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- PDB-7dc7: Crystal structure of D12 Fab-ATP complex -

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Basic information

Entry
Database: PDB / ID: 7dc7
TitleCrystal structure of D12 Fab-ATP complex
Components
  • D12 Fab heavy chain
  • D12 Fab light chain
KeywordsIMMUNE SYSTEM / ANTIBODY / COMPLEX / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKawauchi, H. / Fukami, T.A. / Tatsumi, K. / Torizawa, T. / Mimoto, F.
CitationJournal: Cell Rep / Year: 2020
Title: Exploitation of Elevated Extracellular ATP to Specifically Direct Antibody to Tumor Microenvironment.
Authors: Mimoto, F. / Tatsumi, K. / Shimizu, S. / Kadono, S. / Haraya, K. / Nagayasu, M. / Suzuki, Y. / Fujii, E. / Kamimura, M. / Hayasaka, A. / Kawauchi, H. / Ohara, K. / Matsushita, M. / Baba, T. ...Authors: Mimoto, F. / Tatsumi, K. / Shimizu, S. / Kadono, S. / Haraya, K. / Nagayasu, M. / Suzuki, Y. / Fujii, E. / Kamimura, M. / Hayasaka, A. / Kawauchi, H. / Ohara, K. / Matsushita, M. / Baba, T. / Susumu, H. / Sakashita, T. / Muraoka, T. / Aso, K. / Katada, H. / Tanaka, E. / Nakagawa, K. / Hasegawa, M. / Ayabe, M. / Yamamoto, T. / Tanba, S. / Ishiguro, T. / Kamikawa, T. / Nambu, T. / Kibayashi, T. / Azuma, Y. / Tomii, Y. / Kato, A. / Ozeki, K. / Murao, N. / Endo, M. / Kikuta, J. / Kamata-Sakurai, M. / Ishii, M. / Hattori, K. / Igawa, T.
History
DepositionOct 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 1.2Nov 20, 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

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Assembly

Deposited unit
A: D12 Fab heavy chain
B: D12 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5703
Polymers47,0632
Non-polymers5071
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-26 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.962, 68.085, 102.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody D12 Fab heavy chain


Mass: 24406.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody D12 Fab light chain


Mass: 22656.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47.54 % / Mosaicity: 0.07 °
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8 / Details: 0.1 M HEPES, 32.5 %(w/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.77→56.8 Å / Num. obs: 40596 / % possible obs: 92 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.77-1.866.90.60163430.8580.2450.65100
5.59-56.85.80.03615480.9970.0160.03999.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3235refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NKI

4nki


Resolution: 1.77→41.072 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.27
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2199 1943 4.79 %
Rwork0.1767 --
obs0.1788 40530 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.66 Å2 / Biso mean: 26.0773 Å2 / Biso min: 12.31 Å2
Refinement stepCycle: final / Resolution: 1.77→41.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 31 416 3652
Biso mean--27.39 34.02 -
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.77-1.81210.31521170.23372985100
1.8121-1.86110.22441440.20532953100
1.8611-1.91590.2765930.215175773
1.9159-1.97770.2251080.1943177875
1.9777-2.04840.25261550.17972931100
2.0484-2.13040.24151490.18382963100
2.1304-2.22740.22571730.18462925100
2.2274-2.34480.2817990.193237579
2.3448-2.49170.24211430.18832972100
2.4917-2.6840.23381380.19653020100
2.684-2.95410.23751600.19362988100
2.9541-3.38130.2371630.18813009100
3.3813-4.25940.20351560.1518272890
4.2594-41.0720.16041450.1493203100

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