[English] 日本語
Yorodumi
- PDB-7pzh: Phocaeicola vulgatus sialic acid esterase at 2.06 Angstrom resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pzh
TitlePhocaeicola vulgatus sialic acid esterase at 2.06 Angstrom resolution
ComponentsLysophospholipase L1
KeywordsHYDROLASE / Serine hydrolase / Sialic acid acetyl esterase
Function / homologySGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Lysophospholipase L1
Function and homology information
Biological speciesPhocaeicola vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsScott, H. / Armstrong, Z. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: The structure of Phocaeicola vulgatus sialic acid acetylesterase.
Authors: Scott, H. / Davies, G.J. / Armstrong, Z.
History
DepositionOct 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Lysophospholipase L1
BBB: Lysophospholipase L1
CCC: Lysophospholipase L1
DDD: Lysophospholipase L1
EEE: Lysophospholipase L1
FFF: Lysophospholipase L1
HHH: Lysophospholipase L1
GGG: Lysophospholipase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,01816
Polymers201,8238
Non-polymers1948
Water4,666259
1
AAA: Lysophospholipase L1
BBB: Lysophospholipase L1
hetero molecules


  • defined by author&software
  • Evidence: light scattering, SEC-MALLS
  • 50.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)50,5044
Polymers50,4562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-30 kcal/mol
Surface area16100 Å2
MethodPISA
2
CCC: Lysophospholipase L1
DDD: Lysophospholipase L1
hetero molecules


  • defined by author&software
  • 50.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)50,5044
Polymers50,4562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-31 kcal/mol
Surface area16120 Å2
MethodPISA
3
EEE: Lysophospholipase L1
FFF: Lysophospholipase L1
hetero molecules


  • defined by author&software
  • 50.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)50,5044
Polymers50,4562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-28 kcal/mol
Surface area15870 Å2
MethodPISA
4
HHH: Lysophospholipase L1
GGG: Lysophospholipase L1
hetero molecules


  • defined by author&software
  • 50.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)50,5044
Polymers50,4562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-25 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.233, 93.233, 353.623
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
Lysophospholipase L1 / Sialate O-acetylesterase


Mass: 25227.924 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola vulgatus (bacteria)
Gene: DW869_04095, DWX04_04065, DXA04_10705, ERS852457_01148, ERS852509_00617, ERS852556_01195, F9001_09225, F9Z94_13025, GAS37_03660, GAX98_11820, GAY79_04625, GAY98_11740, GAZ06_07335, GAZ09_07170, ...Gene: DW869_04095, DWX04_04065, DXA04_10705, ERS852457_01148, ERS852509_00617, ERS852556_01195, F9001_09225, F9Z94_13025, GAS37_03660, GAX98_11820, GAY79_04625, GAY98_11740, GAZ06_07335, GAZ09_07170, GAZ65_18905, GAZ76_12675, GAZ90_18550, HKQ51_19175, HUV05_02570, SAMN04487923_100221
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A174J845
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulphate, 0.1 M MOPS/HEPES-Na pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11h, k, l10.8473
pseudo-merohedral11-k, -h, -l20.1527
ReflectionResolution: 2.06→80.74 Å / Num. obs: 106903 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2.06→2.1 Å / Num. unique obs: 5267 / CC1/2: 0.54

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6njc

6njc


Resolution: 2.06→80.742 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.185 / SU B: 3.793 / SU ML: 0.111 / Average fsc free: 0.9606 / Average fsc work: 0.9754 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2258 5355 5.016 %
Rwork0.185 101414 -
all0.187 --
obs-106769 99.988 %
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: 37.958 Å2
Baniso -1Baniso -2Baniso -3
1--0.037 Å2-0 Å2-0 Å2
2---0.037 Å2-0 Å2
3---0.073 Å2
Refinement stepCycle: LAST / Resolution: 2.06→80.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12619 0 62 259 12940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313081
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712425
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6417695
X-RAY DIFFRACTIONr_angle_other_deg1.321.58328906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61451604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97723.333639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.037152411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.721561
X-RAY DIFFRACTIONr_chiral_restr0.0820.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022628
X-RAY DIFFRACTIONr_nbd_refined0.2180.22823
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.212227
X-RAY DIFFRACTIONr_nbtor_refined0.1690.26293
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2421
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0990.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.214
X-RAY DIFFRACTIONr_nbd_other0.2090.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.210
X-RAY DIFFRACTIONr_mcbond_it3.5173.9386413
X-RAY DIFFRACTIONr_mcbond_other3.5173.9376412
X-RAY DIFFRACTIONr_mcangle_it4.5665.8928018
X-RAY DIFFRACTIONr_mcangle_other4.5665.8928019
X-RAY DIFFRACTIONr_scbond_it3.6064.2036668
X-RAY DIFFRACTIONr_scbond_other3.6024.2036666
X-RAY DIFFRACTIONr_scangle_it5.0546.1939677
X-RAY DIFFRACTIONr_scangle_other5.0516.1939677
X-RAY DIFFRACTIONr_lrange_it6.54645.95314743
X-RAY DIFFRACTIONr_lrange_other6.54645.95614744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1130.2983690.2387559X-RAY DIFFRACTION99.8866
2.113-2.1710.2833810.2277287X-RAY DIFFRACTION100
2.171-2.2340.2863750.2277086X-RAY DIFFRACTION99.9732
2.234-2.3030.2963800.2146895X-RAY DIFFRACTION100
2.303-2.3790.2573550.2066695X-RAY DIFFRACTION100
2.379-2.4620.2943200.2076482X-RAY DIFFRACTION100
2.462-2.5550.2773460.2196209X-RAY DIFFRACTION100
2.555-2.6590.2643140.2156025X-RAY DIFFRACTION100
2.659-2.7780.2553310.2045718X-RAY DIFFRACTION100
2.778-2.9130.2462970.1965538X-RAY DIFFRACTION100
2.913-3.0710.2582860.2075199X-RAY DIFFRACTION100
3.071-3.2570.2392360.2054984X-RAY DIFFRACTION100
3.257-3.4820.2362480.1994676X-RAY DIFFRACTION100
3.482-3.7610.2152450.1834320X-RAY DIFFRACTION100
3.761-4.120.1821950.1564001X-RAY DIFFRACTION100
4.12-4.6060.1771950.1413619X-RAY DIFFRACTION100
4.606-5.3180.1731850.1443161X-RAY DIFFRACTION100
5.318-6.5130.2151390.172707X-RAY DIFFRACTION100
6.513-9.2090.148980.1422103X-RAY DIFFRACTION100
9.209-80.740.169600.1581150X-RAY DIFFRACTION99.835

+
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