[English] 日本語
Yorodumi
- PDB-8abv: Crystal structure of SpLdpA in complex with erythro-DGPD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8abv
TitleCrystal structure of SpLdpA in complex with erythro-DGPD
ComponentsSnoaL-like domain-containing protein
KeywordsLYASE / lignin / dehydratase
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / Chem-LJL / Chem-LJU / SnoaL-like domain-containing protein
Function and homology information
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.683 Å
AuthorsZahn, M. / Kuatsjah, E. / Beckham, G.T. / McGeehan, J.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation.
Authors: Kuatsjah, E. / Zahn, M. / Chen, X. / Kato, R. / Hinchen, D.J. / Konev, M.O. / Katahira, R. / Orr, C. / Wagner, A. / Zou, Y. / Haugen, S.J. / Ramirez, K.J. / Michener, J.K. / Pickford, A.R. / ...Authors: Kuatsjah, E. / Zahn, M. / Chen, X. / Kato, R. / Hinchen, D.J. / Konev, M.O. / Katahira, R. / Orr, C. / Wagner, A. / Zou, Y. / Haugen, S.J. / Ramirez, K.J. / Michener, J.K. / Pickford, A.R. / Kamimura, N. / Masai, E. / Houk, K.N. / McGeehan, J.E. / Beckham, G.T.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3716
Polymers30,4501
Non-polymers9215
Water4,197233
1
A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,11418
Polymers91,3513
Non-polymers2,76315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area19460 Å2
ΔGint-154 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.281, 71.281, 86.922
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

21A-303-

SO4

31A-624-

HOH

41A-629-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein SnoaL-like domain-containing protein


Mass: 30450.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: NBRC 103272 / SYK-6 / Gene: SLG_12650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G2IQR8

-
Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-LJU / (1S,2R)-1,2-bis(3-methoxy-4-oxidanyl-phenyl)propane-1,3-diol


Mass: 320.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-LJL / (1R,2S)-1,2-bis(3-methoxy-4-oxidanyl-phenyl)propane-1,3-diol


Mass: 320.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.683→86.922 Å / Num. obs: 23171 / % possible obs: 86.5 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.044 / Net I/σ(I): 13.3
Reflection shellResolution: 1.683→1.782 Å / Redundancy: 19 % / Rmerge(I) obs: 2.506 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1160 / CC1/2: 0.599 / Rpim(I) all: 0.587 / % possible all: 58.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NaLdpA

Resolution: 1.683→86.922 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.618 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1768 1147 4.95 %
Rwork0.148 22023 -
all0.149 --
obs-23170 78.441 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.046 Å20.023 Å20 Å2
2--0.046 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.683→86.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 63 233 2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132137
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161945
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.6492897
X-RAY DIFFRACTIONr_angle_other_deg1.4891.5824469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1725245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5422.063126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18215343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.41515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02525
X-RAY DIFFRACTIONr_nbd_refined0.2120.2434
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21728
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2985
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2180
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.234
X-RAY DIFFRACTIONr_nbd_other0.2010.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.230
X-RAY DIFFRACTIONr_mcbond_it1.6792.033977
X-RAY DIFFRACTIONr_mcbond_other1.682.032976
X-RAY DIFFRACTIONr_mcangle_it2.5023.0371220
X-RAY DIFFRACTIONr_mcangle_other2.5013.0381221
X-RAY DIFFRACTIONr_scbond_it2.792.361159
X-RAY DIFFRACTIONr_scbond_other2.7892.361160
X-RAY DIFFRACTIONr_scangle_it4.3443.4211676
X-RAY DIFFRACTIONr_scangle_other4.3433.4211677
X-RAY DIFFRACTIONr_lrange_it6.15824.6562530
X-RAY DIFFRACTIONr_lrange_other5.92723.9512467
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.683-1.7270.326100.2981550.321550.8350.8037.65660.292
1.727-1.7740.274480.2577590.25821170.8310.82338.120.254
1.774-1.8250.28540.26212280.26220180.8630.85963.52820.251
1.825-1.8820.218970.23216790.23219920.8890.89489.15660.218
1.882-1.9430.183900.23311570.22819310.9190.88764.57790.211
1.943-2.0110.201780.19217820.19218600.930.9271000.169
2.011-2.0870.255520.1839660.18717990.8970.93656.5870.152
2.087-2.1720.172760.15416610.15517370.9520.9561000.127
2.172-2.2690.204500.15910610.16116500.9490.95567.33330.128
2.269-2.380.205760.13215460.13516220.9480.9671000.107
2.38-2.5080.165540.12614520.12715060.9690.9731000.103
2.508-2.660.188760.13613650.1414410.9690.9731000.115
2.66-2.8440.177660.12213100.12513760.9710.9781000.105
2.844-3.0710.158540.11812100.1212640.9770.9821000.103
3.071-3.3640.176500.12411270.12611770.9620.9781000.111
3.364-3.7610.166580.139060.13310760.9680.97889.59110.125
3.761-4.3410.131690.1278780.1279470.9830.9821000.127
4.341-5.3130.161450.1197760.1228210.9830.9861000.124
5.313-7.50.167290.166210.166500.9760.9791000.165
7.5-86.9220.197150.1843840.1843990.9560.9651000.197
Refinement TLS params.Method: refined / Origin x: 25.1264 Å / Origin y: 11.3346 Å / Origin z: 17.4785 Å
111213212223313233
T0.0057 Å2-0.007 Å20.0051 Å2-0.0086 Å2-0.0058 Å2--0.0122 Å2
L0.1143 °20.0215 °2-0.0179 °2-0.1084 °20.0042 °2--0.1038 °2
S-0.0043 Å °0.0034 Å °-0.0214 Å °0.0083 Å °-0.0098 Å °0.0238 Å °0.0232 Å °-0.0287 Å °0.014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA-1 - 242
2X-RAY DIFFRACTION1ALLA301
3X-RAY DIFFRACTION1ALLA401
4X-RAY DIFFRACTION1ALLA501
5X-RAY DIFFRACTION1ALLA502

+
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://pdbjlc1.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