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- PDB-4ma3: Crystal structure of anti-hinge rabbit antibody C2095 -

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Basic information

Entry
Database: PDB / ID: 4ma3
TitleCrystal structure of anti-hinge rabbit antibody C2095
Components
  • C2095 heavy chain
  • C2095 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMalia, T. / Teplyakov, A. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: Structure and specificity of an antibody targeting a proteolytically cleaved IgG hinge.
Authors: Malia, T.J. / Teplyakov, A. / Brezski, R.J. / Luo, J. / Kinder, M. / Sweet, R.W. / Almagro, J.C. / Jordan, R.E. / Gilliland, G.L.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 20, 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: C2095 light chain
H: C2095 heavy chain
A: C2095 light chain
B: C2095 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,11910
Polymers94,5794
Non-polymers5396
Water6,557364
1
L: C2095 light chain
H: C2095 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6376
Polymers47,2902
Non-polymers3474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-67 kcal/mol
Surface area19320 Å2
MethodPISA
2
A: C2095 light chain
B: C2095 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4824
Polymers47,2902
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-51 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.350, 79.440, 65.410
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody C2095 light chain


Mass: 23724.293 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody C2095 heavy chain


Mass: 23565.375 Da / Num. of mol.: 2 / Fragment: FD, SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsHEAVY AND LIGHT CHAINS ARE CHIMERIC MOLECULES EACH COMPRISING A RABBIT VARIABLE DOMAIN AND HUMAN ...HEAVY AND LIGHT CHAINS ARE CHIMERIC MOLECULES EACH COMPRISING A RABBIT VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN.

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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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 23% PEG3350, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 64342 / Num. obs: 64342 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.1 / % possible all: 85.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QOS

3qos
PDB Unreleased entry


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.273 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.141 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21132 1291 2 %RANDOM
Rwork0.17997 ---
all0.18063 62567 --
obs0.18063 62567 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0.42 Å2
2--0 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 0 29 364 6872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226711
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9579183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71824.274234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.906151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3471522
X-RAY DIFFRACTIONr_chiral_restr0.0710.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214996
X-RAY DIFFRACTIONr_mcbond_it2.09624347
X-RAY DIFFRACTIONr_mcangle_it3.36947069
X-RAY DIFFRACTIONr_scbond_it11.121882364
X-RAY DIFFRACTIONr_scangle_it11.367882113
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 96 -
Rwork0.221 4463 -
obs--85.3 %
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)
11.3101-1.0742-0.27473.090.1981.010.04160.04290.0101-0.1328-0.0508-0.11620.022-0.00850.00920.0599-0.02170.01760.062-0.00950.0088-35.255925.9361-27.4396
22.6623-0.7790.39542.6732-0.00752.0989-0.0528-0.14640.070.24040.0186-0.1271-0.11450.18820.03430.1146-0.0497-0.04060.2103-0.0550.1743-9.426947.809-21.0908
30.61250.70030.41852.38870.94621.8469-0.0236-0.04790.00380.1425-0.0226-0.00970.0458-0.08630.04620.08990.01580.00130.0938-0.01320.0307-39.653129.95643.943
43.00791.2190.32364.46070.14011.5873-0.0816-0.0476-0.3417-0.3077-0.0015-0.44510.1440.22630.08310.19150.08810.05680.2198-0.01680.2645-16.33097.467513.5993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 113
2X-RAY DIFFRACTION1H1 - 114
3X-RAY DIFFRACTION2L114 - 219
4X-RAY DIFFRACTION2H115 - 216
5X-RAY DIFFRACTION3A1 - 113
6X-RAY DIFFRACTION3B1 - 114
7X-RAY DIFFRACTION4A114 - 219
8X-RAY DIFFRACTION4B115 - 215

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