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- PDB-5vjq: Complex between HyHEL10 Fab fragment heavy chain mutant (I29F, S5... -

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Basic information

Entry
Database: PDB / ID: 5vjq
TitleComplex between HyHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and Pekin duck egg lysozyme isoform I (DEL-I)
Components
  • HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
  • HyHEL10 light chain Fab fragment
  • Lysozyme
KeywordsHYDROLASE/IMMUNE SYSTEM / lysozyme / hydrolase / HYDROLASE-IMMUNE SYSTEM complex
Function / homologyLysozyme - #10 / Lysozyme / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / :
Function and homology information
Biological speciesMus musculus (house mouse)
Anas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
Model detailsPekin duck lysozyme isoform I (DEL-I)
AuthorsLangley, D.B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Science / Year: 2018
Title: Germinal center antibody mutation trajectories are determined by rapid self/foreign discrimination.
Authors: Burnett, D.L. / Langley, D.B. / Schofield, P. / Hermes, J.R. / Chan, T.D. / Jackson, J. / Bourne, K. / Reed, J.H. / Patterson, K. / Porebski, B.T. / Brink, R. / Christ, D. / Goodnow, C.C.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 29, 2020Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
B: HyHEL10 light chain Fab fragment
I: Lysozyme
C: HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
D: HyHEL10 light chain Fab fragment
J: Lysozyme
E: HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
F: HyHEL10 light chain Fab fragment
K: Lysozyme
G: HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
H: HyHEL10 light chain Fab fragment
L: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,88522
Polymers244,19112
Non-polymers69410
Water17,907994
1
A: HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
B: HyHEL10 light chain Fab fragment
I: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0834
Polymers61,0483
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
D: HyHEL10 light chain Fab fragment
J: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4528
Polymers61,0483
Non-polymers4045
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
F: HyHEL10 light chain Fab fragment
K: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1755
Polymers61,0483
Non-polymers1282
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
H: HyHEL10 light chain Fab fragment
L: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1755
Polymers61,0483
Non-polymers1282
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.650, 132.660, 199.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules IJKL

#3: Protein
Lysozyme


Mass: 14428.297 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Anas platyrhynchos (mallard) / Tissue: egg white / References: UniProt: U3J0P1

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Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F


Mass: 23169.688 Da / Num. of mol.: 4 / Fragment: DEL-I / Mutation: I29F, S52T, Y53F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG heavy chain / Cell (production host): HEK / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: exo-alpha-sialidase
#2: Antibody
HyHEL10 light chain Fab fragment


Mass: 23449.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 1004 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 994 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.69 % / Description: rods
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.75
Details: 100 mM sodium citrate (pH 4.75), 17 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→49.78 Å / Num. obs: 180881 / % possible obs: 98 % / Redundancy: 8.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.035 / Rrim(I) all: 0.105 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.938.10.7830.6420.2860.83894.6
10.41-49.788.60.0450.9980.0170.04896.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.79 Å49.32 Å
Translation6.79 Å49.32 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V8G, 3D9A

5v8g

3d9a


Resolution: 1.9→49.32 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.315 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.148
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 9009 5 %RANDOM
Rwork0.1925 ---
obs0.1946 171765 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74 Å2 / Biso mean: 28.408 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---0.98 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.9→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16683 0 40 994 17717
Biso mean--41.39 30.2 -
Num. residues----2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217363
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214985
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.93123708
X-RAY DIFFRACTIONr_angle_other_deg0.979334887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81252212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41323.908714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03152631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6561591
X-RAY DIFFRACTIONr_chiral_restr0.0920.22643
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023628
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 644 -
Rwork0.249 12115 -
all-12759 -
obs--94.41 %
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)
11.06960.59010.62650.40770.37330.5217-0.0392-0.1620.1487-0.0464-0.06370.075-0.0377-0.09780.1030.0657-0.0087-0.01310.0942-0.0480.1016-46.9843-15.7312-28.9367
20.95860.00640.49410.12740.05520.3271-0.0040.02970.0566-0.0823-0.00360.0161-0.03910.00180.00760.0794-0.02460.00210.1038-0.02330.0652-42.5942-28.5121-40.8373
32.6157-0.1589-0.45241.55410.08021.8551-0.1247-0.2411-0.07970.28510.0784-0.42760.16510.27810.04630.0810.0191-0.08430.1187-0.02030.1782-7.0646-17.5457-14.4934
40.83310.5018-0.56490.6605-0.44560.6325-0.0546-0.0754-0.1175-0.0775-0.0328-0.10810.07070.07740.08740.1108-0.01330.01550.0732-0.00310.05151.25713.6614-29.3779
50.9173-0.0013-0.44110.3345-0.0920.3610.00660.05260.0083-0.1290.0024-0.03680.0314-0.012-0.00910.1349-0.0231-0.0010.08590.00410.0157-4.409327.0265-40.1337
61.6897-0.3101-0.08571.41440.12591.4645-0.1307-0.025-0.06010.14680.06230.2586-0.1288-0.14860.06840.07910.00610.04250.06270.00540.0769-37.139613.7706-11.6501
70.3749-0.0774-0.20450.8088-0.2610.6190.0161-0.03310.03410.0346-0.0642-0.11310.06550.18070.04810.04320.04320.00450.16290.01760.0276-27.661928.64618.7957
80.49510.3201-0.28941.4163-0.17880.9116-0.02750.11980.0207-0.1621-0.0120.01370.0945-0.06720.03950.06780.05290.00050.15750.00560.0052-41.533229.8486.6293
91.81891.28230.022.55620.07960.06440.1365-0.1258-0.25790.1175-0.1174-0.12150.1388-0.0057-0.01910.406-0.01050.00250.17560.02520.0805-45.6546-6.681833.5372
100.6909-0.3352-0.0791.49470.35690.56260.06240.2309-0.02570.0246-0.07580.18830.0391-0.13590.01330.02840.0033-0.03160.26570.00810.0927-18.1417-26.707218.3834
110.40670.10390.34241.03210.31790.64040.07550.2670.01-0.1469-0.0283-0.04550.02020.1277-0.04720.04270.07530.00810.27390.01850.0541-3.3956-27.33017.2552
122.14370.39430.17832.2633-0.01981.54280.0484-0.27750.37890.3531-0.1074-0.2768-0.18390.09780.0590.0886-0.0188-0.07330.10880.00080.2426-3.65929.373835.3429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 213
2X-RAY DIFFRACTION2B1 - 212
3X-RAY DIFFRACTION3I1 - 129
4X-RAY DIFFRACTION4C1 - 213
5X-RAY DIFFRACTION5D1 - 213
6X-RAY DIFFRACTION6J1 - 129
7X-RAY DIFFRACTION7E1 - 213
8X-RAY DIFFRACTION8F1 - 212
9X-RAY DIFFRACTION9K1 - 128
10X-RAY DIFFRACTION10G1 - 212
11X-RAY DIFFRACTION11H1 - 212
12X-RAY DIFFRACTION12L1 - 129

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