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- PDB-4put: Crystal structure of the Arabidopsis thaliana TOP2 oligopeptidase -

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Basic information

Entry
Database: PDB / ID: 4put
TitleCrystal structure of the Arabidopsis thaliana TOP2 oligopeptidase
ComponentsCytosolic oligopeptidase A
KeywordsHYDROLASE / oligopeptidase
Function / homology
Function and homology information


oligopeptidase A / peptide metabolic process / apoplast / response to cadmium ion / chloroplast / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Neurolysin/Thimet oligopeptidase, N-terminal domain / Neurolysin; domain 3 - #40 / Neurolysin/Thimet oligopeptidase, domain 2 / Peptidase M3A/M3B catalytic domain / Peptidase family M3 / Neurolysin; domain 3 / Neutral zinc metallopeptidases, zinc-binding region signature. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable cytosolic oligopeptidase A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3 Å
AuthorsWang, R. / Rajagopalan, K. / Tong, L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structure of the Arabidopsis thaliana TOP2 oligopeptidase.
Authors: Wang, R. / Rajagopalan, K. / Sadre-Bazzaz, K. / Moreau, M. / Klessig, D.F. / Tong, L.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: 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_struct_conn_angle / software / struct_conn / struct_ref_seq_dif / 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 / _software.name / _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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Cytosolic oligopeptidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4173
Polymers81,3161
Non-polymers1012
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.740, 168.740, 175.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Cytosolic oligopeptidase A / Thimet metalloendopeptidase 2 / Zincin-like metalloproteases family protein 2


Mass: 81316.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYOP, TOP2, At5g10540, F12B17.110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q949P2, oligopeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 4.44 Å3/Da / Density % sol: 72.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 220 mM ammonium acetate and 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 30200 / Num. obs: 29598 / % possible obs: 98 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.5 / % possible all: 97.1

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PRIME-Xrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 3→48.09 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 149597.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: OPLS 2005X / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1404 5 %RANDOM
Rwork0.207 ---
all0.207 30200 --
obs0.207 28322 94 %-
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.28 Å20 Å20 Å2
2--5.28 Å20 Å2
3----10.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5517 0 2 0 5519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.018
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.8
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d23
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d2.05
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it2.342.5
X-RAY DIFFRACTIONo_mcangle_it3.854
X-RAY DIFFRACTIONo_scbond_it3.883.5
X-RAY DIFFRACTIONo_scangle_it6.035
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.386 141 5.6 %
Rwork0.341 2380 -
obs--85.7 %

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