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- PDB-1jtp: Degenerate interfaces in antigen-antibody complexes -

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Basic information

Entry
Database: PDB / ID: 1jtp
TitleDegenerate interfaces in antigen-antibody complexes
Components
  • LYSOZYME C
  • Single-Domain Antibody
KeywordsAntibody / Hydrolase / immunoglobulin / heavy chain antibody / VHH / interface
Function / homology
Function and homology information


glycosaminoglycan binding / 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 / 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
FORMIC ACID / : / Lysozyme C
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Meleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDecanniere, K. / Transue, T.R. / Desmyter, A. / Maes, D. / Muyldermans, S. / Wyns, L.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Degenerate interfaces in antigen-antibody complexes.
Authors: Decanniere, K. / Transue, T.R. / Desmyter, A. / Maes, D. / Muyldermans, S. / Wyns, L.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme
Authors: Desmyter, A. / Transue, T.R. / Ghahroudi, M.A. / Thi, M.H. / Poortmans, F. / Hamers, R. / Muyldermans, S. / Wyns, L.
History
DepositionAug 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE ARG IS PART OF THE HEMAGLUTAMINE-TAG, WHILE THE ENTRY IN THE GB DATABASE REPRESENTS THE ...SEQUENCE ARG IS PART OF THE HEMAGLUTAMINE-TAG, WHILE THE ENTRY IN THE GB DATABASE REPRESENTS THE SAME MOLECULE WITH A HIS-TAG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-Domain Antibody
B: Single-Domain Antibody
L: LYSOZYME C
M: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,36215
Polymers59,9714
Non-polymers39111
Water5,368298
1
A: Single-Domain Antibody
L: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1467
Polymers29,9852
Non-polymers1615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-46 kcal/mol
Surface area11550 Å2
MethodPISA
2
B: Single-Domain Antibody
M: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2158
Polymers29,9852
Non-polymers2306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-33 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.123, 69.375, 113.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Single-Domain Antibody


Mass: 15757.232 Da / Num. of mol.: 2 / Fragment: VH DOMAIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pHEN1 / Production host: Escherichia coli (E. coli) / References: GenBank: 2392447
#2: Protein LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C


Mass: 14228.105 Da / Num. of mol.: 2 / Fragment: ENZYME / Source method: isolated from a natural source / Details: Purchased from Sigma / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P00703, lysozyme
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2M Na Formate, 100mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.98089 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998
RadiationMonochromator: 0.98089 Angstrom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98089 Å / Relative weight: 1
ReflectionResolution: 1.9→17 Å / Num. all: 42348 / Num. obs: 40619 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2 / Num. unique all: 3873 / Rsym value: 0.417 / % possible all: 92

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 1MEL

1mel


Resolution: 1.9→17 Å / Isotropic thermal model: isotropic / Cross valid method: Free-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Eng & Huber
Details: overall anisotropic B-factor and bulk solvent correction used
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 4149 -Random
Rwork0.1841 ---
all-40619 --
obs-40619 10.21 %-
Displacement parametersBiso mean: 20.38 Å2
Baniso -1Baniso -2Baniso -3
1--4.087 Å20 Å20 Å2
2---0.162 Å20 Å2
3---4.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 5 316 4329

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