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- PDB-3d9a: High Resolution Crystal Structure Structure of HyHel10 Fab Comple... -

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Basic information

Entry
Database: PDB / ID: 3d9a
TitleHigh Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
Components
  • Heavy Chain of HyHel10 Antibody Fragment (Fab)
  • Light Chain of HyHel10 Antibody Fragment (Fab)
  • Lysozyme C
KeywordsHYDROLASE/IMMUNE SYSTEM / Lysozyme / HyHel10 / Fab / Antibody / Antigen / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Hydrolase / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsDeSantis, M.E. / Li, M. / Shanmuganathan, A. / Acchione, M. / Walter, R. / Wlodawer, A. / Smith-Gill, S.
CitationJournal: Mol.Immunol. / Year: 2009
Title: Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies.
Authors: Acchione, M. / Lipschultz, C.A. / DeSantis, M.E. / Shanmuganathan, A. / Li, M. / Wlodawer, A. / Tarasov, S. / Smith-Gill, S.J.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 1.4Aug 30, 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_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Lysozyme C
L: Light Chain of HyHel10 Antibody Fragment (Fab)
H: Heavy Chain of HyHel10 Antibody Fragment (Fab)


Theoretical massNumber of molelcules
Total (without water)60,5653
Polymers60,5653
Non-polymers00
Water12,304683
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-24 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.842, 77.385, 89.115
Angle α, β, γ (deg.)90.000, 96.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Antibody Light Chain of HyHel10 Antibody Fragment (Fab)


Mass: 23449.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Antibody Heavy Chain of HyHel10 Antibody Fragment (Fab)


Mass: 22784.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M di-Ammonium Citrate; 20% PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 166019 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.039 / Χ2: 1.121 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.233.90.58111001.041100
1.23-1.2640.485110681.0441100
1.26-1.2940.394111231.0511100
1.29-1.334.10.32111251.0561100
1.33-1.374.10.262111081.0511100
1.37-1.424.10.205111061.0641100
1.42-1.484.10.164111051.1531100
1.48-1.554.10.127110721.2491100
1.55-1.634.20.095110721.251100
1.63-1.734.20.071112121.2261100
1.73-1.864.20.053110831.1141100
1.86-2.054.20.04111191.099199.9
2.05-2.354.20.034112121.0991100
2.35-2.964.20.029111291.031199.7
2.96-503.80.027103851.305191.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0057refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NDM

1ndm


Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.299 / SU ML: 0.029 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 5014 3 %RANDOM
Rwork0.19 ---
obs0.191 165981 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.09 Å2
2--0.35 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 0 683 4936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224377
X-RAY DIFFRACTIONr_bond_other_d0.0020.022904
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9345975
X-RAY DIFFRACTIONr_angle_other_deg0.9163.0057068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6075555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03224.185184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27515690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0481522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
X-RAY DIFFRACTIONr_mcbond_it0.8281.52755
X-RAY DIFFRACTIONr_mcbond_other0.211.51117
X-RAY DIFFRACTIONr_mcangle_it1.57524471
X-RAY DIFFRACTIONr_scbond_it2.27931622
X-RAY DIFFRACTIONr_scangle_it3.394.51501
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 352 -
Rwork0.247 11795 -
all-12147 -
obs--98.63 %
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)
10.36580.14450.05740.6560.01971.46030.05190.12870.0021-0.0051-0.0439-0.00350.0841-0.0513-0.008-0.02940.01870.0020.00820.0037-0.03365.47528.217412.6465
20.7312-0.7102-0.12140.88990.29751.0436-0.0606-0.02260.07010.06980.0515-0.0344-0.0151-0.07260.0091-0.0156-0.0059-0.0008-0.0387-0.0088-0.00013.846819.715838.7346
31.2427-0.44031.05940.8892-0.03151.78710.0850.03890.0561-0.1104-0.1062-0.0873-0.13270.14320.0212-0.03370.05120.03970.06910.0479-0.064111.251720.772575.1895
40.593-0.46320.29750.6812-0.48071.35120.0133-0.0235-0.01370.00390.0057-0.01520.03140.0481-0.019-0.0205-0.0098-0.0089-0.04260.0081-0.00316.29431.518939.7038
50.7934-0.1398-0.93471.12710.83211.7749-0.00590.0535-0.0951-0.0618-0.09580.05050.1249-0.05030.1016-0.02230.0780.010.05160.0132-0.06157.88335.830571.9497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1CA601 - 7291 - 129
2X-RAY DIFFRACTION2LB1 - 1071 - 107
3X-RAY DIFFRACTION3LB108 - 213108 - 213
4X-RAY DIFFRACTION4HC301 - 4121 - 112
5X-RAY DIFFRACTION5HC413 - 509113 - 209

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