[English] 日本語
Yorodumi
- PDB-7x2x: Crystal Structure of hetero-Diels-Alderase PycR1 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x2x
TitleCrystal Structure of hetero-Diels-Alderase PycR1 in complex with 10-hydroxy-8E-humulene
ComponentsPycR1
KeywordsBIOSYNTHETIC PROTEIN / Complex
Function / homologyChem-80N
Function and homology information
Biological speciesLeptobacillium sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsZhou, J. / Lu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91856202 China
CitationJournal: To Be Published
Title: Calcium-dependent glycosylated enzyme in the tandem hetero-Diels-Alder reaction
Authors: Zhou, J. / Lu, J.
History
DepositionFeb 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: 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: PycR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,35120
Polymers42,9541
Non-polymers3,39619
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint29 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.616, 78.616, 163.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

21A-899-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein PycR1


Mass: 42954.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptobacillium sp. (fungus) / Production host: Escherichia coli (E. coli)

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(6-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpb6-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

-
Non-polymers , 6 types, 474 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-80N / (1R,2E,6E,9E)-2,5,5,9-tetramethylcycloundeca-2,6,9-trien-1-ol


Mass: 220.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH=6.0, 0.2 M Ammonium chloride, 20%(w/v) PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.58→45.93 Å / Num. obs: 70881 / % possible obs: 100 % / Redundancy: 25.9 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.026 / Rrim(I) all: 0.098 / Net I/σ(I): 20.9
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 25.5 % / Rmerge(I) obs: 1.699 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3458 / CC1/2: 0.804 / Rpim(I) all: 0.484 / Rrim(I) all: 1.767 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X2N

7x2n


Resolution: 1.58→45.93 Å / SU ML: 0.1524 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 3565 5.04 %
Rwork0.1644 67214 -
obs0.1657 70779 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.45 Å2
Refinement stepCycle: LAST / Resolution: 1.58→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 219 457 3370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242981
X-RAY DIFFRACTIONf_angle_d1.21344061
X-RAY DIFFRACTIONf_chiral_restr0.0763477
X-RAY DIFFRACTIONf_plane_restr0.0079501
X-RAY DIFFRACTIONf_dihedral_angle_d21.2867496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.30411450.24332652X-RAY DIFFRACTION100
1.6-1.620.26521300.22822635X-RAY DIFFRACTION100
1.62-1.650.25331390.2232638X-RAY DIFFRACTION100
1.65-1.670.23711400.2142669X-RAY DIFFRACTION100
1.67-1.70.25141380.20442647X-RAY DIFFRACTION100
1.7-1.730.21791420.19392631X-RAY DIFFRACTION100
1.73-1.760.221400.18532663X-RAY DIFFRACTION100
1.76-1.80.22831510.1752636X-RAY DIFFRACTION99.96
1.8-1.830.19531430.1742655X-RAY DIFFRACTION100
1.83-1.870.19181400.18262673X-RAY DIFFRACTION100
1.87-1.920.20271460.17482668X-RAY DIFFRACTION100
1.92-1.960.18731350.16922644X-RAY DIFFRACTION100
1.96-2.020.21231550.17522662X-RAY DIFFRACTION100
2.02-2.080.23311170.17262672X-RAY DIFFRACTION100
2.08-2.140.19851520.16982665X-RAY DIFFRACTION100
2.14-2.220.21211420.16712691X-RAY DIFFRACTION100
2.22-2.310.18491370.16762679X-RAY DIFFRACTION100
2.31-2.410.21481400.16532692X-RAY DIFFRACTION100
2.42-2.540.19961300.16872707X-RAY DIFFRACTION100
2.54-2.70.19051620.16592700X-RAY DIFFRACTION100
2.7-2.910.21091610.17322686X-RAY DIFFRACTION100
2.91-3.20.15771340.15812738X-RAY DIFFRACTION100
3.2-3.670.16921630.15722732X-RAY DIFFRACTION100
3.67-4.620.1661420.13712811X-RAY DIFFRACTION100
4.62-45.930.16311410.15822968X-RAY DIFFRACTION99.94

+
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