[English] 日本語
Yorodumi
- PDB-7e30: Crystal structure of a novel alpha/beta hydrolase in apo form in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7.0E+30
TitleCrystal structure of a novel alpha/beta hydrolase in apo form in complex with citrate
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / alpha/beta dehydrogenase
Function / homologyCITRIC ACID
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsGao, J. / Han, X. / Zheng, Y.Y. / Liu, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2022
Title: Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase.
Authors: Pfaff, L. / Gao, J. / Li, Z. / Jackering, A. / Weber, G. / Mican, J. / Chen, Y. / Dong, W. / Han, X. / Feiler, C.G. / Ao, Y.F. / Badenhorst, C.P.S. / Bednar, D. / Palm, G.J. / Lammers, M. / ...Authors: Pfaff, L. / Gao, J. / Li, Z. / Jackering, A. / Weber, G. / Mican, J. / Chen, Y. / Dong, W. / Han, X. / Feiler, C.G. / Ao, Y.F. / Badenhorst, C.P.S. / Bednar, D. / Palm, G.J. / Lammers, M. / Damborsky, J. / Strodel, B. / Liu, W. / Bornscheuer, U.T. / Wei, R.
History
DepositionFeb 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: 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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha/beta hydrolase
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4478
Polymers55,7082
Non-polymers7396
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-77 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.974, 97.086, 99.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 258 or resid 401))
21(chain B and (resid 1 through 258 or resid 401))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 258 or resid 401))A0
211(chain B and (resid 1 through 258 or resid 401))B0

-
Components

#1: Protein alpha/beta hydrolase


Mass: 27853.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.42 Å3/Da / Density % sol: 49.11 % / Mosaicity: 0.353 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD, PEG 1500, NaAc

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 20, 2020
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→25 Å / Num. obs: 77551 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Χ2: 1.026 / Net I/σ(I): 17.1 / Num. measured all: 384676
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.56-1.623.20.475860.8380.2660.4841.03399.6
1.62-1.683.50.32476860.9110.20.3841.08599.9
1.68-1.764.10.25676910.9410.1440.2951.10399.9
1.76-1.854.80.20376500.9690.1020.2281.184100
1.85-1.975.70.15577090.9850.0710.1711.261100
1.97-2.125.70.1177140.9910.0510.1211.161100
2.12-2.335.70.08577460.9940.0390.0941.01499.9
2.33-2.675.70.07277900.9950.0330.0790.92100
2.67-3.365.80.0678450.9960.0270.0660.77100
3.36-255.50.06481340.9950.0290.0710.83299.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZRQ

5zrq


Resolution: 1.56→24.55 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1712 3866 4.99 %
Rwork0.1494 73583 -
obs0.1504 77449 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.5 Å2 / Biso mean: 20.1243 Å2 / Biso min: 8.56 Å2
Refinement stepCycle: final / Resolution: 1.56→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 47 555 4526
Biso mean--32.35 32.03 -
Num. residues----516
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1582X-RAY DIFFRACTION6.844TORSIONAL
12B1582X-RAY DIFFRACTION6.844TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.56-1.620.22323730.199672087581
1.62-1.680.2163910.180172967687
1.68-1.760.20483860.164472897675
1.76-1.850.1793830.152272617644
1.85-1.970.17293790.148173227701
1.97-2.120.17433900.141673207710
2.12-2.330.17933870.141173547741
2.33-2.670.18883850.149873957780
2.67-3.360.16553910.148874387829
3.36-24.550.14634010.142977008101

+
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