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Basic information

Entry
Database: PDB / ID: 5cp7
TitleCrystal Structure of an Antigen-Binding Fragment of Monoclonal Antibody against Sulfonamides
Components
  • Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
  • Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
KeywordsIMMUNE SYSTEM / Antigen-Binding Fragment / Anti-Sulfonamides Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsWang, Z. / Shen, J. / Li, C. / Li, Y. / Wen, K. / Yu, X. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31372475 China
CitationJournal: Anal. Chem. / Year: 2019
Title: Class-specific Monoclonal Antibodies and Dihydropteroate Synthase in Bioassays used for the Detection of Sulfonamides: Structural Insights into Recognition Diversity.
Authors: Li, C. / Liang, X. / Wen, K. / Li, Y. / Zhang, X. / Ma, M. / Yu, X. / Yu, W. / Shen, J. / Wang, Z.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 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: Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
B: Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
C: Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
D: Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
E: Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
F: Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
G: Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
H: Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7


Theoretical massNumber of molelcules
Total (without water)188,9188
Polymers188,9188
Non-polymers00
Water181
1
A: Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
H: Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7


Theoretical massNumber of molelcules
Total (without water)47,2292
Polymers47,2292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-18 kcal/mol
Surface area19930 Å2
MethodPISA
2
B: Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
C: Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7


Theoretical massNumber of molelcules
Total (without water)47,2292
Polymers47,2292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-17 kcal/mol
Surface area20230 Å2
MethodPISA
3
D: Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
E: Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7


Theoretical massNumber of molelcules
Total (without water)47,2292
Polymers47,2292
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-18 kcal/mol
Surface area19820 Å2
MethodPISA
4
F: Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7
G: Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7


Theoretical massNumber of molelcules
Total (without water)47,2292
Polymers47,2292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-18 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.103, 96.510, 138.624
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody
Light Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7 / L Chain of Fab 4C7


Mass: 24109.832 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody
Heavy Chain of Antigen-Binding Fragment of Monoclonal Antibody of 4C7 / H Chain of Fab 4C7


Mass: 23119.646 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium phosphate dibasic, 20% PEG3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 46968 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.132 / Χ2: 0.918 / Net I/av σ(I): 12.847 / Net I/σ(I): 6.3 / Num. measured all: 215824
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.114.50.56446370.56899.7
3.11-3.234.50.41446170.58999.7
3.23-3.384.50.31646350.62499.7
3.38-3.564.50.32246541.3999.7
3.56-3.784.50.2646501.50599.6
3.78-4.074.40.19846571.41799.4
4.07-4.484.70.11346981.10399.9
4.48-5.124.80.08147260.85499.7
5.12-6.444.80.06447580.6199.5
6.44-304.70.04449360.60899.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NLD

1nld


Resolution: 3.01→29.88 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.811 / SU B: 5.0053 / SU ML: 0.397 / Cross valid method: THROUGHOUT / ESU R Free: 0.525 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3019 2274 5.1 %RANDOM
Rwork0.2604 ---
obs0.2626 42540 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.82 Å2 / Biso mean: 31.754 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.55 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 3.01→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13141 0 0 1 13142
Biso mean---2 -
Num. residues----1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0213521
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212316
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9518463
X-RAY DIFFRACTIONr_angle_other_deg0.6913.00228471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12951707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40824.037540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.953152136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5221563
X-RAY DIFFRACTIONr_chiral_restr0.0580.22094
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023038
LS refinement shellResolution: 3.014→3.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 133 -
Rwork0.314 2180 -
all-2313 -
obs--67.59 %
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)
12.10690.05711.32950.37850.05981.6741-0.0132-0.05890.21790.0423-0.01830.0586-0.1535-0.05850.03140.0752-0.05390.07110.088-0.02850.192227.320929.427658.2659
22.230.2604-1.78380.4674-0.40292.44650.0595-0.18770.2446-0.041-0.022-0.0777-0.02380.1026-0.03750.03060.0422-0.02960.1254-0.12840.1864-21.98631.328881.4273
31.5928-0.5706-1.07330.3310.45531.5627-0.0248-0.12360.01560.03720.0333-0.01140.12720.0981-0.00850.110.0727-0.02930.1187-0.02450.1749-28.276315.524577.5723
41.3746-0.82071.41330.5309-1.01314.1370.1373-0.0061-0.0783-0.1548-0.05730.0995-0.2552-0.08-0.080.41730.0234-0.18890.1274-0.02720.1492-21.202717.284115.6174
51.7291-0.511.01410.1646-0.13913.86280.20220.13030.1468-0.1494-0.0057-0.0285-1.07920.044-0.19650.7732-0.0031-0.04850.10060.09130.1766-23.205235.739516.0864
61.5365-0.2505-1.31440.04450.1225.07960.17280.38370.2586-0.0147-0.0507-0.0351-0.8837-0.389-0.12210.6156-0.02890.16810.25410.13630.173822.478825.8137-3.6829
71.67940.5359-1.43310.2409-0.1073.7503-0.24410.2878-0.0897-0.17860.1636-0.04450.0776-0.23040.08050.4116-0.19870.13250.2574-0.00880.065827.87658.4482-2.9646
81.78751.03381.33440.77091.03122.26950.0731-0.0696-0.06070.0643-0.0665-0.01480.0118-0.0733-0.00650.0734-0.02380.03450.13820.02220.131923.913812.724162.1435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION2B1 - 214
3X-RAY DIFFRACTION3C1 - 218
4X-RAY DIFFRACTION4D2 - 212
5X-RAY DIFFRACTION5E1 - 218
6X-RAY DIFFRACTION6F4 - 212
7X-RAY DIFFRACTION7G1 - 218
8X-RAY DIFFRACTION8H1 - 212

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