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- PDB-7rg7: Crystal structure of nanoclamp8:VHH in complex with MTX -

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Basic information

Entry
Database: PDB / ID: 7rg7
TitleCrystal structure of nanoclamp8:VHH in complex with MTX
Componentsnano CLostridial Antibody Mimetic Protein 8 VHH
KeywordsIMMUNE SYSTEM
Function / homologyMETHOTREXATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsGuo, Z. / Peat, T. / Newman, J. / Alexandrov, K.
Funding support Australia, Canada, 4items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160100973 Australia
Australian Research Council (ARC)DP150100936 Australia
Canada Excellence Research Chair AwardCE200100029 Canada
National Health and Medical Research Council (NHMRC, Australia)APP1113262 Australia
CitationJournal: Nat Commun / Year: 2021
Title: Design of a methotrexate-controlled chemical dimerization system and its use in bio-electronic devices.
Authors: Guo, Z. / Smutok, O. / Johnston, W.A. / Walden, P. / Ungerer, J.P.J. / Peat, T.S. / Newman, J. / Parker, J. / Nebl, T. / Hepburn, C. / Melman, A. / Suderman, R.J. / Katz, E. / Alexandrov, K.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 18, 2023Group: Author supporting evidence / Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_audit_support / pdbx_initial_refinement_model
Item: _pdbx_audit_support.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nano CLostridial Antibody Mimetic Protein 8 VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0314
Polymers32,5281
Non-polymers5033
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.121, 95.882, 118.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-754-

HOH

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Components

#1: Antibody nano CLostridial Antibody Mimetic Protein 8 VHH


Mass: 32528.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% (w/v) PEG 4000, 0.2 M DL-malate-imidazole pH 6.0, 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.83→59.05 Å / Num. obs: 27424 / % possible obs: 99.5 % / Redundancy: 13.7 % / CC1/2: 1 / Net I/σ(I): 16.7
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 13.6 % / Num. unique obs: 1597 / CC1/2: 1 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QXV

3qxv


Resolution: 1.83→59.05 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.276 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20236 1377 5 %RANDOM
Rwork0.14939 ---
obs0.15205 26016 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.023 Å2
Baniso -1Baniso -2Baniso -3
1-7.29 Å20 Å20 Å2
2---1.14 Å20 Å2
3----6.15 Å2
Refinement stepCycle: 1 / Resolution: 1.83→59.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 35 390 2470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212334
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9523181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7925301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23624.22109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32115389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.141515
X-RAY DIFFRACTIONr_chiral_restr0.1840.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211854
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_it1.8261.51432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.78122308
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8743902
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4054.5873
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.64532334
X-RAY DIFFRACTIONr_sphericity_free7.853407
X-RAY DIFFRACTIONr_sphericity_bonded3.65232268
LS refinement shellResolution: 1.83→1.876 Å
RfactorNum. reflection% reflection
Rfree0.426 98 -
Rwork0.246 1802 -
obs--95.57 %
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)
10.12080.0231-0.06470.08450.20510.36470.002-0.01280.0046-0.0028-0.0085-0.00180.0015-0.00430.00650.02450.007900.08880.00130.046718.18916.51155.147
20.00750.30350.9433-0.55581.67532.8148-0.04470.00150.04030.0387-0.04350.052-0.25690.0040.08820.05870.01990.00620.08720.01130.059610.46918.83241.029
30.3365-0.0328-0.0640.03470.14150.0646-0.00980.0590.0617-0.00190.04660.0565-0.0008-0.0353-0.03680.0460.0035-0.01820.11610.03960.035516.46924.86343.493
40.07840.0292-0.10610.36970.41060.6566-0.0122-0.02210.0021-0.00820.00380.00170.01350.01380.0084-0.00350.00080.00020.09090.00790.038518.37416.26454.515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 298
2X-RAY DIFFRACTION2A301
3X-RAY DIFFRACTION3A302 - 303
4X-RAY DIFFRACTION4A401 - 790

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