[English] 日本語
Yorodumi
- PDB-9iq5: CatM, SnoaL-like protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iq5
TitleCatM, SnoaL-like protein
ComponentsSnoaL-like domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Homologous of AkaM / catalyzing tandem cyclization.
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / SnoaL-like domain-containing protein
Function and homology information
Biological speciesStreptantibioticus cattleyicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsZhang, B. / Zhu, A. / Ma, X.X. / Ge, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22277051,81925033, 22193071 China
CitationJournal: To Be Published
Title: Tandem Michael addition and Knoevenagel condensation catalyzed by NTF2-Like Enzymes as iminium catalysis
Authors: Liu, C.L. / Zhang, B. / Ge, H.M.
History
DepositionJul 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SnoaL-like domain-containing protein
B: SnoaL-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)29,0972
Polymers29,0972
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-12 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.092, 61.985, 99.609
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 3 through 121)
d_2ens_1(chain "B" and ((resid 3 through 4 and (name N...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 3 - 121 / Label seq-ID: 3 - 121

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.943107759689, -0.0295911266557, -0.33116781069), (0.0257157762366, -0.999539980438, 0.0160787548534), (-0.33149125549, 0.00664776115191, 0.943434870463)Vector: 8. ...NCS oper: (Code: given
Matrix: (-0.943107759689, -0.0295911266557, -0.33116781069), (0.0257157762366, -0.999539980438, 0.0160787548534), (-0.33149125549, 0.00664776115191, 0.943434870463)
Vector: 8.92469390834, 53.9402682118, 1.20330639919)

-
Components

#1: Protein SnoaL-like domain-containing protein


Mass: 14548.470 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptantibioticus cattleyicolor (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria)
Gene: SCATT_01420
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G8X1I4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M Ammonium sulfate 0.1 M Sodium HEPES 7.5 2 % v/v PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.06→38.82 Å / Num. obs: 16707 / % possible obs: 95.14 % / Redundancy: 11.3 % / Biso Wilson estimate: 43.66 Å2 / CC1/2: 0.997 / Net I/σ(I): 17.92
Reflection shellResolution: 2.06→2.13 Å / Num. unique obs: 1466 / CC1/2: 0.756

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9IQ3

9iq3


Resolution: 2.06→38.82 Å / SU ML: 0.2903 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.198
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2697 792 4.76 %
Rwork0.2364 15850 -
obs0.238 16642 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.94 Å2
Refinement stepCycle: LAST / Resolution: 2.06→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 47 1873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961852
X-RAY DIFFRACTIONf_angle_d1.06212491
X-RAY DIFFRACTIONf_chiral_restr0.0608281
X-RAY DIFFRACTIONf_plane_restr0.0105322
X-RAY DIFFRACTIONf_dihedral_angle_d14.5744679
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.699677901917 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.190.35531290.30742472X-RAY DIFFRACTION91.39
2.19-2.360.37711410.29842515X-RAY DIFFRACTION92.61
2.36-2.60.33411350.27882749X-RAY DIFFRACTION99.93
2.6-2.970.32141310.27522548X-RAY DIFFRACTION92.99
2.97-3.740.2621240.24332675X-RAY DIFFRACTION95.59
3.74-38.820.22661320.20182891X-RAY DIFFRACTION98.15
Refinement TLS params.Method: refined / Origin x: 2.46919687774 Å / Origin y: 27.1762397647 Å / Origin z: 10.9766063844 Å
111213212223313233
T0.375960948784 Å2-0.00232098605819 Å2-0.0246507826097 Å2-0.376474038344 Å20.00433321505015 Å2--0.266314498021 Å2
L2.38127979349 °20.346066668854 °2-0.441635684575 °2-5.12084934211 °21.31343963935 °2--3.71891716171 °2
S-0.0868017434301 Å °-0.0625218886331 Å °0.225976865895 Å °-0.284699198818 Å °0.0309445658256 Å °0.561297421448 Å °-0.475054986842 Å °-0.00652540739876 Å °0.0220618122275 Å °
Refinement TLS groupSelection details: all

+
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