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- PDB-5az2: Crystal structure of the Fab fragment of 9E5, a murine monoclonal... -

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Basic information

Entry
Database: PDB / ID: 5az2
TitleCrystal structure of the Fab fragment of 9E5, a murine monoclonal antibody specific for human epiregulin
Components
  • anti-human epiregulin antibody 9E5 Fab heavy chain
  • anti-human epiregulin antibody 9E5 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin / Monoclonal antibody / Epidermal growth factor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.603 Å
AuthorsKado, Y. / Mizohata, E. / Nagatoishi, S. / Iijima, M. / Shinoda, K. / Miyafusa, T. / Nakayama, T. / Yoshizumi, T. / Sugiyama, A. / Kawamura, T. ...Kado, Y. / Mizohata, E. / Nagatoishi, S. / Iijima, M. / Shinoda, K. / Miyafusa, T. / Nakayama, T. / Yoshizumi, T. / Sugiyama, A. / Kawamura, T. / Lee, Y.H. / Matsumura, H. / Doi, H. / Fujitani, H. / Kodama, T. / Shibasaki, Y. / Tsumoto, K. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Cabinet Office, Government of Japan and the Japan Society for the Promotion of Science Japan
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES
Authors: Kado, Y. / Mizohata, E. / Nagatoishi, S. / Iijima, M. / Shinoda, K. / Miyafusa, T. / Nakayama, T. / Yoshizumi, T. / Sugiyama, A. / Kawamura, T. / Lee, Y.H. / Matsumura, H. / Doi, H. / ...Authors: Kado, Y. / Mizohata, E. / Nagatoishi, S. / Iijima, M. / Shinoda, K. / Miyafusa, T. / Nakayama, T. / Yoshizumi, T. / Sugiyama, A. / Kawamura, T. / Lee, Y.H. / Matsumura, H. / Doi, H. / Fujitani, H. / Kodama, T. / Shibasaki, Y. / Tsumoto, K. / Inoue, T.
History
DepositionSep 16, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: anti-human epiregulin antibody 9E5 Fab heavy chain
L: anti-human epiregulin antibody 9E5 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,2952
Polymers47,2952
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-24 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.000, 79.830, 59.980
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody anti-human epiregulin antibody 9E5 Fab heavy chain


Mass: 23688.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody anti-human epiregulin antibody 9E5 Fab light chain


Mass: 23606.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCEs OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCEs OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: HEPES Na, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 48127 / % possible obs: 95.3 % / Redundancy: 4 % / Net I/σ(I): 16.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.603→17.274 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 2354 5.08 %
Rwork0.1927 --
obs0.1949 46334 91.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.603→17.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 0 279 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073445
X-RAY DIFFRACTIONf_angle_d1.1814697
X-RAY DIFFRACTIONf_dihedral_angle_d13.51256
X-RAY DIFFRACTIONf_chiral_restr0.048530
X-RAY DIFFRACTIONf_plane_restr0.006603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6031-1.63580.3141370.26112559X-RAY DIFFRACTION90
1.6358-1.67140.28161370.24182659X-RAY DIFFRACTION95
1.6714-1.71020.27711460.23162658X-RAY DIFFRACTION94
1.7102-1.75290.27711610.21792580X-RAY DIFFRACTION93
1.7529-1.80030.24511500.21252584X-RAY DIFFRACTION93
1.8003-1.85320.26321160.21192567X-RAY DIFFRACTION90
1.8532-1.9130.25151360.20752554X-RAY DIFFRACTION90
1.913-1.98120.23871440.2012648X-RAY DIFFRACTION94
1.9812-2.06040.21991610.1862725X-RAY DIFFRACTION97
2.0604-2.1540.19561640.18422757X-RAY DIFFRACTION98
2.154-2.26740.23361510.18652728X-RAY DIFFRACTION97
2.2674-2.40910.26061460.19342665X-RAY DIFFRACTION95
2.4091-2.59450.2441260.20362647X-RAY DIFFRACTION93
2.5945-2.85460.28621260.1982690X-RAY DIFFRACTION94
2.8546-3.26520.22241350.1822683X-RAY DIFFRACTION95
3.2652-4.10470.22091190.17622410X-RAY DIFFRACTION84
4.1047-17.27480.2193990.18341866X-RAY DIFFRACTION65
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)
10.83790.27891.01620.52180.40262.52370.0026-0.03340.0708-0.0132-0.00970.04240.0874-0.09160.00530.1536-0.00850.04180.1459-0.02010.1855-4.9475-18.3567-11.5603
20.5345-0.07540.57250.3473-0.25790.8836-0.04990.04090.0092-0.03310.0092-0.0309-0.04830.03110.03550.1684-0.00340.01340.1838-0.01040.18446.3034-4.9448-14.8192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resseq 1:222)
2X-RAY DIFFRACTION2(chain L and resseq 1:213)

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