002 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2.
Authors: Stewart, A. / Dershwitz, P. / Stewart Jr., C. / Sawaya, M.R. / Yeates, T.O. / Semrau, J.D. / Zischka, H. / DiSpirito, A.A. / Bobik, T.A.
History
DepositionDec 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / struct_ncs_dom / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monooxygenase
B: Monooxygenase
C: Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,13130
Polymers180,7923
Non-polymers4,33927
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.347, 96.765, 135.206
Angle α, β, γ (deg.)90.00, 116.41, 90.00
Int Tables number5
Space group name H-MC121
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 472 or resid 474 through 532 or resid 601 through 603))
21(chain B and (resid 3 through 472 or resid 474 through 532 or resid 601 through 603))
31(chain C and (resid 3 through 472 or resid 474 through 532 or resid 601 through 603))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVAL(chain A and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))AA3 - 4723 - 472
12ARGARGASPASP(chain A and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))AA474 - 532474 - 532
13FADFADGOLGOL(chain A and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))AD - F601 - 603
21VALVALVALVAL(chain B and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))BB3 - 4723 - 472
22ARGARGASPASP(chain B and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))BB474 - 532474 - 532
23FADFADGOLGOL(chain B and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))BL - N601 - 603
31VALVALVALVAL(chain C and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))CC3 - 4723 - 472
32ARGARGASPASP(chain C and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))CC474 - 532474 - 532
33FADFADBRBR(chain C and (resid 3 through 472 or resid 474 through 532 or resid 700 through 901))CAA - CA601 - 603

NCS oper:
IDCodeMatrixVector
1given(-0.996000144492, -0.0841297303179, 0.030098183481), (-0.0891541168903, 0.958103570664, -0.272193114023), (-0.00593764378651, -0.273787757865, -0.961771806631)77.0524603609, 0.991840061122, 34.8569661804
2given(0.996307419365, -0.0821368006749, -0.0250014418371), (0.0858329535877, 0.959832849297, 0.267120956663), (0.00205674438154, -0.268280538588, 0.963338633305)3.32760622005, -47.5132648357, 34.9463299061

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Monooxygenase


Mass: 60263.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylocystis sp. SB2 (bacteria) / Gene: CTY30_04200 / Plasmid: pET41a / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 5 types, 159 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 49.01 % / Description: yellow color
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG3350, 0.1 M Bis-Tris propane pH 6.5, 0.2 M Sodium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2020 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.61→121.1 Å / Num. obs: 52358 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.079 / Rrim(I) all: 0.149 / Χ2: 0.93 / Net I/σ(I): 6.4 / Num. measured all: 184364 / Scaling rejects: 10
Reflection shellResolution: 2.61→2.75 Å / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 1.692 / Num. measured all: 27645 / Num. unique obs: 7601 / CC1/2: 0.461 / Rpim(I) all: 1.033 / Rrim(I) all: 1.986 / Χ2: 0.85 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
autoPROC1.0.5data processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IHG

3ihg


Resolution: 2.61→59.95 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 1999 3.82 %
Rwork0.2043 50271 -
obs0.2062 52271 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.12 Å2 / Biso min: 42.02 Å2
Refinement stepCycle: final / Resolution: 2.61→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12160 0 412 133 12705
Biso mean--81.97 71.8 -
Num. residues----1593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812622
X-RAY DIFFRACTIONf_angle_d0.99417155
X-RAY DIFFRACTIONf_dihedral_angle_d15.0794759
X-RAY DIFFRACTIONf_chiral_restr0.0561920
X-RAY DIFFRACTIONf_plane_restr0.0092264
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7637X-RAY DIFFRACTION7.978TORSIONAL
12B7637X-RAY DIFFRACTION7.978TORSIONAL
13C7637X-RAY DIFFRACTION7.978TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.670.39961420.39053567X-RAY DIFFRACTION100
2.67-2.740.35241420.34863571X-RAY DIFFRACTION100
2.74-2.820.42531410.32493553X-RAY DIFFRACTION100
2.82-2.910.31661430.28883601X-RAY DIFFRACTION100
2.91-3.020.30191420.26983579X-RAY DIFFRACTION100
3.02-3.140.33271430.26333584X-RAY DIFFRACTION100
3.14-3.280.28051420.25383587X-RAY DIFFRACTION100
3.28-3.460.31311430.22483562X-RAY DIFFRACTION100
3.46-3.670.27121420.1983596X-RAY DIFFRACTION100
3.67-3.960.21641420.18343575X-RAY DIFFRACTION100
3.96-4.350.25081430.17493604X-RAY DIFFRACTION100
4.35-4.980.20591420.16033577X-RAY DIFFRACTION99
4.98-6.280.25451450.20173646X-RAY DIFFRACTION100
6.28-59.950.19681470.15953670X-RAY DIFFRACTION99
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)
11.2737-0.1229-0.15950.31990.13980.6899-0.1171-0.07890.126-0.0341-0.0127-0.00640.00670.1869-00.60450.01-0.05710.5586-0.01440.54822.5966-10.24053.1877
21.50160.0089-0.68620.1194-0.11090.77830.00580.23770.113-0.0036-0.0590.027-0.0832-0.095900.5576-0.0223-0.02210.50520.02140.534355.4585-11.709234.4952
30.8784-0.0341-0.09960.67240.23830.51680.0439-0.18520.0424-0.02770.03030.00210.07360.112900.5957-0.06680.0350.6419-0.06970.602126.6489-54.541640.8182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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