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- PDB-5vpg: CRYSTAL STRUCTURE OF DER P 1 COMPLEXED WITH FAB 4C1 -

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Basic information

Entry
Database: PDB / ID: 5vpg
TitleCRYSTAL STRUCTURE OF DER P 1 COMPLEXED WITH FAB 4C1
Components
  • Der p 1 allergen
  • FAB 4C1 - HEAVY CHAIN
  • FAB 4C1 - LIGHT CHAIN
KeywordsHYDROLASE/IMMUNE SYSTEM / ALLERGEN-ANTIBODY COMPLEX / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space / metal ion binding
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Dermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChruszcz, M. / Vailes, L.D. / Chapman, M.D. / Pomes, A. / Minor, W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular Determinants For Antibody Binding On Group 1 House Dust Mite Allergens.
Authors: Chruszcz, M. / Pomes, A. / Glesner, J. / Vailes, L.D. / Osinski, T. / Porebski, P.J. / Majorek, K.A. / Heymann, P.W. / Platts-Mills, T.A. / Minor, W. / Chapman, M.D.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 3RVW
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / database_2
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Der p 1 allergen
C: FAB 4C1 - LIGHT CHAIN
D: FAB 4C1 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,25813
Polymers76,5013
Non-polymers75810
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-2 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.803, 61.764, 223.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules CD

#2: Antibody FAB 4C1 - LIGHT CHAIN


Mass: 23808.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)
#3: Antibody FAB 4C1 - HEAVY CHAIN


Mass: 27677.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Der p 1 allergen


Mass: 25014.805 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 99-320 / Source method: isolated from a natural source
Source: (natural) Dermatophagoides pteronyssinus (European house dust mite)
References: UniProt: Q3HWZ5
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 438 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.1M NA CACODYLATE, 15% W/V PEG4000, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2009 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 47483 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 26
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.535 / % possible all: 89.5

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3F5V, 3RVV

3f5v

3rvv
PDB Unreleased entry


Resolution: 1.95→45.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.438 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2401 5.1 %RANDOM
Rwork0.156 ---
obs0.158 45003 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 28.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5085 0 47 429 5561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225350
X-RAY DIFFRACTIONr_bond_other_d0.0030.023542
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9467300
X-RAY DIFFRACTIONr_angle_other_deg2.28338619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8225669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94823.83235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36215824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8331530
X-RAY DIFFRACTIONr_chiral_restr0.1010.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216032
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021104
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_it0.8291.53307
X-RAY DIFFRACTIONr_mcbond_other0.1271.51333
X-RAY DIFFRACTIONr_mcangle_it1.51925381
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.72732043
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2884.51919
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 160 -
Rwork0.17 3094 -
obs--87.64 %
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)
10.74020.2346-0.27050.9402-0.32621.0244-0.00210.03550.046-0.08930.0217-0.0188-0.0475-0.015-0.01960.1459-0.0061-0.0120.08640.00880.1281-20.701-1.19-8.664
21.65830.7525-0.31972.1692-0.41931.39950.0784-0.1968-0.11050.2677-0.0718-0.060.0383-0.0325-0.00660.21790.0031-0.02290.11280.01210.1167-33.193-7.76528.602
34.5450.90583.95354.3716-1.43768.649-0.4726-0.40870.02851.5240.3022-0.1443-1.5488-0.60760.17041.10420.1181-0.07840.17590.02140.0311-25.366-7.89364.7
41.7136-0.02560.53051.01130.03741.8330.055-0.06070.09880.1277-0.0469-0.1359-0.02380.094-0.0080.195-0.0061-0.02370.1280.00050.148-13.41-1.06425.709
53.3414.2125-2.59077.6104-5.31795.4303-0.0554-0.2274-0.60.8501-0.4603-1.0808-0.34190.58160.51580.4853-0.0049-0.20640.19290.07020.2716-12.528-13.43857.458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 222
2X-RAY DIFFRACTION2C1 - 104
3X-RAY DIFFRACTION3C105 - 211
4X-RAY DIFFRACTION4D1 - 119
5X-RAY DIFFRACTION5D120 - 222

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