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- PDB-6fpc: Structure of the PRO-PRO endopeptidase (PPEP-2) from Paenibacillu... -

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Basic information

Entry
Database: PDB / ID: 6fpc
TitleStructure of the PRO-PRO endopeptidase (PPEP-2) from Paenibacillus alvei
ComponentsPRO-PRO endopeptidase
KeywordsHYDROLASE / Endopeptidase / Metalloprotease / Zinc
Function / homologyPro-Pro endopeptidase / Metallopeptidase, catalytic domain superfamily / metallopeptidase activity / extracellular region / metal ion binding / : / Pro-Pro endopeptidase
Function and homology information
Biological speciesPaenibacillus alvei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsWeeks, S.D. / Klychnikov, O.I. / Hensbergen, P.J. / Strelkov, S.V.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Discovery of a new Pro-Pro endopeptidase, PPEP-2, provides mechanistic insights into the differences in substrate specificity within the PPEP family.
Authors: Klychnikov, O.I. / Shamorkina, T.M. / Weeks, S.D. / van Leeuwen, H.C. / Corver, J. / Drijfhout, J.W. / van Veelen, P.A. / Sluchanko, N.N. / Strelkov, S.V. / Hensbergen, P.J.
History
DepositionFeb 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRO-PRO endopeptidase
B: PRO-PRO endopeptidase
C: PRO-PRO endopeptidase
D: PRO-PRO endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,77636
Polymers84,5954
Non-polymers3,18032
Water10,845602
1
A: PRO-PRO endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5515
Polymers21,1491
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PRO-PRO endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9369
Polymers21,1491
Non-polymers7878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PRO-PRO endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,33613
Polymers21,1491
Non-polymers1,18712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PRO-PRO endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9529
Polymers21,1491
Non-polymers8038
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.900, 84.900, 113.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
PRO-PRO endopeptidase / PPEP-2


Mass: 21148.814 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus alvei (bacteria) / Gene: PAV_1c07830 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: K4ZRC1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Paenibacillus alvei (bacteria) / Strain: DSM 29 / Gene: PAV_1c07830 / Plasmid: pETRUK / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS / References: Pro-Pro endopeptidase
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.2 M Ammonium Sulphate 0.2 M Cadmium Sulphate, 0.01 M Zinc Chloride pH 9.0 adjusted with Ammonium hydroxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2017
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.75→113.27 Å / Num. obs: 80890 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.26 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.917 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→84.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.107 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2136 2.65 %RANDOM
Rwork0.176 ---
obs0.177 80730 99.8 %-
Displacement parametersBiso mean: 33.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.3356 Å20 Å20 Å2
2---0.3356 Å20 Å2
3---0.6712 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.75→84.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 88 602 6296
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015800HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.987882HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1947SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes965HARMONIC5
X-RAY DIFFRACTIONt_it5800HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion14.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion752SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7338SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2211 155 2.58 %
Rwork0.2107 5847 -
all0.2109 6002 -
obs--99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7771-0.0225-0.10751.16780.00561.05170.0398-0.08960.23270.06340.01-0.125-0.06840.0857-0.0498-0.08070.01150.0206-0.0465-0.0268-0.0026-1.9676-17.81184.7455
20.9629-0.1445-0.28611.1918-0.41741.0481-0.0863-0.0539-0.02720.0121-0.0049-0.13270.1630.14770.0912-0.03930.02710.0135-0.02440.0128-0.06659.9887-42.4454-7.2434
30.99860.35480.09390.9572-0.0710.5772-0.06490.21450.1102-0.15020.12690.09970.067-0.098-0.062-0.0709-0.0051-0.00520.04140.0325-0.0814-7.2579-26.1804-30.0918
40.06680.4317-0.3351.8972-0.59260.3430.03290.0143-0.05340.1513-0.05130.18240.00380.00640.0184-0.0211-0.0110.0328-0.0390.0055-0.0124-22.0385-44.18229.1938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|31 - 215 }
2X-RAY DIFFRACTION2{ B|31 - 216 }
3X-RAY DIFFRACTION3{ C|29 - 216 }
4X-RAY DIFFRACTION4{ D|30 - 215 }

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