[English] 日本語
Yorodumi
- PDB-3es1: Crystal structure of protein with a cupin-like fold and unknown f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3es1
TitleCrystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution
ComponentsCupin 2, conserved barrel domain protein
Keywordsstructural genomics / unknown function / YP_001165807.1 / protein with a cupin-like fold and unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Cupin domain
Function / homology
Function and homology information


Ubiquitin Ligase Nedd4; Chain: W; - #150 / : / Ubiquitin Ligase Nedd4; Chain: W; / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / Single Sheet / RmlC-like jelly roll fold / Jelly Rolls ...Ubiquitin Ligase Nedd4; Chain: W; - #150 / : / Ubiquitin Ligase Nedd4; Chain: W; / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / Single Sheet / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cupin 2, conserved barrel domain protein
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 6, 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: Cupin 2, conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9912
Polymers18,9561
Non-polymers351
Water3,387188
1
A: Cupin 2, conserved barrel domain protein
hetero molecules

A: Cupin 2, conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9824
Polymers37,9112
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area6350 Å2
ΔGint-52 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.330, 78.330, 107.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-227-

HOH

-
Components

#1: Protein Cupin 2, conserved barrel domain protein


Mass: 18955.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria)
Gene: YP_001165807.1, Saro_3421, / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A4XEC0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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 (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2M NaThioCyanate, 20.0% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92522,0.97932,0.97879
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 11, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.925221
20.979321
30.978791
ReflectionResolution: 1.91→28.665 Å / Num. obs: 15326 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.05 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 13.43
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.0112.1221272830197.4
1.98-2.060.0112.9222112828197.6
2.06-2.150.0114208412666197.5
2.15-2.260.0114.8213052725197.8
2.26-2.410.0115.9233692972197.9
2.41-2.590.0117.5213232711198.2
2.59-2.850.01110.7220572808198.4
2.85-3.260.01118.2222802832198.5
3.26-4.10.01133221382828198.9
4.1-28.6650.01144225892872198.2

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→28.665 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.399 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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. 4.ONE CHLORIDE ION FROM CRYSTALLIZATION WAS MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 765 5 %RANDOM
Rwork0.17 ---
obs0.172 15326 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.37 Å2 / Biso mean: 22.97 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.91→28.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 1 188 1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211299
X-RAY DIFFRACTIONr_bond_other_d0.0020.02870
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9611771
X-RAY DIFFRACTIONr_angle_other_deg1.41332124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89123.72959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22315210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0221512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211476
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02250
X-RAY DIFFRACTIONr_mcbond_it0.8151.5831
X-RAY DIFFRACTIONr_mcbond_other0.2261.5337
X-RAY DIFFRACTIONr_mcangle_it1.32321347
X-RAY DIFFRACTIONr_scbond_it2.0973468
X-RAY DIFFRACTIONr_scangle_it3.0844.5424
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 53 -
Rwork0.205 1047 -
all-1100 -
obs--96.58 %
Refinement TLS params.Method: refined / Origin x: 54.2608 Å / Origin y: 22.7422 Å / Origin z: 15.0084 Å
111213212223313233
T0.0041 Å2-0.0307 Å2-0.0067 Å2--0.0414 Å20.0031 Å2---0.0164 Å2
L0.2197 °20.0976 °2-0.0336 °2-0.3199 °2-0.0817 °2--0.4971 °2
S-0.0146 Å °0.0042 Å °0.0034 Å °-0.0202 Å °-0.0206 Å °-0.0653 Å °-0.0684 Å °0.019 Å °0.0353 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