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- PDB-8pkc: Structure of Api m1 in complex with the AM1-4 nanobody -

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Basic information

Entry
Database: PDB / ID: 8pkc
TitleStructure of Api m1 in complex with the AM1-4 nanobody
Components
  • AM1-4 nanobody
  • Phospholipase A2
KeywordsALLERGEN / antibody / nanobody
Function / homology
Function and homology information


phospholipase A2 activity / phospholipase A2 / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 domain superfamily
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Apis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsAagaard, J.B. / Gandini, R. / Spillner, E. / Miehe, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research0135-00061B Denmark
Citation
Journal: To be published
Title: Nanobody-based IgG formats as blocking antibodies of the major honeybee venom allergen Api m 1
Authors: Aagaard, J.B.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJun 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2
B: Phospholipase A2
C: AM1-4 nanobody
D: AM1-4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5826
Polymers58,1394
Non-polymers4422
Water00
1
A: Phospholipase A2
C: AM1-4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2913
Polymers29,0702
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase A2
D: AM1-4 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2913
Polymers29,0702
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.600, 93.600, 189.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 10 or resid 12...
d_2ens_1(chain "B" and (resid 2 through 10 or resid 12...
d_1ens_2(chain "C" and (resid 4 through 11 or resid 13...
d_2ens_2(chain "D" and (resid 4 through 11 or resid 13...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ILEILEGLYGLYAA2 - 102 - 10
d_12ens_1GLYGLYGLYGLYAA12 - 2212 - 22
d_13ens_1PHEPHEASPASPAA24 - 11924 - 119
d_14ens_1SERSERGLNGLNAA121 - 127121 - 127
d_15ens_1PHEPHETYRTYRAA129 - 134129 - 134
d_21ens_1ILEILEGLYGLYBB2 - 102 - 10
d_22ens_1GLYGLYGLYGLYBB12 - 2212 - 22
d_23ens_1PHEPHEASPASPBB24 - 11924 - 119
d_24ens_1SERSERGLNGLNBB121 - 127121 - 127
d_25ens_1PHEPHETYRTYRBB129 - 134129 - 134
d_11ens_2GLNGLNGLYGLYCC4 - 114 - 11
d_12ens_2VALVALLEULEUCC13 - 1913 - 19
d_13ens_2LEULEUTHRTHRCC21 - 2921 - 29
d_14ens_2SERSERSERSERCC3131
d_15ens_2TYRTYRLYSLYSCC33 - 4433 - 44
d_16ens_2ARGARGALAALACC46 - 7646 - 76
d_17ens_2SERSERPROPROCC78 - 8978 - 89
d_18ens_2ASPASPSERSERCC91 - 12891 - 128
d_21ens_2GLNGLNGLYGLYDD4 - 114 - 11
d_22ens_2VALVALLEULEUDD13 - 1913 - 19
d_23ens_2LEULEUTHRTHRDD21 - 2921 - 29
d_24ens_2SERSERSERSERDD3131
d_25ens_2TYRTYRLYSLYSDD33 - 4433 - 44
d_26ens_2ARGARGALAALADD46 - 7646 - 76
d_27ens_2SERSERPROPRODD78 - 8978 - 89
d_28ens_2ASPASPSERSERDD91 - 12891 - 128

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.256581908939, -0.959266540436, 0.118209256848), (-0.966269247275, 0.25178940142, -0.0540910260854), (0.0221238734375, -0.128100748365, -0.991514363231)51.3617293703, 35.5933368134, -58.8570198036
2given(-0.217159686744, -0.966231102721, 0.138705178664), (-0.975337408204, 0.209033263779, -0.0708663163352), (0.0394792427791, -0.150673656519, -0.987794937536)51.7005774964, 36.9889795614, -57.8612134398

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Components

#1: Protein Phospholipase A2 / bvPLA2 / Allergen Api m I / Phosphatidylcholine 2-acylhydrolase


Mass: 15274.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Apis mellifera (honey bee) / References: UniProt: P00630, phospholipase A2
#2: Antibody AM1-4 nanobody


Mass: 13795.243 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1M sodium citrate pH 5.5, 15% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 4.1→46.8 Å / Num. obs: 7086 / % possible obs: 99.83 % / Redundancy: 13.6 % / Biso Wilson estimate: 39.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1177 / Net I/σ(I): 16.12
Reflection shellResolution: 4.1→4.247 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.9098 / Num. unique obs: 687 / CC1/2: 0.897 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→46.8 Å / SU ML: 0.441 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2957 709 10.01 %
Rwork0.2583 6374 -
obs0.262 7083 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.15 Å2
Refinement stepCycle: LAST / Resolution: 4.1→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 28 0 4066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434156
X-RAY DIFFRACTIONf_angle_d0.80245600
X-RAY DIFFRACTIONf_chiral_restr0.0621586
X-RAY DIFFRACTIONf_plane_restr0.0058724
X-RAY DIFFRACTIONf_dihedral_angle_d12.64041506
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.958639947851
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS1.10146890133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.420.34051380.26941237X-RAY DIFFRACTION100
4.42-4.860.25071380.24521238X-RAY DIFFRACTION99.85
4.86-5.560.32821390.26561258X-RAY DIFFRACTION100
5.56-70.31011420.291274X-RAY DIFFRACTION100
7.01-46.80.26351520.23641367X-RAY DIFFRACTION99.8
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
121.481039823245.3701893285-33.9548080945
2-1.5762548032628.0634434674-30.6027272099
314.718051838355.3726996889-60.7378568177
4-13.305140040538.51103846-5.63490650182
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 134 )AA2 - 1341 - 133
22chain 'B' and (resid 1 through 134 )BC1 - 1341 - 134
33chain 'C' and (resid 2 through 129 )CE2 - 1291 - 128
44chain 'D' and (resid 2 through 128 )DF2 - 1281 - 127

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