[English] 日本語
Yorodumi
- PDB-4n21: Crystal structure of the GP2 Core Domain from the California Acad... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n21
TitleCrystal structure of the GP2 Core Domain from the California Academy of Science Virus
ComponentsGP2 Ectodomain
KeywordsVIRAL PROTEIN / CAS Virus / Post-Fusion Conformation / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homologyHelix Hairpins - #210 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / membrane / identical protein binding / Glycoprotein
Function and homology information
Biological speciesCAS virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsMalashkevich, V.N. / Koellhoffer, J.F. / Dai, Z. / Toro, R. / Lai, J.R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural Characterization of the Glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus-Like Species.
Authors: Koellhoffer, J.F. / Dai, Z. / Malashkevich, V.N. / Stenglein, M.D. / Liu, Y. / Toro, R. / S Harrison, J. / Chandran, K. / Derisi, J.L. / Almo, S.C. / Lai, J.R.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GP2 Ectodomain
B: GP2 Ectodomain
C: GP2 Ectodomain
D: GP2 Ectodomain
E: GP2 Ectodomain
F: GP2 Ectodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,36417
Polymers91,0646
Non-polymers1,30011
Water4,179232
1
A: GP2 Ectodomain
B: GP2 Ectodomain
C: GP2 Ectodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,35910
Polymers45,5323
Non-polymers8277
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14350 Å2
ΔGint-179 kcal/mol
Surface area20450 Å2
MethodPISA
2
D: GP2 Ectodomain
E: GP2 Ectodomain
F: GP2 Ectodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0057
Polymers45,5323
Non-polymers4734
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13870 Å2
ΔGint-169 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.676, 46.713, 109.451
Angle α, β, γ (deg.)102.320, 89.990, 119.980
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
GP2 Ectodomain


Mass: 15177.354 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAS virus / Gene: GP2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J7H5L9*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M lithium sulfate, 0.1 M MES-NaOH, pH 6, 35% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.213
11h,-h-k,-l20.151
11-H-K, K, -K-L30.161
11K, -H-K, H+K+L40.168
11-H-K, H, K+L50.146
11K, H, -H-K-L60.161
ReflectionResolution: 2→50 Å / Num. obs: 51572 / % possible obs: 97.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.059 / Χ2: 1.059 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0320.44726621.079196.9
2.03-2.0720.36524271.106196.9
2.07-2.1120.31525741.151197
2.11-2.1520.2625471.123197.1
2.15-2.220.21525961.103197.5
2.2-2.2520.19126191.124197.4
2.25-2.3120.14825121.062197.5
2.31-2.3720.1426121.071197.7
2.37-2.4420.12225911.09197.9
2.44-2.5220.11825701.107197.8
2.52-2.6120.09426671.097198.2
2.61-2.7120.0825251.024198.1
2.71-2.8420.07225400.983198.3
2.84-2.9920.06726161.027198.3
2.99-3.1720.06225950.988198.3
3.17-3.4220.05725801.026198.1
3.42-3.7620.04825960.982198
3.76-4.3120.0426021.024198.1
4.31-5.4320.03725780.93198.2
5.43-5020.04125631.096196.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å39.22 Å
Translation5.53 Å39.22 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G2K

4g2k


Resolution: 1.99→39.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2244 / WRfactor Rwork: 0.1765 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8833 / SU B: 3.44 / SU ML: 0.051 / SU R Cruickshank DPI: 0.038 / SU Rfree: 0.0332 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 2596 5 %RANDOM
Rwork0.1681 ---
obs0.1704 51570 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.83 Å2 / Biso mean: 53.8724 Å2 / Biso min: 20.66 Å2
Baniso -1Baniso -2Baniso -3
1--22.77 Å2-22.49 Å27.92 Å2
2--44.84 Å2-9.02 Å2
3----22.07 Å2
Refinement stepCycle: LAST / Resolution: 1.99→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5972 0 88 232 6292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196247
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.978430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5025769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55226.234308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.158151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4561512
X-RAY DIFFRACTIONr_chiral_restr0.080.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024544
LS refinement shellResolution: 1.992→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 153 -
Rwork0.203 3356 -
all-3509 -
obs--88.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.079-0.03130.11760.3063-0.40681.4026-0.0280.0063-0.0077-0.0122-0.02220.08040.02480.07210.05020.0213-0.02530.00940.0969-0.01340.058920.673413.631551.3651
20.1195-0.0734-0.18280.35990.1210.28430.01560.0168-0.0005-0.0085-0.0289-0.0449-0.0189-0.03380.01330.0109-0.02150.01350.1084-0.00240.054724.970915.00551.3899
30.1316-0.1098-0.02290.40310.25320.18130.01540.0207-0.0355-0.01230.0006-0.0038-0.0010.0168-0.0160.0233-0.01610.0240.1013-0.00770.059323.984510.645850.6968
40.0699-0.05450.18490.3165-0.17770.5101-0.0025-0.0004-0.00690.0173-0.0082-0.02590.0082-0.0260.01060.0204-0.02020.02860.1038-0.00450.05861.6838-2.384855.6932
50.1248-0.0739-0.06410.28640.46280.987-0.021-0.00560.04350.0187-0.0328-0.01120.058-0.00970.05380.0239-0.02310.0120.0938-0.00630.05440.65222.028455.0023
60.1163-0.08820.10140.323-0.4260.8027-0.0254-0.01-0.0110.0365-0.00850.0379-0.07450.00030.03390.0267-0.01960.01350.0937-0.01670.0598-2.5159-1.014156.4055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A229 - 351
2X-RAY DIFFRACTION2B229 - 351
3X-RAY DIFFRACTION3C228 - 351
4X-RAY DIFFRACTION4D229 - 351
5X-RAY DIFFRACTION5E230 - 350
6X-RAY DIFFRACTION6F228 - 351

+
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