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- PDB-4n23: Crystal structure of the GP2 Core Domain from the California Acad... -

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Basic information

Entry
Database: PDB / ID: 4n23
TitleCrystal structure of the GP2 Core Domain from the California Academy of Science Virus, monoclinic symmetry
ComponentsGP2 Ectodomain
KeywordsVIRAL PROTEIN / Marburg Virus / Post-Fusion Conformation / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homologyTLV/ENV coat polyprotein / Helix Hairpins - #210 / Helix Hairpins / host cell plasma membrane / Orthogonal Bundle / Mainly Alpha / identical protein binding / membrane / Glycoprotein
Function and homology information
Biological speciesCAS virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP2 Ectodomain
B: GP2 Ectodomain
C: GP2 Ectodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1238
Polymers45,5323
Non-polymers5915
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-156 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.866, 46.718, 109.474
Angle α, β, γ (deg.)90.000, 104.280, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-402-

MPD

21B-535-

HOH

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Components

#1: Protein GP2 Ectodomain


Mass: 15177.354 Da / Num. of mol.: 3
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


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MCSG4-D10 - 0.2 M lithium sulfate, 0.1 M MES-NaOH, pH 6, 35% MPD, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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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, L10.299
111/2H+3/2K, 1/2H-1/2K, -1/2H-1/2K-L20.347
111/2H-3/2K, -1/2H-1/2K, -1/2H+1/2K-L30.354
ReflectionResolution: 2→50 Å / Num. obs: 27014 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.072 / Χ2: 0.983 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.033.70.49113621199.9
2.03-2.073.70.4212731.023199.8
2.07-2.113.70.35813841.0351100
2.11-2.153.70.29712791.039199.8
2.15-2.23.80.25513811.058199.9
2.2-2.253.70.21713511.0511100
2.25-2.313.80.17613520.9631100
2.31-2.373.70.16313330.93199.9
2.37-2.443.70.14413380.935199.9
2.44-2.523.80.13913480.917199.8
2.52-2.613.80.1113760.979199.9
2.61-2.713.80.09313170.937199.9
2.71-2.843.80.08713390.951100
2.84-2.993.80.08113581.038199.9
2.99-3.173.70.08213541.132199.9
3.17-3.423.60.07713541.09199.7
3.42-3.763.50.06513620.967199.9
3.76-4.313.60.05513700.815199.9
4.31-5.433.70.04413760.864199.8
5.43-503.60.04614070.939198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.89 Å39.21 Å
Translation1.89 Å39.21 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N21

4n21


Resolution: 2→39.21 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2323 / WRfactor Rwork: 0.1842 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8177 / SU B: 5.458 / SU ML: 0.078 / SU R Cruickshank DPI: 0.0378 / SU Rfree: 0.0346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1350 5 %RANDOM
Rwork0.1762 ---
obs0.1788 26977 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.85 Å2 / Biso mean: 52.4457 Å2 / Biso min: 16.54 Å2
Baniso -1Baniso -2Baniso -3
1-30.71 Å2-0 Å24.09 Å2
2---10.14 Å20 Å2
3----20.57 Å2
Refinement stepCycle: LAST / Resolution: 2→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 40 131 3157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193106
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.9674181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6765378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30626.169154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63615617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.593156
X-RAY DIFFRACTIONr_chiral_restr0.080.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022258
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 103 -
Rwork0.207 1766 -
all-1869 -
obs--96.14 %
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)
10.5231-0.04440.70910.2276-0.0441.0566-0.01580.04060.0112-0.03540.00040.0409-0.03120.09650.01540.0997-0.01820.02570.0231-0.0060.136510.912623.03550.8486
20.5988-0.0215-0.38720.2131-0.11432.6125-0.04490.02030.0847-0.0135-0.053-0.020.0669-0.0540.09790.09240.00920.00610.01690.01130.138613.935226.486651.4911
30.5855-0.01940.12990.19110.18531.456-0.02860.0525-0.0545-0.01580.0068-0.0116-0.0542-0.02120.02180.08820.00760.01990.00840.00430.124515.347622.237450.1907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A229 - 351
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1C401
4X-RAY DIFFRACTION2B230 - 351
5X-RAY DIFFRACTION2B401
6X-RAY DIFFRACTION3C228 - 351
7X-RAY DIFFRACTION3C402 - 403

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