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- PDB-8d8p: Crystal structure of a novel fatty acid decarboxylase from Rothia... -

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Basic information

Entry
Database: PDB / ID: 8d8p
TitleCrystal structure of a novel fatty acid decarboxylase from Rothia nasimurium
ComponentsDecarboxylase
KeywordsOXIDOREDUCTASE / fatty acid decarboxylase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PALMITIC ACID / Cytochrome
Similarity search - Component
Biological speciesRothia nasimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsVieira, P.S. / Murakami, M.T. / Zanphorlin, L.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2019/08855-1 Brazil
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Crystal structure of a novel fatty acid decarboxylase from Rothia nasimurium
Authors: Vieira, P.S. / Murakami, M.T. / Zanphorlin, L.M.
History
DepositionJun 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Decarboxylase
B: Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,57618
Polymers94,6772
Non-polymers2,89916
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-194 kcal/mol
Surface area32000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.545, 203.380, 316.351
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

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Components

#1: Protein Decarboxylase


Mass: 47338.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rothia nasimurium (bacteria) / Gene: A7979_11370 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1RQ53
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25 % (w/v) PEG3500, 15% (w/v) 2-Methil-2,4-pentanediol, 0.1 M Imidazole (pH 6.5) and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRUS / Beamline: MANACA / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.75→49.02 Å / Num. obs: 24500 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 74.46 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.35 / Net I/σ(I): 5.9
Reflection shellResolution: 2.75→2.92 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 3873 / CC1/2: 0.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IZO

1izo


Resolution: 2.75→48.41 Å / SU ML: 0.5089 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.7749
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 1226 5.01 %
Rwork0.228 23268 -
obs0.2301 24494 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.51 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6514 0 182 25 6721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00486828
X-RAY DIFFRACTIONf_angle_d0.83119282
X-RAY DIFFRACTIONf_chiral_restr0.041996
X-RAY DIFFRACTIONf_plane_restr0.01341214
X-RAY DIFFRACTIONf_dihedral_angle_d10.4189956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.42471340.38142547X-RAY DIFFRACTION99.63
2.86-2.990.40451330.3532525X-RAY DIFFRACTION99.92
2.99-3.150.40651350.34942563X-RAY DIFFRACTION100
3.15-3.350.32971350.31672562X-RAY DIFFRACTION99.93
3.35-3.60.35151360.26052579X-RAY DIFFRACTION100
3.6-3.970.26531340.22212554X-RAY DIFFRACTION100
3.97-4.540.23521370.18312593X-RAY DIFFRACTION99.93
4.54-5.720.25431380.19242632X-RAY DIFFRACTION99.89
5.72-48.410.18771440.17962713X-RAY DIFFRACTION99.37
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)
16.512093296781.37741211834-1.754050190074.50075722537-0.6074525328060.432403140820.128846872403-0.1123061562470.3756112363920.5385138275680.0290220728836-0.310427860317-0.1375646178350.196263826697-0.066392474360.572593266930.0436845212082-0.06730579770030.683388014731-0.03453985678680.42616430753815.4758434383-7.65348010411-10.8442118407
21.51951254627-0.1623377309180.3343857123421.22024114030.2621150380350.5237507567540.05933987120740.226322206259-0.180565495876-0.210811446371-0.1065152298180.1286866992930.0159580572044-0.08086022460960.06400924091220.6524088310540.05173181990650.00171400026510.793380396122-0.04335983065140.400197399204-3.69543470332-24.6952032545-19.0853441829
31.422972032430.131653310782-0.1234433806732.94173824625-0.2267384473240.07992704878340.0371652510410.244950653458-0.143682212869-0.467013407272-0.1152610108540.03951834138360.270910865951-0.178005951330.05317363734680.5173537619620.05349204647640.02266080025710.682258306485-0.0883818490150.381904686313-7.88659524303-28.3339041807-18.7538663099
41.30640302592-0.5935856602790.08279698108462.18634614703-0.2747190124111.14917551731-0.003741053459670.400459237772-0.115136373216-0.436687082865-0.111231259027-0.023990532560.0747782927489-0.009050923823580.1275221957620.6035634686060.06244951885330.008573498679440.852890771053-0.02869173411610.3830253429162.7777089748-14.8413691323-25.9205789282
52.54439438609-1.17500730841.415813382824.53862721451-1.784626271385.131457868610.2703687974861.215213207670.0778254133723-1.03226405576-0.1306100192730.387797765168-0.0951471840496-0.213181955087-0.1298788780540.6882060550550.1183213405650.01036596696860.9096916493080.01339519874380.4531557976861.60019969083-41.4870076717-72.6399086065
60.6226404846370.2140758488310.8539788195371.048931006030.5606424116553.70806730769-0.146132169154-0.1083780302320.1545245623940.1708543272770.1382264218690.230480451486-0.514117798006-0.4534087829770.02764228108950.6539355459840.1510081616710.1000455486310.7254426115430.0123100096140.5098092941132.49745048163-35.1180733356-54.6745145713
71.299239040680.006216643925150.0447858319012.427378564551.32132347836.280344658190.396900378884-0.4482377598140.4080339955040.06649684166960.39607632864-0.575281546041-1.313314926551.26699106422-0.7052293451191.05058528856-0.2707147457970.004471674894020.857109956648-0.1302921910150.61238091319230.2793974294-24.2262534729-57.0961614297
82.768258950062.047855539631.330721502125.896337325233.659627590577.983347691410.0450136661770.3270876510150.1303717869050.1227523698460.306959058389-0.314807781164-0.4661667206780.985660236517-0.3518804324960.6266183022560.05536345605720.02015311691920.690045021252-0.08632324759930.54992467079427.1964983409-39.1567868321-57.4097266159
91.60647724791-0.2529247335330.958369200591.72667358536-0.6763508394675.2338014782-0.0100275955121-0.196186914860.2691776762650.4088432839880.0915816639053-0.241179052927-1.084464815560.329409467985-0.06024255697490.651572316556-0.01613912326950.0590331665220.637052831958-0.1316310467160.48893491253321.8968077562-29.3027324028-53.0395769898
102.27499788221-0.1298759150950.5532520498393.75965072883-0.6685398027273.78056515702-0.1409979259330.1361954224370.2975178333090.1924546200960.3979463184690.670512561787-0.618119990485-0.746386265324-0.2131563788210.7555509953140.2206261035070.03412566146050.7061712062380.004631659452970.492142918698-0.540238519616-30.896193201-63.3724940065
115.00675449135-0.9486128500331.031506441475.402835215881.908533594651.03929517383-0.389386401629-0.4951621020280.726171610723-0.2902283832980.0295065977494-0.402126801598-0.569606535754-0.1700744923390.2849109075180.9946181590740.195367898574-0.008015835030040.610251615798-0.03816010873120.5798212290137.27602117278-20.0796435888-57.213194075
122.25187893745-0.174144168184-0.8752582142811.678643278110.3097362760816.46821936751-0.132076155146-0.1690186267860.303009676342-0.3527601047520.0676503734636-0.366314434424-1.688769921820.9660068814380.04937221684240.884374811741-0.19028409836-0.02769549651240.603233999187-0.02719705907080.53943555889624.3822276252-26.262970474-70.2968642728
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 49 )AA10 - 491 - 40
22chain 'A' and (resid 50 through 183 )AA50 - 18341 - 174
33chain 'A' and (resid 184 through 278 )AA184 - 278175 - 269
44chain 'A' and (resid 279 through 429 )AA279 - 429270 - 420
55chain 'B' and (resid 10 through 32 )BD10 - 321 - 23
66chain 'B' and (resid 33 through 110 )BD33 - 11024 - 101
77chain 'B' and (resid 111 through 155 )BD111 - 155102 - 146
88chain 'B' and (resid 156 through 183 )BD156 - 183147 - 174
99chain 'B' and (resid 184 through 299 )BD184 - 299175 - 290
1010chain 'B' and (resid 300 through 348 )BD300 - 348291 - 339
1111chain 'B' and (resid 349 through 380 )BD349 - 380340 - 371
1212chain 'B' and (resid 381 through 429 )BD381 - 429372 - 420

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