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- PDB-8ipc: The recombinant NZ-1 Fab complexed with the PDZ tandem fragment o... -

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Basic information

Entry
Database: PDB / ID: 8ipc
TitleThe recombinant NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 181 and 184
Components
  • Putative zinc metalloprotease aq_1964
  • The recombinantly-expressed heavy chain of the monoclonal antibody NZ-1
  • The recombinantly-expressed light chain of the monoclonal antibody NZ-1
KeywordsIMMUNE SYSTEM/HYDROLASE / PDZ domain Fab / HYDROLASE / IMMUNE SYSTEM-HYDROLASE complex
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 profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Putative zinc metalloprotease aq_1964
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Aquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAdachi, Y. / Nogi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02561 Japan
CitationJournal: Protein Expr.Purif. / Year: 2023
Title: Recombinant production of antibody antigen-binding fragments with an N-terminal human growth hormone tag in mammalian cells.
Authors: Adachi, Y. / Kaneko, M.K. / Kato, Y. / Nogi, T.
History
DepositionMar 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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
H: The recombinantly-expressed heavy chain of the monoclonal antibody NZ-1
L: The recombinantly-expressed light chain of the monoclonal antibody NZ-1
A: Putative zinc metalloprotease aq_1964


Theoretical massNumber of molelcules
Total (without water)68,0373
Polymers68,0373
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.935, 75.086, 173.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody The recombinantly-expressed heavy chain of the monoclonal antibody NZ-1


Mass: 23553.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody The recombinantly-expressed light chain of the monoclonal antibody 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) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Protein Putative zinc metalloprotease aq_1964


Mass: 21135.703 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% (wt/vol) polyethylene glycol 3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris-HCl (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→45.82 Å / Num. obs: 35390 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 46.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3029 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.32 Å / SU ML: 0.3567 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 33.7384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2698 3308 4.98 %
Rwork0.2427 63063 -
obs0.2442 35351 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.38 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 0 106 4802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214794
X-RAY DIFFRACTIONf_angle_d0.53726511
X-RAY DIFFRACTIONf_chiral_restr0.0414744
X-RAY DIFFRACTIONf_plane_restr0.005832
X-RAY DIFFRACTIONf_dihedral_angle_d5.0436664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.35621550.352624X-RAY DIFFRACTION99.82
2.23-2.260.43811520.35992633X-RAY DIFFRACTION99.79
2.26-2.30.36071470.33912555X-RAY DIFFRACTION99.93
2.3-2.340.34021340.31292703X-RAY DIFFRACTION100
2.34-2.380.321330.29912641X-RAY DIFFRACTION99.96
2.38-2.420.3661580.32692594X-RAY DIFFRACTION99.78
2.42-2.470.39681430.30552641X-RAY DIFFRACTION99.78
2.47-2.520.36451450.29782598X-RAY DIFFRACTION99.78
2.52-2.570.42721220.30292640X-RAY DIFFRACTION99.82
2.57-2.630.33061400.29072608X-RAY DIFFRACTION99.89
2.63-2.70.34221110.29972676X-RAY DIFFRACTION99.29
2.7-2.770.31931330.29382621X-RAY DIFFRACTION99.85
2.77-2.850.34011480.28232636X-RAY DIFFRACTION99.89
2.85-2.950.35421380.30022629X-RAY DIFFRACTION99.93
2.95-3.050.42721410.28412646X-RAY DIFFRACTION100
3.05-3.170.33211290.27892599X-RAY DIFFRACTION99.93
3.17-3.320.33391230.27642656X-RAY DIFFRACTION99.86
3.32-3.490.30461640.26072614X-RAY DIFFRACTION99.78
3.49-3.710.26951230.23572643X-RAY DIFFRACTION99.64
3.71-40.27231170.22692630X-RAY DIFFRACTION98.49
4-4.40.22021210.19722639X-RAY DIFFRACTION99.93
4.4-5.030.15971170.17652639X-RAY DIFFRACTION99.89
5.03-6.330.22941660.19882596X-RAY DIFFRACTION99.75
6.34-38.320.16841480.20152602X-RAY DIFFRACTION99.06

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