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- PDB-3ro0: Crystal structure of Bacillus amyloliquefaciens pyroglutamyl pept... -

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Basic information

Entry
Database: PDB / ID: 3ro0
TitleCrystal structure of Bacillus amyloliquefaciens pyroglutamyl peptidase I and terpyridine platinum(II)
ComponentsPyrrolidone-carboxylate peptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
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
2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride / Pyrrolidone-carboxylate peptidase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 25, 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 ...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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Pyrrolidone-carboxylate peptidase
B: Pyrrolidone-carboxylate peptidase
C: Pyrrolidone-carboxylate peptidase
D: Pyrrolidone-carboxylate peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8269
Polymers97,5074
Non-polymers2,3195
Water17,258958
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-62 kcal/mol
Surface area31530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)290.320, 45.520, 67.990
Angle α, β, γ (deg.)90.00, 91.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

21D-958-

HOH

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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: Chemical
ChemComp-TPT / 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride


Mass: 463.799 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H11ClN3Pt
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 958 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.8 M 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 8, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 142153 / Num. obs: 123673 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 30.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2 / Num. unique all: 6118 / % possible all: 43.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RNZ

3rnz


Resolution: 1.5→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 5971 -RANDOM
Rwork0.179 ---
all0.18 118603 --
obs0.18 112632 83.1 %-
Solvent computationBsol: 51.1062 Å2
Displacement parametersBiso mean: 20.5411 Å2
Baniso -1Baniso -2Baniso -3
1-2.544 Å20 Å20.217 Å2
2---5.733 Å20 Å2
3---3.189 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6345 0 95 958 7398
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.99
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_mcbond_it1.2971.5
X-RAY DIFFRACTIONc_scbond_it2.2772
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scangle_it3.3272.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.289 258 -
Rwork0.26 --
obs-4774 35.48 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3tpt.param

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