[English] 日本語
Yorodumi
- PDB-2prx: Crystal structure of Thioesterase superfamily protein (ZP_0083725... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2prx
TitleCrystal structure of Thioesterase superfamily protein (ZP_00837258.1) from Shewanella loihica PV-4 at 1.65 A resolution
ComponentsThioesterase superfamily protein
KeywordsHYDROLASE / ZP_00837258.1 / Thioesterase superfamily protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyThioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Thioesterase superfamily protein
Function and homology information
Biological speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Thioesterase superfamily protein (ZP_00837258.1) from Shewanella loihica PV-4 at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioesterase superfamily protein
B: Thioesterase superfamily protein


Theoretical massNumber of molelcules
Total (without water)34,9102
Polymers34,9102
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-9 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.501, 38.501, 172.247
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Thioesterase superfamily protein


Mass: 17454.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: PV-4 / Gene: ZP_00837258.1, Shew_3755 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QJH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.1141.71TWO CRYSTALS WERE USED FOR THE SOLUTION THIS STRUCTURE. A 1.99A MAD DATA SET COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN INITIAL MODEL. THE MODEL WAS THEN REFINED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO AN ENHANCED RESOLUTION OF 1.5A.
2TWO CRYSTALS WERE USED FOR THE SOLUTION THIS STRUCTURE. A 1.99A MAD DATA SET COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN INITIAL MODEL. THE MODEL WAS THEN REFINED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO AN ENHANCED RESOLUTION OF 1.5A.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop9NANODROP, 2.4M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop8NANODROP, 2.4M (NH4)2SO4, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
21001
12
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.91837
SYNCHROTRONSSRL BL9-220.97927, 0.97941, 0.91162
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 23, 2007Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDFeb 15, 2007Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979271
30.979411
40.911621
ReflectionResolution: 1.5→86.066 Å / Num. obs: 35176 / % possible obs: 76.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.542.70.1834.1557721000.18361.3
1.54-1.582.70.1534.8568321290.15364.9
1.58-1.632.70.1345.5574821260.13465.5
1.63-1.682.70.1126.2573921130.11267.4
1.68-1.732.80.1057.2579420850.10570.4
1.73-1.792.80.0938592221150.09372.6
1.79-1.862.80.0799.4604621220.07974
1.86-1.9430.0710.4607720520.0775.3
1.94-2.0230.06311.4603419850.06375.5
2.02-2.123.20.05612.8618119580.05679.8
2.12-2.243.20.05712.2614919440.05781.9
2.24-2.373.10.05911.7582218760.05983.7
2.37-2.543.10.05612.3552017990.05685.8
2.54-2.7430.04814.1518117150.04886.5
2.74-330.04415.7486316160.04489.4
3-3.3530.04614.1442114800.04692.1
3.35-3.872.90.04215.6398913570.04292.7
3.87-4.7430.03716.7351711740.03797.3
4.74-6.713.20.04116.529089130.04196.9
6.71-86.074.30.04514.922375170.04599

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
SHELXrefinement
MolProbity3beta29model building
SOLVEphasing
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→28.736 Å / Num. parameters: 6902 / Num. restraintsaints: 9250 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. DATA IS TETARTOHEDRALLY TWINNED. REFINEMENT WAS PERFORMED WITH THE TWIN OPERATORS (K,H,-L), (-K,-H,-L), AND (-H,-K,L) AND THE RESPECTIVE TWIN FRACTIONS OF 0.28, 0.19, 0.15. 4. THE NOMINAL RESOLUTION IS 1.65 A WITH 7312 OBSERVED REFLECTIONS BETWEEN 1.65-1.50 (64.2% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. 5. THE R-FREE SET WAS GENERATED USING THE TWIN LAWS.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1811 -RANDOM EXPANDED BY TWIN LAW
Rwork0.199 ---
all0.203 35176 --
obs0.199 35102 72.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1975) 201-228
Displacement parametersBiso mean: 15.625 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 0 9 1714
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0.064
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0

+
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