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- PDB-4mc7: Crystal structure of a subtype N11 neuraminidase-like protein of ... -

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Entry
Database: PDB / ID: 4mc7
TitleCrystal structure of a subtype N11 neuraminidase-like protein of A/flat-faced bat/Peru/033/2010 (H18N11)
ComponentsNEURAMINIDASE
KeywordsVIRAL PROTEIN / bat / influenza
Function / homologyNeuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.99 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Stevens, J.
CitationJournal: Plos Pathog. / Year: 2013
Title: New world bats harbor diverse influenza a viruses.
Authors: Tong, S. / Zhu, X. / Li, Y. / Shi, M. / Zhang, J. / Bourgeois, M. / Yang, H. / Chen, X. / Recuenco, S. / Gomez, J. / Chen, L.M. / Johnson, A. / Tao, Y. / Dreyfus, C. / Yu, W. / McBride, R. / ...Authors: Tong, S. / Zhu, X. / Li, Y. / Shi, M. / Zhang, J. / Bourgeois, M. / Yang, H. / Chen, X. / Recuenco, S. / Gomez, J. / Chen, L.M. / Johnson, A. / Tao, Y. / Dreyfus, C. / Yu, W. / McBride, R. / Carney, P.J. / Gilbert, A.T. / Chang, J. / Guo, Z. / Davis, C.T. / Paulson, J.C. / Stevens, J. / Rupprecht, C.E. / Holmes, E.C. / Wilson, I.A. / Donis, R.O.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEURAMINIDASE
B: NEURAMINIDASE
C: NEURAMINIDASE
D: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,58213
Polymers162,4974
Non-polymers1,0859
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-93 kcal/mol
Surface area49730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.374, 164.358, 214.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A75 - 437
2111B75 - 437
3111C75 - 437
4111D75 - 437

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Components

#1: Protein
NEURAMINIDASE


Mass: 40624.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/flat-faced bat/Peru/033/2010 (H18N11) / Production host: Trichoplusia ni (cabbage looper)
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca

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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: 3.35 Å3/Da / Density % sol: 63.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 mM calcium acetate, 10% PEG8000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 27, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→44.835 Å / Num. all: 39587 / Num. obs: 39587 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.99→3.11 Å / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0111refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.99→44.835 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / SU B: 42.396 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26009 2121 5.1 %RANDOM
Rwork0.21431 ---
all0.22 39587 --
obs0.21667 39587 93.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.133 Å2
Baniso -1Baniso -2Baniso -3
1-4.01 Å20 Å2-0 Å2
2---0.31 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.99→44.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11164 0 61 0 11225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211528
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.94515684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37251448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85324.16500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56151780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9651552
X-RAY DIFFRACTIONr_chiral_restr0.0910.21712
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218832
Refine LS restraints NCS

Ens-ID: 1 / Number: 2791 / Refine-ID: X-RAY DIFFRACTION / Weight position: 0.05

Dom-IDAuth asym-IDTypeRms dev position (Å)
1ATIGHT POSITIONAL0.05
2BTIGHT POSITIONAL0.06
3CTIGHT POSITIONAL0.05
4DTIGHT POSITIONAL0.05
1ATIGHT THERMAL11.05
2BTIGHT THERMAL12.58
3CTIGHT THERMAL10.22
4DTIGHT THERMAL10.6
LS refinement shellResolution: 2.99→3.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 111 -
Rwork0.339 2638 -
obs--88.45 %
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)
10.4694-0.6868-0.0141.25440.67411.7795-0.05080.0030.040.1135-0.0167-0.03420.1496-0.07990.06760.1689-0.0269-0.01690.0357-0.02960.067956.774624.07181.175
20.9036-1.27910.27971.9735-0.57280.5265-0.1804-0.19240.25870.31980.2114-0.4409-0.0160.1913-0.0310.14220.0724-0.15960.2081-0.16970.264219.682166.979265.4586
31.5464-0.83421.05671.4096-0.23021.3856-0.2185-0.04840.12530.2883-0.06580.0247-0.2473-0.14130.28430.35890.1082-0.20250.2054-0.1830.215939.55356.6983100.2611
41.3656-1.23930.45251.83950.14391.27070.31530.47520.1217-0.3225-0.3766-0.0326-0.09150.00160.06120.23310.1646-0.05630.3803-0.07750.196337.141734.45345.932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 437
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B75 - 437
4X-RAY DIFFRACTION2B501
5X-RAY DIFFRACTION3C75 - 437
6X-RAY DIFFRACTION3C501
7X-RAY DIFFRACTION4D75 - 437
8X-RAY DIFFRACTION4D501

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