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- PDB-4u3x: Structure of a human VH antibody domain binding to the cleft of h... -

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Basic information

Entry
Database: PDB / ID: 4u3x
TitleStructure of a human VH antibody domain binding to the cleft of hen egg lysozyme
Components
  • Human VH domain antibody
  • Lysozyme C
KeywordsIMMUNE SYSTEM / Human VH domain antibody / Phage display / Antibody-antigen complex structure / 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 speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.26 Å
AuthorsRouet, R. / Langley, D.B. / Christ, D.
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
DepositionJul 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / entity_src_nat / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _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 1.3Nov 8, 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: Human VH domain antibody
B: Lysozyme C
C: Human VH domain antibody
D: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1346
Polymers55,0094
Non-polymers1242
Water1,820101
1
A: Human VH domain antibody
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5673
Polymers27,5052
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-5 kcal/mol
Surface area10480 Å2
MethodPISA
2
C: Human VH domain antibody
D: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5673
Polymers27,5052
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-6 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.070, 39.240, 100.180
Angle α, β, γ (deg.)90.00, 104.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Human VH 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) / Strain (production host): K-12 / Variant (production host): BL21-Gold (DE3)
#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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 300 mM sodium citrate, 16% PEG 3350 / PH range: 5.5

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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: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.26→97.14 Å / Num. obs: 24456 / % possible obs: 98.6 % / Redundancy: 1.5 % / Net I/σ(I): 2.4

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementStarting model: 1LYZ, 1OHQ

1lyz

1ohq


Resolution: 2.26→97.14 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 15.494 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24839 1252 5.2 %RANDOM
Rwork0.1893 ---
obs0.1923 22746 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.923 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.35 Å2
2---0.38 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.26→97.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 8 101 3685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023674
X-RAY DIFFRACTIONr_bond_other_d0.0010.023187
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9125000
X-RAY DIFFRACTIONr_angle_other_deg0.90637243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82423.418158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98515495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6041523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02938
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_it0.9621.5251938
X-RAY DIFFRACTIONr_mcbond_other0.9491.5241937
X-RAY DIFFRACTIONr_mcangle_it1.5942.2812412
X-RAY DIFFRACTIONr_mcangle_other1.5942.2832413
X-RAY DIFFRACTIONr_scbond_it1.1591.5491736
X-RAY DIFFRACTIONr_scbond_other1.1591.5491736
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.752.2922589
X-RAY DIFFRACTIONr_long_range_B_refined3.33212.1724150
X-RAY DIFFRACTIONr_long_range_B_other3.32512.1534141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.263→2.322 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 94 -
Rwork0.267 1599 -
obs--94.74 %
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)
12.21650.52420.02531.90790.57851.4306-0.0003-0.07130.04850.03480.01940.01150.04950.0249-0.01910.03170.0032-0.02650.12480.00630.0246-11.2947-10.876910.2523
22.95780.65560.39730.84230.37560.78960.00650.06330.04140.0166-0.0042-0.0206-0.05930.0354-0.00230.0650.0019-0.02170.1166-0.00160.0093-28.0872-22.1913-10.2981
35.2869-0.91640.51832.44910.74421.6562-0.2071-0.24580.40820.13960.1992-0.13870.0784-0.01560.00790.07980.0265-0.05920.1341-0.02090.0592-28.12633.985865.2592
41.83220.24191.17251.4540.32053.28880.0858-0.0783-0.02650.0617-0.025-0.08860.07220.167-0.06070.1129-0.0209-0.00890.1655-0.01060.0069-37.6506-6.227640.6618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 120
2X-RAY DIFFRACTION2B1 - 201
3X-RAY DIFFRACTION3C2 - 119
4X-RAY DIFFRACTION4D1 - 128

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