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- PDB-3kzz: Crystal structure of SNAP-tag bound to its substrate benzylguanine -

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Basic information

Entry
Database: PDB / ID: 3kzz
TitleCrystal structure of SNAP-tag bound to its substrate benzylguanine
ComponentsSNAP-tag
KeywordsTRANSFERASE / protein tag / protein engineering / benzylguanine / substrate binding
Function / homologyMethylated DNA-protein cysteine methyltransferase domain / Double Stranded RNA Binding Domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta / 6-(benzyloxy)-9H-purin-2-amine
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSchmitt, S. / Pojer, F. / Schiltz, M. / Johnsson, K.
CitationJournal: To be Published
Title: SNAP-tag structure
Authors: Schmitt, S. / Mollwitz, B. / Pojer, F. / Bannwarth, M. / Schiltz, M. / Johnsson, K.
History
DepositionDec 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Assembly

Deposited unit
A: SNAP-tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7123
Polymers19,4051
Non-polymers3072
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 77.160, 64.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein SNAP-tag


Mass: 19405.201 Da / Num. of mol.: 1 / Mutation: C145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OBG / 6-(benzyloxy)-9H-purin-2-amine / o6-benzylguanine


Mass: 241.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N5O / Comment: antineoplastic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE SEQUENCE HAS BEEN DEPOSITED TO EMBL WITH ACCESSION NUMBER FR727225. 2. RESIDUE CYS145ALA IS A MUTATION.

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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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG3350, 100 mM BisTris pH 6.5, 400 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979653 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 29, 2009
RadiationMonochromator: double crystal monochromator (with either Si (111) or Si (311)) between two cylindrical parabolic mirrors.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979653 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 16155 / Num. obs: 16100 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 29.64 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 32.17
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 6.11 / Num. unique all: 2505 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CCP4phasermodel building
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
CCP4phaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KZY

3kzy


Resolution: 1.89→38.58 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.679 / SU ML: 0.082 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22215 805 5 %RANDOM
Rwork0.1871 ---
obs0.18884 15293 100 %-
all-16098 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.838 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.89→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 19 114 1348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221279
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9831742
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97824.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1815203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.877155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021979
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_it0.9021.5790
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57621266
X-RAY DIFFRACTIONr_scbond_it2.2953489
X-RAY DIFFRACTIONr_scangle_it3.6894.5474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.893→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 57 -
Rwork0.216 1082 -
obs--100 %

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