[English] 日本語
Yorodumi
- PDB-8gzi: Crystal Structure of ApiI in complex with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gzi
TitleCrystal Structure of ApiI in complex with SAH
ComponentsApiI
KeywordsBIOSYNTHETIC PROTEIN / complex
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesApiospora montagnei NRRL 25634 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12209677016 Å
AuthorsZhou, J.H. / Lu, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91856202 China
CitationJournal: To Be Published
Title: Crystal Structure of ApiI in complex with SAH
Authors: Zhou, J.H. / Lu, J.Y.
History
DepositionSep 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ApiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2194
Polymers43,6801
Non-polymers5393
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.024, 98.024, 80.257
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

-
Components

#1: Protein ApiI


Mass: 43680.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apiospora montagnei NRRL 25634 (fungus)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M MES pH6, 20%(w/v)PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.12→37.522 Å / Num. obs: 25591 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 32.7129451443 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.028 / Rsym value: 0.092 / Net I/σ(I): 20
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1855 / CC1/2: 0.996 / Rpim(I) all: 0.185 / Rrim(I) all: 0.606 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WUP

7wup


Resolution: 2.12209677016→37.5214098838 Å / SU ML: 0.243882300324 / Cross valid method: FREE R-VALUE / σ(F): 1.33646519919 / Phase error: 25.2735300356
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253678668743 1245 4.89540736081 %
Rwork0.202601129552 24187 -
obs0.205122000596 25432 99.4680851064 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.2051386468 Å2
Refinement stepCycle: LAST / Resolution: 2.12209677016→37.5214098838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 36 139 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008047015724182970
X-RAY DIFFRACTIONf_angle_d0.9274660670434024
X-RAY DIFFRACTIONf_chiral_restr0.0542997095621471
X-RAY DIFFRACTIONf_plane_restr0.006149569875516
X-RAY DIFFRACTIONf_dihedral_angle_d8.083207847011810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1221-2.20710.2667087479971530.2092511843942632X-RAY DIFFRACTION99.7492836676
2.2071-2.30750.3485400865341350.2809116930622547X-RAY DIFFRACTION96.2325080732
2.3075-2.42910.2786182260591370.2094513601462692X-RAY DIFFRACTION99.9293535853
2.4291-2.58130.2735818845441170.2074187800522706X-RAY DIFFRACTION99.9292035398
2.5813-2.78050.251024472521310.2120785490432651X-RAY DIFFRACTION100
2.7805-3.06020.2527912125331060.2183385441592732X-RAY DIFFRACTION100
3.0602-3.50280.2440119077321390.2117674259682723X-RAY DIFFRACTION99.9650716032
3.5028-4.4120.2545772868931600.1826847586832709X-RAY DIFFRACTION100

+
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