[English] 日本語
Yorodumi
- PDB-8d8p: Crystal structure of a novel fatty acid decarboxylase from Rothia... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more