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- PDB-1nmc: COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CH... -

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Entry
Database: PDB / ID: 1nmc
TitleCOMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CHAIN ANTIBODY WITH A 15 RESIDUE LINKER AND INFLUENZA VIRUS NEURAMINIDASE
Components
  • (SINGLE CHAIN ...Single-chain variable fragment) x 2
  • NEURAMINIDASE
KeywordsCOMPLEX (SINGLE-CHAIN ANTIBODY/ANTIGEN) / COMPLEX (SINGLE-CHAIN ANTIBODY-ANTIGEN) / HYDROLASE / COMPLEX (SINGLE-CHAIN ANTIBODY-ANTIGEN) complex
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / ec:3.2.1.18: / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / integral component of membrane / metal ion binding
Glycoside hydrolase, family 34 / Sialidase, Influenza viruses A/B / Sialidase superfamily / Neuraminidase
Neuraminidase / gb:501094:
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMalby, R.L. / Mccoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Three-dimensional structures of single-chain Fv-neuraminidase complexes.
Authors: Malby, R.L. / McCoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M.
#1: Journal: Proteins / Year: 1993
Title: Recombinant Antineuraminidase Single Chain Antibody: Expression, Characterization, and Crystallization in Complex with Antigen
Authors: Malby, R.L. / Caldwell, J.B. / Gruen, L.C. / Harley, V.R. / Ivancic, N. / Kortt, A.A. / Lilley, G.G. / Power, B.E. / Webster, R.G. / Colman, P.M. / Hudson, P.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 21, 1997 / Release: Sep 23, 1998
RevisionDateData content typeGroupProviderType
1.0Sep 23, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: NEURAMINIDASE
H: SINGLE CHAIN ANTIBODY
L: SINGLE CHAIN ANTIBODY
A: NEURAMINIDASE
B: SINGLE CHAIN ANTIBODY
C: SINGLE CHAIN ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,22326
Polymers138,5716
Non-polymers3,65120
Water3,243180
1
N: NEURAMINIDASE
H: SINGLE CHAIN ANTIBODY
L: SINGLE CHAIN ANTIBODY
hetero molecules

N: NEURAMINIDASE
H: SINGLE CHAIN ANTIBODY
L: SINGLE CHAIN ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,22326
Polymers138,5716
Non-polymers3,65120
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
2
A: NEURAMINIDASE
B: SINGLE CHAIN ANTIBODY
C: SINGLE CHAIN ANTIBODY
hetero molecules

A: NEURAMINIDASE
B: SINGLE CHAIN ANTIBODY
C: SINGLE CHAIN ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,22326
Polymers138,5716
Non-polymers3,65120
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Unit cell
γ
α
β
Length a, b, c (Å)144.400, 144.400, 227.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.998491, 0.05492, -0.000553), (-0.054921, 0.998491, -0.000301), (0.000536, 0.000331, 1)
Vector: 0.1759, 3.9769, 113.4122)

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Components

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Protein/peptide , 1 types, 2 molecules NA

#1: Protein/peptide NEURAMINIDASE /


Mass: 43723.770 Da / Num. of mol.: 2 / Fragment: RESIDUES 82 - 468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: N9 / Variant: A/TERN/AUSTRALIA/G70C/75 / Cell (production host): EGG / Production host: Gallus gallus (chicken) / References: UniProt: P03472, EC: 3.2.1.18

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SINGLE CHAIN ... , 2 types, 4 molecules HBLC

#2: Protein/peptide SINGLE CHAIN ANTIBODY


Mass: 13399.659 Da / Num. of mol.: 2
Fragment: VH AND VL DOMAINS OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIFTEEN RESIDUE POLYPEPTIDE LINKER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 501094
#3: Protein/peptide SINGLE CHAIN ANTIBODY


Mass: 12162.203 Da / Num. of mol.: 2
Fragment: VH AND VL DOMAINS OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIFTEEN RESIDUE POLYPEPTIDE LINKER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 501094

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Non-polymers , 5 types, 200 molecules

#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Calcium
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O / Water

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Details

Nonpolymer detailsTHE THREE OLIGOSACCHARIDES COVALENTLY ATTACHED TO N9 NEURAMINIDASE ARE NUMBERED BY THE ASN RESIDUE ...THE THREE OLIGOSACCHARIDES COVALENTLY ATTACHED TO N9 NEURAMINIDASE ARE NUMBERED BY THE ASN RESIDUE TO WHICH THEY ARE ATTACHED.

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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: 4 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.6
Details: NC10 SCFV(15) AND N9 NA WERE MIXED TOGETHER (SCFV(15) IN SLIGHT MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOUR DIFFUSION AGAINST PHOSPHATE BUFFER 1.3M PH6.8.
PH range: 6.6-6.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Malby, R.L., (1993) Proteins: Struct.,Funct., Genet., 16, 57.
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
15 mg/mlNC10scFvdrop
210 mg/mlN9NAdrop
31.7 Mpotassium phosphatedrop
41.3 Mphosphatereservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: PHOTON FACTORY / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 67425 / % possible obs: 80 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.104
Reflection shellResolution: 2.5→2.6 Å / % possible all: 70
Reflection
*PLUS
Num. measured all: 156708

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Processing

Software
NameVersionClassification
WEISdata collection
PROTEINdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
PROTEINdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NCA
Resolution: 2.5→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: A POSTERIORI / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 -10 %RANDOM
Rwork0.22 ---
Obs0.22 64026 80 %-
Displacement parametersBiso mean: 23 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9734 0 224 180 10138
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT
LS refinement shellResolution: 2.5→2.65 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.36 9223 -
Obs--70 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1PARHCSDX.PROTOPHCSDX.PRO
2PARAM19.SOLTOPH19.SOL
3PARAM1.CHOTOPH1.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47

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