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- PDB-4pgj: Human heavy-chain domain antibody in complex with hen egg-white l... -

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Basic information

Entry
Database: PDB / ID: 4pgj
TitleHuman heavy-chain domain antibody in complex with hen egg-white lysozyme
Components
  • Human heavy chain domain antibody
  • Lysozyme C
KeywordsIMMUNE SYSTEM/HYDROLASE / antibody human dAb cleft binder dAb-HEL complex / IMMUNE SYSTEM-HYDROLASE 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 speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsChrist, D. / Langley, D.B. / Rouet, R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Fully Human VH Single Domains That Rival the Stability and Cleft Recognition of Camelid Antibodies.
Authors: Rouet, R. / Dudgeon, K. / Christie, M. / Langley, D. / Christ, D.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2May 27, 2015Group: Structure summary
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / entity_src_nat / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Human heavy chain domain antibody
B: Lysozyme C
C: Human heavy chain domain antibody
D: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)55,0094
Polymers55,0094
Non-polymers00
Water00
1
A: Human heavy chain domain antibody
B: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)27,5052
Polymers27,5052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-8 kcal/mol
Surface area10280 Å2
MethodPISA
2
C: Human heavy chain domain antibody
D: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)27,5052
Polymers27,5052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-8 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.070, 40.310, 137.020
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number5
Space group name H-MI121
DetailsAuthors report assembly confirmed by gel filtration and MALLS

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Components

#1: Antibody Human heavy chain domain antibody


Mass: 13173.522 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: Protein at 4.4 mg/mL in 50 mM Tris (pH 7.5) amd 150 mM NaCl. Well solution contained 28% (w/v) PEG1500, 100 mM Na-citrate (pH 5.4). 400 nL of well solution and protein solution were combined.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.6→49.08 Å / Num. obs: 16831 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 9

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Processing

SoftwareName: REFMAC / Version: 5.6.0111 / Classification: refinement
RefinementResolution: 2.6→49.08 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.879 / SU B: 24.287 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.699 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 851 5.1 %RANDOM
Rwork0.22482 ---
obs0.22788 15980 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.675 Å2
Baniso -1Baniso -2Baniso -3
1--3.4 Å2-0 Å2-0.5 Å2
2--2.38 Å20 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 2.6→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 0 0 3380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213471
X-RAY DIFFRACTIONr_bond_other_d0.0010.022145
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9094744
X-RAY DIFFRACTIONr_angle_other_deg1.0123.0085137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4815475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73823.333135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22215389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6081516
X-RAY DIFFRACTIONr_chiral_restr0.090.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 54 -
Rwork0.379 1106 -
obs--99.32 %
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)
12.6159-1.50710.95295.0414-1.02131.74810.1541-0.0718-0.00020.449-0.0741-0.1384-0.13550.1837-0.080.1857-0.1106-0.07310.1913-0.02870.119242.7136-24.5172-11.7432
22.6522-0.39650.64711.6065-0.89093.91220.0271-0.21080.05660.1836-0.04550.2307-0.1467-0.24150.01840.0707-0.01110.03030.0654-0.01310.136822.3488-12.5435-26.7083
33.09871.6692-0.53472.64691.02043.608-0.2340.4704-0.1265-0.29740.2477-0.0725-0.1049-0.4262-0.01370.0797-0.0668-0.01130.3241-0.00020.0582-21.0433-28.6557-57.871
42.81330.2298-0.24431.30180.63163.4558-0.00840.0808-0.0349-0.0506-0.0148-0.0759-0.0548-0.08450.02310.0323-0.0025-0.00740.06010.0140.1678-7.3075-16.7186-36.9905
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 120
2X-RAY DIFFRACTION2B1 - 128
3X-RAY DIFFRACTION3C3 - 120
4X-RAY DIFFRACTION4D1 - 128

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