[English] 日本語
Yorodumi
- PDB-7msy: Structure of CalU17 from the Calicheamicin Biosynthesis Pathway o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7msy
TitleStructure of CalU17 from the Calicheamicin Biosynthesis Pathway of Micromonospora echinospora
ComponentsCalU17
KeywordsUNKNOWN FUNCTION / Enediyne biosynthetic pathway / Calicheamicin Biosynthesis
Function / homologySulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / metal ion binding / CalU17
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.21 Å
AuthorsKosgei, A.J. / Miller, M.D. / Xu, W. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM115261 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA217255 United States
National Science Foundation (NSF, United States)STC-1231306 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina.
Authors: Kosgei, A.J. / Miller, M.D. / Bhardwaj, M. / Xu, W. / Thorson, J.S. / Van Lanen, S.G. / Phillips Jr., G.N.
History
DepositionMay 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CalU17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,97711
Polymers35,2891
Non-polymers68810
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-44 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.465, 53.465, 223.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-689-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein CalU17


Mass: 35289.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is CalU17 structure with the tag cleaved and soaked in Calcium to find out if the calcium binding site is conserved.
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calU17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KND1

-
Non-polymers , 5 types, 234 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Magnesium formate dihydrate 20% w/v PEG 3,350 pH 7.0;

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.5497 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2019
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5497 Å / Relative weight: 1
ReflectionResolution: 2.21→48.23 Å / Num. obs: 16890 / % possible obs: 97.8 % / Redundancy: 20.735 % / Biso Wilson estimate: 62.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.096 / Χ2: 1.049 / Net I/σ(I): 19.79 / Num. measured all: 350217
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
2.21-2.263.2212.6580.25298912389283.12775
2.26-2.337.5481.9090.658703122311532.05294.30.334
2.33-2.3912.0361.3961.3113962116311601.45999.70.641
2.39-2.4715.4561.12.0117574113711371.1371000.82
2.47-2.5520.6950.813.4523634114211420.8311000.95
2.55-2.6424.7180.5725.6726349106610660.5841000.974
2.64-2.7426.1720.4237.9927193103910390.4311000.988
2.74-2.8525.960.30310.9726349101510150.3091000.994
2.85-2.9825.1690.23414.18246919819810.2391000.995
2.98-3.1224.7110.17718.2227849229220.1811000.997
3.12-3.2924.9030.13623.47221898918910.1391000.998
3.29-3.4926.0060.10130.96220018468460.1031000.999
3.49-3.7325.8680.08437.61206177977970.0861000.999
3.73-4.0324.9560.07243.69186927497490.0741000.999
4.03-4.4124.0380.06347.69168997037030.0641000.999
4.41-4.9423.9560.06150.6152846386380.0621000.999
4.94-5.725.5030.05952.25145625715710.0611000.999
5.7-6.9824.0980.05652.15120254994990.0571000.999
6.98-9.8721.6820.04656.2787164024020.0481001
9.87-48.2319.9360.04160.650042532510.04299.20.999

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.17.1phasing
XSCALEVERSION Mar 15, 2019data scaling
XDS0.86data reduction
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7ML6

7ml6


Resolution: 2.21→48.23 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 840 4.98 %
Rwork0.1837 16043 -
obs0.1864 16883 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.27 Å2 / Biso mean: 73.7953 Å2 / Biso min: 48.48 Å2
Refinement stepCycle: final / Resolution: 2.21→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 84 225 2613
Biso mean--101.88 68.49 -
Num. residues----292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.350.49281090.4522318242786
2.35-2.530.41931690.358126322801100
2.53-2.780.2661450.188126702815100
2.78-3.180.30771170.208127252842100
3.18-4.010.23651330.148827662899100
4.01-48.230.18991670.162529323099100
Refinement TLS params.Method: refined / Origin x: 22.2761 Å / Origin y: 0.8286 Å / Origin z: 38.6378 Å
111213212223313233
T0.5651 Å20.0228 Å20.0243 Å2-0.6731 Å20.0468 Å2--0.6164 Å2
L1.3401 °20.1853 °2-0.1008 °2-1.5325 °2-0.5008 °2--1.298 °2
S-0.0224 Å °-0.0045 Å °-0.0583 Å °-0.0016 Å °-0.016 Å °-0.05 Å °0.1297 Å °0.0293 Å °-0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 307
2X-RAY DIFFRACTION1allB2
3X-RAY DIFFRACTION1allC401 - 408
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allS2 - 327
6X-RAY DIFFRACTION1allE1 - 2

+
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