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- PDB-5b6f: Crystal structure of the Fab fragment of an anti-Leukotriene C4 m... -

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Basic information

Entry
Database: PDB / ID: 5b6f
TitleCrystal structure of the Fab fragment of an anti-Leukotriene C4 monoclonal antibody complexed with LTC4
Components(anti-leukotriene C4 monoclonal antibody immunoglobulin ...) x 2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBLIN / ANTI-LEUKOTRIENE C4 ANTIBODY / LEUKOTRIENE C4 / FAB FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-LTX
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSugahara, M. / Ago, H. / Saino, H. / Miyano, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and TechnologyS1311005 Japan
RIKEN Japan
Citation
Journal: To Be Published
Title: Crystal structure of the Fab fragment of an anti-Leukotriene C4 monoclonal antibody complexed with LTC4
Authors: Sugahara, M. / Ago, H. / Saino, H. / Miyano, M. / Yamamoto, S. / Takahashi, Y.
#1: Journal: To Be Published
Title: The Y54(L)W Mutation of Anti-leukotriene C4 Single-chain Antibody Increases Affinity to Leukotriene E4
Authors: Kawakami, Y. / Kinoshita, M. / Mori, Y. / Okochi, S. / Hirano, S. / Shimoda, I. / Kanzaki, K. / Suzuki-Yamamoto, T. / Kimotoi, M. / Hori, T.
History
DepositionMay 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_poly ...entity / entity_poly / entity_poly_seq / entity_src_nat / exptl_crystal / exptl_crystal_grow / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq
Item: _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code ..._entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _exptl_crystal_grow.pdbx_details / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain
B: anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain
C: anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain
D: anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain
E: anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain
F: anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain
G: anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain
H: anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,52022
Polymers208,6608
Non-polymers3,86014
Water22,6811259
1
A: anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain
B: anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0825
Polymers52,1652
Non-polymers9173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-47 kcal/mol
Surface area19290 Å2
MethodPISA
2
C: anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain
D: anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1786
Polymers52,1652
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-35 kcal/mol
Surface area19120 Å2
MethodPISA
3
E: anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain
F: anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0825
Polymers52,1652
Non-polymers9173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-39 kcal/mol
Surface area19150 Å2
MethodPISA
4
G: anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain
H: anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1786
Polymers52,1652
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-35 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.600, 173.980, 75.460
Angle α, β, γ (deg.)90.00, 90.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain


Mass: 26369.650 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA
#2: Antibody
anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain


Mass: 25795.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA

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Non-polymers , 4 types, 1273 molecules

#3: Chemical
ChemComp-LTX / (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-(2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid / Leukotriene C4


Mass: 625.774 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H47N3O9S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1259 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE OF THE HEAVY CHAIN HAS BEEB DEPOSITED TO GENBANK WITH ACCESSION NUMBER AB538879, LIGHT ...SEQUENCE OF THE HEAVY CHAIN HAS BEEB DEPOSITED TO GENBANK WITH ACCESSION NUMBER AB538879, LIGHT CHAIN HAS BEEN DEPOSITED TO GENBANK WITH ACCESSION NUMBER AB538878.

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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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 0.1 microL (0.1M MES-NaOH pH 6.0, 36% (w/v) PEGMME 5000, 0.2M NH4 sulfate, 0.6mM LTC4) + 0.1 microL (15mg/ml Fab, 10mM Na phosphate 7.0, 140mM NaCl) in paraffin oil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→39.26 Å / Num. obs: 177824 / % possible obs: 91.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.4 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
CNSrefinement
REFMACrefinement
iMOSFLMdata processing
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→37.728 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 24.19
Details: THE STRUCTURAL FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2224 8137 4.98 %
Rwork0.1953 --
obs0.1966 163413 73.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13191 0 250 1259 14700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513854
X-RAY DIFFRACTIONf_angle_d0.94118823
X-RAY DIFFRACTIONf_dihedral_angle_d13.1884949
X-RAY DIFFRACTIONf_chiral_restr0.0612097
X-RAY DIFFRACTIONf_plane_restr0.0052397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1750.29657310.25714299X-RAY DIFFRACTION68
2.175-2.26210.2857450.240814331X-RAY DIFFRACTION68
2.2621-2.36510.27617500.236914320X-RAY DIFFRACTION68
2.3651-2.48970.2597880.229814522X-RAY DIFFRACTION69
2.4897-2.64570.27057870.228414670X-RAY DIFFRACTION70
2.6457-2.84990.26657630.223615107X-RAY DIFFRACTION72
2.8499-3.13660.22898110.202215944X-RAY DIFFRACTION75
3.1366-3.59010.2098820.185716542X-RAY DIFFRACTION79
3.5901-4.5220.18179360.165717360X-RAY DIFFRACTION83
4.522-37.73380.19229440.168718181X-RAY DIFFRACTION86

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