[English] 日本語
Yorodumi
- PDB-8p8f: Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p8f
TitleCrystal structure of the lipase SpL from Sphingomonas sp. HXN-200 in complex with N-benzyl-picolinamide
ComponentsLipase
KeywordsHYDROLASE / alpha-beta hydrolase / lipase / SpL
Function / homologyLipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / : / Lipase
Function and homology information
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMokos, D. / Gruber, K. / Daniel, B.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science Fund Austria
Austrian Research Promotion Agency Austria
CitationJournal: Acs Catalysis / Year: 2024
Title: Biocatalytic Heteroaromatic Amide Formation in Water Enabled by a Catalytic Tetrad and Two Access Tunnels.
Authors: Zukic, E. / Mokos, D. / Weber, M. / Stix, N. / Ditrich, K. / Ferrario, V. / Muller, H. / Willrodt, C. / Gruber, K. / Daniel, B. / Kroutil, W.
History
DepositionJun 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4014
Polymers70,9762
Non-polymers4242
Water9,908550
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-4 kcal/mol
Surface area23080 Å2
Unit cell
Length a, b, c (Å)60.833, 60.833, 217.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 6 - 314 / Label seq-ID: 20 - 328

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Lipase


Mass: 35488.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Gene: LH19_08550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N7I173
#2: Chemical ChemComp-XBW / ~{N}-(phenylmethyl)pyridine-2-carboxamide


Mass: 212.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5 mg/ml SPL, 0.02 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 22% w/v Poly(acrylic acid sodium salt) 5,100

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.8→46.62 Å / Num. obs: 72849 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.06 / Rrim(I) all: 0.154 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-46.6213.30.0746070.9950.030.079
1.8-1.8411.70.74343380.8350.3360.817

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.618 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2277 3612 4.964 %
Rwork0.1886 69153 -
all0.191 --
obs-72765 99.977 %
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: 24.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.177 Å20 Å20 Å2
2---0.177 Å2-0 Å2
3---0.354 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4674 0 32 550 5256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124834
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164503
X-RAY DIFFRACTIONr_angle_refined_deg1.841.6556602
X-RAY DIFFRACTIONr_angle_other_deg1.0371.57610380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.647538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08210704
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.89910206
X-RAY DIFFRACTIONr_chiral_restr0.1050.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025754
X-RAY DIFFRACTIONr_gen_planes_other0.0210.021057
X-RAY DIFFRACTIONr_nbd_refined0.210.21022
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.24200
X-RAY DIFFRACTIONr_nbtor_refined0.180.22456
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22474
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2342
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5810.22
X-RAY DIFFRACTIONr_nbd_other0.2420.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.26
X-RAY DIFFRACTIONr_mcbond_it2.9762.4152470
X-RAY DIFFRACTIONr_mcbond_other2.9732.4152470
X-RAY DIFFRACTIONr_mcangle_it3.6264.3313084
X-RAY DIFFRACTIONr_mcangle_other3.6254.3333085
X-RAY DIFFRACTIONr_scbond_it4.3182.8282364
X-RAY DIFFRACTIONr_scbond_other4.3172.8292365
X-RAY DIFFRACTIONr_scangle_it6.064.9873518
X-RAY DIFFRACTIONr_scangle_other6.0594.9873519
X-RAY DIFFRACTIONr_lrange_it6.72124.3885557
X-RAY DIFFRACTIONr_lrange_other6.61924.0475436
X-RAY DIFFRACTIONr_ncsr_local_group_10.0650.0510127
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.065020.05008
12AX-RAY DIFFRACTIONLocal ncs0.065020.05008
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
1.8-1.8470.2692470.24951520.2553990.9490.9581000.236
1.847-1.8970.2922390.25749900.25952290.9430.9561000.239
1.897-1.9520.3382290.32348360.32350660.9270.93899.98030.315
1.952-2.0120.2552500.22346780.22549280.9520.9671000.203
2.012-2.0780.2562450.21545340.21747800.9510.97199.97910.199
2.078-2.1510.252190.20644680.20846880.9550.97299.97870.191
2.151-2.2320.2542120.21542360.21744480.9580.971000.198
2.232-2.3230.282140.22941060.23243210.9460.96599.97690.217
2.323-2.4260.2341940.19639430.19841390.9670.97899.95170.187
2.426-2.5440.261920.20337600.20639520.960.9781000.198
2.544-2.6810.2531920.19335540.19637460.9630.9791000.193
2.681-2.8430.2771760.18833570.19235330.9570.9791000.193
2.843-3.0380.2442090.18431590.18833680.9620.9781000.197
3.038-3.2810.2191500.18429420.18630920.9710.9791000.201
3.281-3.5920.2291580.1927430.19229010.970.9811000.206
3.592-4.0130.2051080.16824730.1725840.9760.98499.88390.188
4.013-4.6280.1751260.14121650.14322930.9810.98899.91280.169
4.628-5.6540.1871310.13718070.1419380.9810.9891000.165
5.654-7.9380.176850.14914220.15115070.9820.9871000.18
7.938-46.6180.13360.148280.148660.9910.98699.76910.18

+
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