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- PDB-4zxn: Crystal structure of rat coronavirus strain New-Jersey Hemaggluti... -

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Basic information

Entry
Database: PDB / ID: 4zxn
TitleCrystal structure of rat coronavirus strain New-Jersey Hemagglutinin-Esterase
ComponentsHE protein
KeywordsVIRAL PROTEIN / Hemagglutinins / Coronavirus
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / metal ion binding / plasma membrane
Similarity search - Function
Hemagglutinin-esterase / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin-esterase
Similarity search - Component
Biological speciesRat coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBakkers, M.J.G. / Feitsma, L.J. / Huizinga, E.G. / de Groot, R.J.
CitationJournal: To Be Published
Title: Crystal structures of murine coronavirus hemagglutinin-esterases reveal structural basis for esterase substrate specificity
Authors: Bakkers, M.J.G. / Feitsma, L.J. / Huizinga, E.G. / de Groot, R.J.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0269
Polymers43,6111
Non-polymers1,4168
Water1,60389
1
A: HE protein
hetero molecules

A: HE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,05318
Polymers87,2212
Non-polymers2,83116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)60.710, 184.370, 76.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

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Components

#1: Protein HE protein / E3 glycoprotein


Mass: 43610.688 Da / Num. of mol.: 1 / Fragment: UNP residues 22-400 / Mutation: S40A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rat coronavirus (strain NJ) / Gene: HE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q3HS77, sialate O-acetylesterase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Bis Tris propane pH 7.5, 0.2M Sodium fluoride, 20% w/v PEG 3350
PH range: 7.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.2→35.49 Å / Num. obs: 22281 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.121 / Net I/σ(I): 8.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLM7.09data reduction
Aimless0.1.27data scaling
PHASER2.5.1phasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BCoV

Resolution: 2.2→35.49 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.603 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27826 1141 5.1 %RANDOM
Rwork0.2319 ---
obs0.23412 21128 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.989 Å2
Baniso -1Baniso -2Baniso -3
1--4.49 Å20 Å2-0 Å2
2--3.09 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 86 89 3101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023114
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.9624237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4935370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91324.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22115453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8621512
X-RAY DIFFRACTIONr_chiral_restr0.0610.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212429
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1260.391477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.2330.5851845
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3930.4861637
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined1.3233.6014724
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 73 -
Rwork0.294 1568 -
obs--100 %
Refinement TLS params.Method: refined / Details: Chain A / Origin x: -13.66 Å / Origin y: -26.355 Å / Origin z: -8.934 Å
111213212223313233
T0.8703 Å2-0.1016 Å2-0.0579 Å2-0.0366 Å2-0.0046 Å2--0.0447 Å2
L0.6719 °20.0363 °2-0.2181 °2-3.0971 °20.2672 °2--1.802 °2
S0.0862 Å °0.0159 Å °-0.149 Å °0.081 Å °-0.1237 Å °0.163 Å °0.3613 Å °-0.2338 Å °0.0375 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 388
2X-RAY DIFFRACTION1A - W601 - 689

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