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- PDB-6icc: The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicu... -

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Basic information

Entry
Database: PDB / ID: 6icc
TitleThe NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 181 and 186
Components
  • Heavy chain of antigen binding fragment, Fab of NZ-1
  • Light chain of antigen binding fragment, Fab of NZ-1
  • PDZ tandem fragment with PA tag
KeywordsSIGNALING PROTEIN / protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative zinc metalloprotease aq_1964
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTamura, R. / Oi, R. / Kaneko, M.K. / Kato, Y. / Nogi, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science26291016 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101078 Japan
Japan Agency for Medical Research and Development (AMED)16am0101020j0005 Japan
CitationJournal: Protein Sci. / Year: 2019
Title: Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins.
Authors: Tamura, R. / Oi, R. / Akashi, S. / Kaneko, M.K. / Kato, Y. / Nogi, T.
History
DepositionSep 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PDZ tandem fragment with PA tag
H: Heavy chain of antigen binding fragment, Fab of NZ-1
L: Light chain of antigen binding fragment, Fab of NZ-1


Theoretical massNumber of molelcules
Total (without water)67,4783
Polymers67,4783
Non-polymers00
Water4,522251
1
A: PDZ tandem fragment with PA tag

H: Heavy chain of antigen binding fragment, Fab of NZ-1
L: Light chain of antigen binding fragment, Fab of NZ-1


Theoretical massNumber of molelcules
Total (without water)67,4783
Polymers67,4783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area5830 Å2
ΔGint-35 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.938, 84.293, 185.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PDZ tandem fragment with PA tag


Mass: 20721.291 Da / Num. of mol.: 1 / Fragment: UNP residues 115-181 and 185-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: aq_1964 / Production host: Escherichia coli (E. coli)
References: UniProt: O67776, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Antibody Heavy chain of antigen binding fragment, Fab of NZ-1


Mass: 23409.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse)
#3: Antibody Light chain of antigen binding fragment, Fab of NZ-1


Mass: 23347.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAuthors state that four residues of the host protein, that is 182, 183, 184 and 185 were deleted ...Authors state that four residues of the host protein, that is 182, 183, 184 and 185 were deleted and 12 residues, GVAMPGAEDDVV, were inserted in place of them.

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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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12-15%(wt./vol.) PEG 3350, 200mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→48.23 Å / Num. obs: 54069 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.94 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3874 / CC1/2: 0.873 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wkl, 4yo0

3wkl

4yo0


Resolution: 2→48.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.299 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.166
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 2701 5 %RANDOM
Rwork0.21272 ---
obs0.215 51283 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.625 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å20 Å2
2---0.26 Å20 Å2
3----3.37 Å2
Refinement stepCycle: 1 / Resolution: 2→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4725 0 0 251 4976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124911
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.6466697
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7324.972640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49222.723213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68715832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1071524
X-RAY DIFFRACTIONr_chiral_restr0.080.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023723
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_it2.6154.5532503
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8036.8173134
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3294.8542408
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.96462.0027206
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 185 -
Rwork0.312 3684 -
obs--99.97 %

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