[English] 日本語
Yorodumi
- PDB-7pzg: Phocaeicola vulgatus sialic acid esterase at 1.44 Angstrom resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pzg
TitlePhocaeicola vulgatus sialic acid esterase at 1.44 Angstrom resolution
ComponentsLysophospholipase L1
KeywordsHYDROLASE / Serine hydrolase / Sialic acid acetyl esterase
Function / homologySGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / lysophospholipase activity / SGNH hydrolase superfamily / Hydrolases; Acting on ester bonds / metal ion binding / MALONIC ACID / SGNH/GDSL hydrolase family protein
Function and homology information
Biological speciesPhocaeicola vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,67316
Polymers100,9124
Non-polymers76212
Water12,538696
1
AAA: Lysophospholipase L1
DDD: Lysophospholipase L1
hetero molecules


  • defined by author&software
  • Evidence: light scattering, SEC-MALLS
  • 50.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)50,8378
Polymers50,4562
Non-polymers3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-37 kcal/mol
Surface area16080 Å2
MethodPISA
2
BBB: Lysophospholipase L1
CCC: Lysophospholipase L1
hetero molecules


  • defined by author&software
  • 50.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)50,8378
Polymers50,4562
Non-polymers3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-34 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.269, 90.150, 76.579
Angle α, β, γ (deg.)90.000, 99.289, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Lysophospholipase L1 / Sialate O-acetylesterase


Mass: 25227.924 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 18 % (w/v) PEG 3350, 200 mM sodium malonate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.44→70.434 Å / Num. obs: 168248 / % possible obs: 97.7 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 18.3
Reflection shellResolution: 1.44→1.46 Å / Num. unique obs: 7900 / CC1/2: 0.712

-
Processing

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

6njc


Resolution: 1.44→70.434 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.172 / SU B: 1.156 / SU ML: 0.044 / Average fsc free: 0.9248 / Average fsc work: 0.9304 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.203 8262 4.913 %
Rwork0.177 159915 -
all0.178 --
obs-168177 97.573 %
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: 22.426 Å2
Baniso -1Baniso -2Baniso -3
1--0.072 Å2-0 Å20.685 Å2
2---0.424 Å2-0 Å2
3---0.258 Å2
Refinement stepCycle: LAST / Resolution: 1.44→70.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 48 696 7094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176239
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.6448920
X-RAY DIFFRACTIONr_angle_other_deg1.5291.58214505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92523.259316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.062151201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9821530
X-RAY DIFFRACTIONr_chiral_restr0.10.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021326
X-RAY DIFFRACTIONr_nbd_refined0.2290.21355
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.26029
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23284
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2480
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.213
X-RAY DIFFRACTIONr_nbd_other0.1640.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.225
X-RAY DIFFRACTIONr_mcbond_it1.8532.1573224
X-RAY DIFFRACTIONr_mcbond_other1.8482.1563223
X-RAY DIFFRACTIONr_mcangle_it2.5263.2334037
X-RAY DIFFRACTIONr_mcangle_other2.5253.2344038
X-RAY DIFFRACTIONr_scbond_it2.9562.4583373
X-RAY DIFFRACTIONr_scbond_other2.9552.4583374
X-RAY DIFFRACTIONr_scangle_it4.373.5574883
X-RAY DIFFRACTIONr_scangle_other4.373.5584884
X-RAY DIFFRACTIONr_lrange_it7.14326.5727737
X-RAY DIFFRACTIONr_lrange_other7.14126.577737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.4770.2695680.27111313X-RAY DIFFRACTION93.0821
1.477-1.5180.2585450.2511315X-RAY DIFFRACTION95.7224
1.518-1.5620.2685500.23811046X-RAY DIFFRACTION96.7381
1.562-1.610.2495760.21110781X-RAY DIFFRACTION96.8449
1.61-1.6630.2275400.20610500X-RAY DIFFRACTION97.0976
1.663-1.7210.2215310.19510102X-RAY DIFFRACTION97.4253
1.721-1.7860.2254890.1869860X-RAY DIFFRACTION97.5401
1.786-1.8590.2144820.1819498X-RAY DIFFRACTION97.8144
1.859-1.9410.2134910.1829100X-RAY DIFFRACTION97.9773
1.941-2.0360.2064560.1798754X-RAY DIFFRACTION98.2505
2.036-2.1460.1984510.1778284X-RAY DIFFRACTION98.4669
2.146-2.2760.2023860.1737937X-RAY DIFFRACTION98.7424
2.276-2.4330.1993790.1667459X-RAY DIFFRACTION98.8399
2.433-2.6280.213910.1666939X-RAY DIFFRACTION99.0005
2.628-2.8790.1913390.1666375X-RAY DIFFRACTION99.2608
2.879-3.2180.2083170.1725823X-RAY DIFFRACTION99.4493
3.218-3.7150.192810.1755137X-RAY DIFFRACTION99.5956
3.715-4.5480.1532070.1514404X-RAY DIFFRACTION99.762
4.548-6.4240.2121950.1863378X-RAY DIFFRACTION99.8603
6.424-70.4340.2880.161910X-RAY DIFFRACTION98.9109

+
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://pdbjlvh1.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