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- PDB-8c4x: PAM Protease -

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Basic information

Entry
Database: PDB / ID: 8c4x
TitlePAM Protease
Components(Protease) x 2
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family
Similarity search - Domain/homology
Biological speciesActinomadura keratinilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsNomme, J. / Gavalda, S. / Cioci, G. / Guicherd, M. / Marty, A. / Duquesne, S. / Ben Khaled, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Institute of Agricultural Research (INRAE) France
CitationJournal: Nature / Year: 2024
Title: An engineered enzyme embedded into PLA to make self-biodegradable plastic.
Authors: Guicherd, M. / Ben Khaled, M. / Gueroult, M. / Nomme, J. / Dalibey, M. / Grimaud, F. / Alvarez, P. / Kamionka, E. / Gavalda, S. / Noel, M. / Vuillemin, M. / Amillastre, E. / Labourdette, D. ...Authors: Guicherd, M. / Ben Khaled, M. / Gueroult, M. / Nomme, J. / Dalibey, M. / Grimaud, F. / Alvarez, P. / Kamionka, E. / Gavalda, S. / Noel, M. / Vuillemin, M. / Amillastre, E. / Labourdette, D. / Cioci, G. / Tournier, V. / Kitpreechavanich, V. / Dubois, P. / Andre, I. / Duquesne, S. / Marty, A.
History
DepositionJan 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation
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.title / _citation.year
Revision 1.2Jul 31, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5126
Polymers36,1102
Non-polymers4034
Water7,134396
1
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1235
Polymers27,7201
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protease


Theoretical massNumber of molelcules
Total (without water)8,3901
Polymers8,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.482, 64.175, 62.959
Angle α, β, γ (deg.)90.00, 96.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protease


Mass: 27720.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura keratinilytica (bacteria) / Gene: prt / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0U5AS91
#2: Protein Protease


Mass: 8389.620 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura keratinilytica (bacteria) / Gene: prt / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0U5AS91

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Non-polymers , 4 types, 400 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 40% MPD 0.1M Sodium Citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.52→62.6 Å / Num. obs: 48618 / % possible obs: 98.24 % / Redundancy: 3.8 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.38
Reflection shellResolution: 1.52→1.57 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 18284

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Processing

Software
NameVersionClassification
PHENIXv1.19refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→62.6 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1765 2468 5.08 %
Rwork0.1501 --
obs0.1514 48618 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→62.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 25 396 2943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062651
X-RAY DIFFRACTIONf_angle_d0.923639
X-RAY DIFFRACTIONf_dihedral_angle_d9.45409
X-RAY DIFFRACTIONf_chiral_restr0.053429
X-RAY DIFFRACTIONf_plane_restr0.009476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.550.21671380.20712575X-RAY DIFFRACTION98
1.55-1.580.19521290.20282512X-RAY DIFFRACTION98
1.58-1.610.23711380.20062541X-RAY DIFFRACTION97
1.61-1.650.22891400.18162530X-RAY DIFFRACTION98
1.65-1.690.1961430.17622589X-RAY DIFFRACTION99
1.69-1.740.20761380.16492544X-RAY DIFFRACTION99
1.74-1.790.23561650.17342534X-RAY DIFFRACTION99
1.79-1.850.1791300.17342554X-RAY DIFFRACTION98
1.85-1.910.18821440.16112526X-RAY DIFFRACTION97
1.91-1.990.18671370.14472550X-RAY DIFFRACTION98
1.99-2.080.17281410.13952574X-RAY DIFFRACTION99
2.08-2.190.17321530.142551X-RAY DIFFRACTION99
2.19-2.330.16791410.14672581X-RAY DIFFRACTION99
2.33-2.510.1841920.1442573X-RAY DIFFRACTION97
2.51-2.760.18291130.14912605X-RAY DIFFRACTION99
2.76-3.160.17021430.14812621X-RAY DIFFRACTION99
3.16-3.980.15331600.13112544X-RAY DIFFRACTION97
3.98-62.60.14251230.13172646X-RAY DIFFRACTION98

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