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- PDB-4n21: Crystal structure of the GP2 Core Domain from the California Acad... -

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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 / 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: 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
Revision 1.4Oct 30, 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
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

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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


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 44.09 %
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

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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, L10.213
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

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Phasing

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

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