[English] 日本語
Yorodumi
- PDB-3cjy: Crystal structure of putative thioesterase (YP_496845.1) from Nov... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cjy
TitleCrystal structure of putative thioesterase (YP_496845.1) from Novosphingobium aromaticivorans DSM 12444 at 1.70 A resolution
ComponentsPutative thioesterase
KeywordsHYDROLASE / YP_496845.1 / Putative thioesterase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / Acyl-CoA thioesterase C-terminal domain / Acyl-CoA thioesterase, double hotdog domain / Acyl-CoA thioesterase, double hotdog domain / : / Acyl-CoA thioesterase N-terminal domain / Porin / HotDog domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acyl-CoA thioesterase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative thioesterase (YP_496845.1) from Novosphingobium aromaticivorans DSM 12444 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Putative thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8699
Polymers27,0981
Non-polymers7718
Water3,477193
1
A: Putative thioesterase
hetero molecules

A: Putative thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,73818
Polymers54,1962
Non-polymers1,54216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area4550 Å2
ΔGint-20.5 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.053, 111.755, 74.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Putative thioesterase


Mass: 27097.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: YP_496845.1, Saro_1571 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2G812

-
Non-polymers , 5 types, 201 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.19
Details: NANODROP, 0.19M Calcium chloride, 19.6% PEG 400, 5.0% Glycerol, 0.1M HEPES pH 7.19, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97932, 0.97914
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 29, 2008 / Details: Flat 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
20.979321
30.979141
ReflectionResolution: 1.7→29.161 Å / Num. obs: 28153 / % possible obs: 100 % / Redundancy: 4 % / Biso Wilson estimate: 17.089 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.744.10.6361.2833520520.636100
1.74-1.794.10.5071.5810619920.507100
1.79-1.844.10.3972795319560.397100
1.84-1.94.10.3312.4766118790.331100
1.9-1.964.10.2553758418610.255100
1.96-2.034.10.2113.7722717740.211100
2.03-2.114.10.1714.5700317160.171100
2.11-2.194.10.1445.3676616590.144100
2.19-2.294.10.126.3648015860.12100
2.29-2.44.10.1116.8627115340.111100
2.4-2.534.10.1076.9592414550.107100
2.53-2.694.10.0957.7556013580.095100
2.69-2.874.10.0878.2536613210.087100
2.87-3.140.0729.7487612040.072100
3.1-3.440.05711.4451111240.057100
3.4-3.840.04913.3405010130.049100
3.8-4.393.90.04413.735889090.044100
4.39-5.383.90.0414.730357820.04100
5.38-7.63.80.04414.723756180.044100
7.6-29.1613.50.03218.312603600.03298.3

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.161 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.029 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.099
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL, PEG AND CALCIUM WERE MODELED BASED ON PURIFICATION, CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. 4. THERE IS UNMODELED DENSITY BETWEEN AMINO ACIDS ASP139 AND ASN141.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1414 5 %RANDOM
Rwork0.173 ---
obs0.174 28130 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.505 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---0.68 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 49 193 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221974
X-RAY DIFFRACTIONr_bond_other_d0.0010.021335
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9932690
X-RAY DIFFRACTIONr_angle_other_deg1.18633251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2565267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23923.19472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94315275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4161515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212260
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02391
X-RAY DIFFRACTIONr_mcbond_it0.9411.51298
X-RAY DIFFRACTIONr_mcbond_other0.2541.5530
X-RAY DIFFRACTIONr_mcangle_it1.60522072
X-RAY DIFFRACTIONr_scbond_it2.4063676
X-RAY DIFFRACTIONr_scangle_it3.7224.5617
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 100 -
Rwork0.242 1946 -
all-2046 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -12.1263 Å / Origin y: -44.1296 Å / Origin z: 3.7875 Å
111213212223313233
T-0.017 Å20.0149 Å20.01 Å2--0.0315 Å2-0.0094 Å2---0.0352 Å2
L0.7355 °20.0484 °20.2721 °2-0.8839 °2-0.1065 °2--0.4209 °2
S0.0035 Å °-0.0359 Å °0.0877 Å °0.0477 Å °-0.0166 Å °0.071 Å °-0.0879 Å °-0.0519 Å °0.0131 Å °

+
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