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- PDB-4yny: Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 -

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Basic information

Entry
Database: PDB / ID: 4yny
TitleCrystal structure of monoclonal anti-human podoplanin antibody NZ-1
Components
  • Heavy chain of antigen binding fragment, Fab
  • Light chain of antigen binding fragment, Fab
KeywordsIMMUNE SYSTEM / Antibodies / Monoclonal / Antibody Affinity / Chromatography / Affinity / Epitopes / Rats / Immunoglobulin Fab Fragments / Kinetics / Protein Binding / Proteins / Recombinant Fusion Proteins / Human podoplanin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 Å
AuthorsFujii, Y. / Kitago, Y. / Arimori, T. / Takagi, J.
CitationJournal: J.Cell.Sci. / Year: 2016
Title: Tailored placement of a turn-forming PA tag into the structured domain of a protein to probe its conformational state
Authors: Fujii, Y. / Matsunaga, Y. / Arimori, T. / Kitago, Y. / Ogasawara, S. / Kaneko, M.K. / Kato, Y. / Takagi, J.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 2.0Feb 5, 2020Group: Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 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: Heavy chain of antigen binding fragment, Fab
B: Light chain of antigen binding fragment, Fab
C: Heavy chain of antigen binding fragment, Fab
D: Light chain of antigen binding fragment, Fab


Theoretical massNumber of molelcules
Total (without water)102,1094
Polymers102,1094
Non-polymers00
Water10,989610
1
A: Heavy chain of antigen binding fragment, Fab
B: Light chain of antigen binding fragment, Fab


Theoretical massNumber of molelcules
Total (without water)51,0542
Polymers51,0542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-25 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: Heavy chain of antigen binding fragment, Fab
D: Light chain of antigen binding fragment, Fab


Theoretical massNumber of molelcules
Total (without water)51,0542
Polymers51,0542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-24 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.883, 57.157, 101.520
Angle α, β, γ (deg.)97.92, 101.53, 105.37
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Heavy chain of antigen binding fragment, Fab


Mass: 25560.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse)
#2: Antibody Light chain of antigen binding fragment, Fab


Mass: 25494.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 610 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, sodium citrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL15A111
SYNCHROTRONPhoton Factory BL-17A20.98
Detector
TypeIDDetectorDate
RAYONIX MX300HE1CCDMar 14, 2014
ADSC QUANTUM 2702CCDFeb 13, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.981
ReflectionResolution: 1.584→31.5 Å / Num. obs: 118170 / % possible obs: 97.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 24.5
Reflection shellHighest resolution: 1.584 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.3 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZAN

1zan


Resolution: 1.584→31.486 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.74
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 5885 4.98 %RANDOM
Rwork0.1684 ---
obs0.1702 118153 97.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.584→31.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6366 0 0 610 6976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176659
X-RAY DIFFRACTIONf_angle_d1.5529111
X-RAY DIFFRACTIONf_dihedral_angle_d13.9534004
X-RAY DIFFRACTIONf_chiral_restr0.1011035
X-RAY DIFFRACTIONf_plane_restr0.011168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5835-1.60150.30881390.27462848X-RAY DIFFRACTION75
1.6015-1.62030.28741840.25743669X-RAY DIFFRACTION95
1.6203-1.64010.30771910.24433636X-RAY DIFFRACTION94
1.6401-1.66090.25941930.21683669X-RAY DIFFRACTION95
1.6609-1.68270.24321750.20253645X-RAY DIFFRACTION96
1.6827-1.70580.21452150.19173660X-RAY DIFFRACTION95
1.7058-1.73010.22491970.18013709X-RAY DIFFRACTION95
1.7301-1.7560.19761890.17693668X-RAY DIFFRACTION96
1.756-1.78340.21141760.17953717X-RAY DIFFRACTION95
1.7834-1.81260.22051780.18373686X-RAY DIFFRACTION96
1.8126-1.84390.21041740.18193681X-RAY DIFFRACTION96
1.8439-1.87740.22762190.18563677X-RAY DIFFRACTION96
1.8774-1.91350.2292010.1773759X-RAY DIFFRACTION97
1.9135-1.95260.23792070.1873846X-RAY DIFFRACTION99
1.9526-1.9950.19562000.17533792X-RAY DIFFRACTION100
1.995-2.04140.21542090.18153873X-RAY DIFFRACTION100
2.0414-2.09240.2151900.183780X-RAY DIFFRACTION100
2.0924-2.1490.18782160.17223844X-RAY DIFFRACTION100
2.149-2.21220.22252090.17283854X-RAY DIFFRACTION100
2.2122-2.28360.21051910.17683861X-RAY DIFFRACTION100
2.2836-2.36520.20342060.18273857X-RAY DIFFRACTION100
2.3652-2.45990.22071820.18363836X-RAY DIFFRACTION100
2.4599-2.57180.22781990.18023838X-RAY DIFFRACTION100
2.5718-2.70730.2242180.18643848X-RAY DIFFRACTION100
2.7073-2.87680.23142060.18113844X-RAY DIFFRACTION100
2.8768-3.09880.2282020.1823837X-RAY DIFFRACTION100
3.0988-3.41030.20552030.17293840X-RAY DIFFRACTION100
3.4103-3.90290.18272170.15683845X-RAY DIFFRACTION100
3.9029-4.91430.16141880.12653840X-RAY DIFFRACTION100
4.9143-31.49270.1692110.14133809X-RAY DIFFRACTION99
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)
11.77491.4777-0.38112.808-0.48952.4904-0.01020.16860.30170.03540.180.4891-0.2595-0.232-0.09580.14770.06080.01580.1420.01750.3029-36.4663-66.357954.7985
22.4924-0.2638-0.13731.4612-1.46886.0238-0.08720.28560.1223-0.07220.17470.19180.1194-0.4331-0.08670.3427-0.1318-0.03510.26580.02490.1987-23.7127-55.229328.1011
32.08570.358-0.4232.6447-0.64682.7773-0.12450.4001-0.0354-0.6190.19810.08280.3-0.2521-0.05890.2394-0.048-0.03440.2225-0.01960.1549-36.9889-86.502244.3223
41.55131.20880.29316.34010.59882.8591-0.04040.05310.08220.09550.1029-0.235-0.28370.74-0.06340.2779-0.1297-0.00240.4076-0.030.1663-10.9212-65.224423.8736
51.51320.0543-0.48362.1796-0.4631.8414-0.05940.0298-0.02760.14890.05080.08970.0335-0.04820.01440.1020.0133-0.00780.1065-0.01780.1379-8.9664-22.1166-29.2568
64.9966-1.6001-1.51083.713-0.18883.7229-0.1077-0.0294-0.0057-0.00880.08170.2114-0.0943-0.40140.03570.2370.0740.0050.27090.01020.159-28.0121-30.0455-6.8596
72.02420.4638-0.6671.826-0.06193.40730.1396-0.31930.26530.4479-0.05950.0969-0.2505-0.0302-0.07230.25820.00080.00970.1601-0.05680.1677-0.976-5.4958-15.7251
83.27121.8691-0.65677.0360.06393.69480.1804-0.0780.1845-0.0068-0.0799-0.2329-0.1335-0.0069-0.09290.15090.0369-0.00320.24650.02140.1512-19.4763-29.34937.9389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 20:137)
2X-RAY DIFFRACTION2(chain A and resseq 138:235)
3X-RAY DIFFRACTION3(chain B and resseq 20:130)
4X-RAY DIFFRACTION4(chain B and resseq 131:229)
5X-RAY DIFFRACTION5(chain C and resseq 20:137)
6X-RAY DIFFRACTION6(chain C and resseq 138:235)
7X-RAY DIFFRACTION7(chain D and resseq 20:130)
8X-RAY DIFFRACTION8(chain D and resseq 131:229)

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