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- PDB-3rnz: Crystal structure of Bacillus Amyloliquefaciens Pyroglutamyl Pept... -

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Basic information

Entry
Database: PDB / ID: 3rnz
TitleCrystal structure of Bacillus Amyloliquefaciens Pyroglutamyl Peptidase I
ComponentsPyrrolidone-carboxylate peptidase
KeywordsHYDROLASE
Function / homology
Function and homology information


pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol
Similarity search - Function
Pyroglutamyl peptidase I, bacterial-type / Pyroglutamyl peptidase I, Glu active site / Pyrrolidone-carboxylate peptidase glutamic acid active site. / Peptidase C15, pyroglutamyl peptidase I-like / Pyroglutamyl peptidase I, Cys active site / Pyrrolidone-carboxylate peptidase cysteine active site. / Peptidase C15, pyroglutamyl peptidase I / Peptidase C15, pyroglutamyl peptidase I-like / Peptidase C15, pyroglutamyl peptidase I-like superfamily / Pyroglutamyl peptidase ...Pyroglutamyl peptidase I, bacterial-type / Pyroglutamyl peptidase I, Glu active site / Pyrrolidone-carboxylate peptidase glutamic acid active site. / Peptidase C15, pyroglutamyl peptidase I-like / Pyroglutamyl peptidase I, Cys active site / Pyrrolidone-carboxylate peptidase cysteine active site. / Peptidase C15, pyroglutamyl peptidase I / Peptidase C15, pyroglutamyl peptidase I-like / Peptidase C15, pyroglutamyl peptidase I-like superfamily / Pyroglutamyl peptidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyrrolidone-carboxylate peptidase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLo, Y.-C. / Wang, A.H.-J.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2011
Title: Terpyridine platinum(II) complexes inhibit cysteine proteases by binding to active-site cysteine.
Authors: Lo, Y.-C. / Su, W.-C. / Ko, T.-P. / Wang, N.-C. / Wang, A.H.-J.
History
DepositionApr 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase
C: Pyrrolidone-carboxylate peptidase
D: Pyrrolidone-carboxylate peptidase


Theoretical massNumber of molelcules
Total (without water)97,5074
Polymers97,5074
Non-polymers00
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-43 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)289.890, 45.360, 68.090
Angle α, β, γ (deg.)90.00, 91.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Pyrrolidone-carboxylate peptidase / 5-oxoprolyl-peptidase / Pyroglutamyl-peptidase I / PGP-I / Pyrase


Mass: 24376.689 Da / Num. of mol.: 4 / Mutation: M58I, A202V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Strain: ATCC49763; RUB 500 / Gene: pcp / Plasmid: pET-23(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46107, pyroglutamyl-peptidase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.8M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 10, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→25 Å / Num. all: 59489 / Num. obs: 59251 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 4.2 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 32.9
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 4 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 8.4 / Num. unique all: 2926 / % possible all: 98.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AUG

1aug


Resolution: 2.01→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2960 5 %RANDOM
Rwork0.174 ---
all0.176 61430 --
obs0.176 58470 95.2 %-
Solvent computationBsol: 50.4074 Å2
Displacement parametersBiso mean: 22.337 Å2
Baniso -1Baniso -2Baniso -3
1-4.462 Å20 Å20.174 Å2
2---5.781 Å20 Å2
3---1.319 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 2.01→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6337 0 0 437 6774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.84
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_mcbond_it1.3471.5
X-RAY DIFFRACTIONc_scbond_it2.2622
X-RAY DIFFRACTIONc_mcangle_it1.9672
X-RAY DIFFRACTIONc_scangle_it3.1592.5
LS refinement shellResolution: 2.01→2.08 Å / Rfactor Rfree error: 0.052
RfactorNum. reflection% reflection
Rfree0.2235 268 -
Rwork0.1727 --
obs-5527 98.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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