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- PDB-3qxw: Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody -

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Basic information

Entry
Database: PDB / ID: 3qxw
TitleFree structure of an anti-methotrexate CDR1-4 Graft VHH Antibody
ComponentsAnti-Methotrexate CDR1-4 Graft VHH
KeywordsIMMUNE SYSTEM / Camelid Single Domain Antibody / Heavy Chain Only / VHH / Antibody / Anti-Hapten Antibody / CDR / Hapten Binding / Small Molecule Sensing / Ligand Binding / Low Molecular Weight Compound / Methotrexate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama Glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFanning, S.W. / Horn, J.R.
CitationJournal: Protein Sci. / Year: 2011
Title: An anti-hapten camelid antibody reveals a cryptic binding site with significant energetic contributions from a nonhypervariable loop.
Authors: Fanning, S.W. / Horn, J.R.
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Structure summary
Revision 1.2Dec 25, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-Methotrexate CDR1-4 Graft VHH
B: Anti-Methotrexate CDR1-4 Graft VHH
C: Anti-Methotrexate CDR1-4 Graft VHH
D: Anti-Methotrexate CDR1-4 Graft VHH
E: Anti-Methotrexate CDR1-4 Graft VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0268
Polymers68,8115
Non-polymers2153
Water5,314295
1
A: Anti-Methotrexate CDR1-4 Graft VHH


Theoretical massNumber of molelcules
Total (without water)13,7621
Polymers13,7621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anti-Methotrexate CDR1-4 Graft VHH


Theoretical massNumber of molelcules
Total (without water)13,7621
Polymers13,7621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Anti-Methotrexate CDR1-4 Graft VHH


Theoretical massNumber of molelcules
Total (without water)13,7621
Polymers13,7621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Anti-Methotrexate CDR1-4 Graft VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8813
Polymers13,7621
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Anti-Methotrexate CDR1-4 Graft VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8582
Polymers13,7621
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.043, 59.167, 131.425
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21A
31B
41C
51D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114E1 - 129
2114A1 - 129
3114B1 - 129
4114C1 - 129
5114D1 - 129

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Components

#1: Antibody
Anti-Methotrexate CDR1-4 Graft VHH


Mass: 13762.164 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama Glama (llama) / Plasmid: pET21(a)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Lithium Sulfate Monohydrate, 0.1M BIS-TRIS, 25% PEG 3000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979 Å
DetectorType: MAR 225 / Detector: CCD / Date: Jul 12, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 50632 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.089 / Rsym value: 0.143

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.578 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23828 2525 5 %RANDOM
Rwork0.18918 ---
obs0.19163 47518 97.51 %-
all-47518 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20.24 Å2
2--0.81 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4733 0 11 295 5039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214887
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9346622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0555615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22322.655226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05815764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4391548
X-RAY DIFFRACTIONr_chiral_restr0.1530.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023777
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.351.53045
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.20624830
X-RAY DIFFRACTIONr_scbond_it3.30831842
X-RAY DIFFRACTIONr_scangle_it4.8284.51792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 902 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1EMEDIUM POSITIONAL0.550.5
2AMEDIUM POSITIONAL0.690.5
3BMEDIUM POSITIONAL0.780.5
4CMEDIUM POSITIONAL0.550.5
5DMEDIUM POSITIONAL0.980.5
1EMEDIUM THERMAL2.442
2AMEDIUM THERMAL1.772
3BMEDIUM THERMAL1.672
4CMEDIUM THERMAL2.292
5DMEDIUM THERMAL1.862
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 156 -
Rwork0.256 3402 -
obs--95.34 %
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)
11.59760.06940.47732.3775-0.70222.3697-0.0281-0.01780.07970.20650.1390.1981-0.1641-0.1702-0.11090.02990.03860.02760.08340.02690.05313.318-6.95448.007
21.55240.1481-0.02951.97760.14672.2465-0.02930.00240.0396-0.0439-0.00070.10390.1155-0.0290.030.01520.0064-0.00810.0105-0.00120.0323-11.532-33.5424.715
30.9927-0.43360.6113.6971-1.19321.27870.0519-0.0515-0.02380.1825-0.1622-0.0954-0.19870.07680.11030.11130.05980.0020.20330.05280.0675-7.229-45.66130.646
41.0416-0.3513-0.17791.63990.26482.0623-0.0780.003-0.0331-0.03290.00150.05040.11610.05340.07640.03020.03110.00060.06010.00960.034713.01-15.47822.115
51.0257-0.20430.42381.4633-0.17712.01980.08490.1193-0.0355-0.2362-0.08150.0928-0.05010.0836-0.00340.2538-0.0122-0.02260.0325-0.00540.0133-19.234-39.16256.629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 131
2X-RAY DIFFRACTION2A3 - 131
3X-RAY DIFFRACTION3C4 - 131
4X-RAY DIFFRACTION4D4 - 131
5X-RAY DIFFRACTION5E3 - 131

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