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- PDB-5vjo: Complex between HyHEL10 Fab fragment heavy chain mutant I29F and ... -

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Basic information

Entry
Database: PDB / ID: 5vjo
TitleComplex between HyHEL10 Fab fragment heavy chain mutant I29F and Pekin duck egg lysozyme isoform I (DEL-I)
Components
  • HyHEL10 heavy chain Fab fragment carrying I29F mutation.
  • HyHEL10 light chain Fab fragment
  • lysozyme isoform I (DEL-I)
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 / Resolution: 2.43 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 1.3Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 I29F mutation.
B: HyHEL10 light chain Fab fragment
C: HyHEL10 heavy chain Fab fragment carrying I29F mutation.
D: HyHEL10 light chain Fab fragment
E: lysozyme isoform I (DEL-I)
F: lysozyme isoform I (DEL-I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,77811
Polymers121,6136
Non-polymers1655
Water81145
1
A: HyHEL10 heavy chain Fab fragment carrying I29F mutation.
B: HyHEL10 light chain Fab fragment
E: lysozyme isoform I (DEL-I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9006
Polymers60,8063
Non-polymers943
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-54 kcal/mol
Surface area23410 Å2
MethodPISA
2
C: HyHEL10 heavy chain Fab fragment carrying I29F mutation.
D: HyHEL10 light chain Fab fragment
F: lysozyme isoform I (DEL-I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8775
Polymers60,8063
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-44 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.020, 102.910, 133.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPROPROAA1 - 2121 - 212
21ASPASPPROPROCC1 - 2121 - 212
12ASPASPARGARGBB1 - 2111 - 211
22ASPASPARGARGDD1 - 2111 - 211
13LYSLYSGLYGLYEE1 - 1261 - 126
23LYSLYSGLYGLYFF1 - 1261 - 126

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules EF

#3: Protein lysozyme isoform I (DEL-I)


Mass: 14428.297 Da / Num. of mol.: 2 / 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, 4 molecules ACBD

#1: Antibody HyHEL10 heavy chain Fab fragment carrying I29F mutation.


Mass: 23171.660 Da / Num. of mol.: 2 / Fragment: DEL-I / Mutation: I29F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: exo-alpha-sialidase
#2: Antibody HyHEL10 light chain Fab fragment


Mass: 23206.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG light chain / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 50 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.52 Å3/Da / Density % sol: 51.25 % / 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: 2.43→47.49 Å / Num. obs: 47296 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.032 / Rrim(I) all: 0.1 / Net I/σ(I): 15.5 / Num. measured all: 459563 / Scaling rejects: 1014
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.43-2.519.50.770.850.2610.814100
9.4-47.4990.0470.9980.0160.0595.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.31data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V8G, 3D9A

5v8g

3d9a


Resolution: 2.43→47.49 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.895 / SU B: 28.682 / SU ML: 0.305 / SU R Cruickshank DPI: 0.5406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.314
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2959 2326 4.9 %RANDOM
Rwork0.2621 ---
obs0.2638 44719 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.12 Å2 / Biso mean: 58.472 Å2 / Biso min: 23.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2--2.66 Å20 Å2
3----1.08 Å2
Refinement stepCycle: final / Resolution: 2.43→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8170 0 5 45 8220
Biso mean--62.36 39.43 -
Num. residues----1092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028397
X-RAY DIFFRACTIONr_bond_other_d0.0020.027096
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.92811487
X-RAY DIFFRACTIONr_angle_other_deg0.976316470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81551086
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81323.934333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.636151186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6811538
X-RAY DIFFRACTIONr_chiral_restr0.0830.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021756
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A117080.05
12C117080.05
21B119480.06
22D119480.06
31E77760.03
32F77760.03
LS refinement shellResolution: 2.429→2.492 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 158 -
Rwork0.333 3245 -
all-3403 -
obs--99.97 %
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)
11.21340.375-1.39090.80180.0692.0349-0.41630.3004-0.0820.15310.02320.24910.6225-0.36390.39310.6304-0.13510.25980.1529-0.05350.40220.7597125.234314.5567
21.43850.9539-0.14650.6709-0.00470.2828-0.1274-0.1747-0.17250.0777-0.0794-0.01480.46660.10260.20680.86610.15930.36240.05840.12330.334624.6432113.230627.8256
30.4164-0.234-0.3220.8319-0.811.8804-0.1440.1987-0.12170.09960.03730.14870.2972-0.29750.10660.4362-0.05050.05550.1738-0.05070.27315.0351135.782338.9612
40.1802-0.2614-0.39930.7791-0.29053.0374-0.06240.01720.06640.25550.041-0.1232-0.21130.03870.02140.3833-0.016-0.01120.20710.05060.218219.9712146.317238.9154
52.0938-0.0402-0.27342.29770.67060.6344-0.4356-0.06280.11170.18130.26290.01080.03580.38760.17270.40660.0948-0.04450.33640.07930.201159.8974139.676516.3424
61.6596-1.23050.99891.1018-0.00753.52580.0107-0.2606-0.08860.15460.17910.00970.4791-0.2248-0.18970.84380.0868-0.02160.06290.04880.142220.8522120.097575.6165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 212
2X-RAY DIFFRACTION2B1 - 211
3X-RAY DIFFRACTION3C1 - 213
4X-RAY DIFFRACTION4D1 - 211
5X-RAY DIFFRACTION5E1 - 127
6X-RAY DIFFRACTION6F1 - 129

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