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- PDB-3qxv: Structure of an Anti-Methotrexate CDR1-4 Graft VHH Antibody in Co... -

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Basic information

Entry
Database: PDB / ID: 3qxv
TitleStructure of an Anti-Methotrexate CDR1-4 Graft VHH Antibody in Complex with Methotrexate
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 / METHOTREXATE
Function and homology information
Biological speciesLama Glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)71,46714
Polymers68,8115
Non-polymers2,6569
Water95553
1
A: Anti-Methotrexate CDR1-4 Graft VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3133
Polymers13,7621
Non-polymers5512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anti-Methotrexate CDR1-4 Graft VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4094
Polymers13,7621
Non-polymers6473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Anti-Methotrexate CDR1-4 Graft VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3133
Polymers13,7621
Non-polymers5512
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)14,2172
Polymers13,7621
Non-polymers4541
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)14,2172
Polymers13,7621
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.669, 57.605, 131.136
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21B
31C
41A
51D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114E1 - 129
2114B1 - 129
3114C1 - 129
4114A1 - 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: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Lithium Sulfate Monohydrate, 0.1M Tris. 25% w/v PEG 3,350, pH 8.5, 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: 2.5→20 Å / Num. obs: 37495 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.73

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 17.457 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27855 1859 5 %RANDOM
Rwork0.22955 ---
obs0.23209 35361 98.75 %-
all-37250 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.323 Å2
Baniso -1Baniso -2Baniso -3
1-5.31 Å20 Å21.09 Å2
2---0.23 Å20 Å2
3----5.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 173 53 4914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214964
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9726716
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8845592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84422.444225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.82815755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8361550
X-RAY DIFFRACTIONr_chiral_restr0.1160.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023821
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_it0.9431.52992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53624742
X-RAY DIFFRACTIONr_scbond_it2.37531972
X-RAY DIFFRACTIONr_scangle_it3.2644.51974
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 882 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1EMEDIUM POSITIONAL0.580.5
2BMEDIUM POSITIONAL0.390.5
3CMEDIUM POSITIONAL0.40.5
4AMEDIUM POSITIONAL0.390.5
5DMEDIUM POSITIONAL0.380.5
1EMEDIUM THERMAL0.962
2BMEDIUM THERMAL2.312
3CMEDIUM THERMAL1.552
4AMEDIUM THERMAL1.312
5DMEDIUM THERMAL1.012
LS refinement shellResolution: 2.111→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 114 -
Rwork0.31 2291 -
obs--87.58 %
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)
11.9912-0.5987-0.75754.01761.42573.8161-0.03080.1508-0.03840.4581-0.22240.160.3216-0.40830.25320.2134-0.11060.02410.3285-0.03470.2658-16.424124.6596-34.8322
22.49230.30720.02214.0559-1.25723.94830.04880.1663-0.2811-0.1609-0.1867-0.0985-0.48910.00390.13780.09210.02540.00050.351-0.01660.3262-8.261215.0037-60.8083
34.2293-1.61260.88952.9576-0.91672.5445-0.02240.25430.06670.1813-0.067-0.11750.18540.21030.08940.148-0.04270.00560.2391-0.00520.27726.4528-2.8081-43.6551
43.4083-0.79521.27183.6851-0.6516.431-0.1173-0.23590.06110.44450.0318-0.1825-0.1979-0.13520.08550.4788-0.0313-0.0330.3013-0.00840.247614.9571-12.9311-17.8666
53.33810.15960.46424.4918-1.62068.2303-0.16150.0178-0.00070.3519-0.1988-0.3877-0.02091.38350.36030.9127-0.1488-0.01530.63650.05760.2968-5.750920.6188-8.9453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 131
2X-RAY DIFFRACTION2B4 - 131
3X-RAY DIFFRACTION3C4 - 131
4X-RAY DIFFRACTION4D3 - 131
5X-RAY DIFFRACTION5E4 - 129

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