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- PDB-1r6v: Crystal structure of fervidolysin from Fervidobacterium pennivora... -

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Basic information

Entry
Database: PDB / ID: 1r6v
TitleCrystal structure of fervidolysin from Fervidobacterium pennivorans, a keratinolytic enzyme related to subtilisin
Componentssubtilisin-like serine protease
KeywordsHYDROLASE / subtilisin / sandwich domain / propeptide
Function / homology
Function and homology information


protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidase activity / serine-type endopeptidase activity / calcium ion binding / cell surface / proteolysis
Similarity search - Function
Immunoglobulin-like - #1800 / Fervidolysin domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8/S53 domain / 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. ...Immunoglobulin-like - #1800 / Fervidolysin domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8/S53 domain / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesFervidobacterium pennivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKim, J.S. / Kluskens, L.D. / de Vos, W.M. / Huber, R. / van der Oost, J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of fervidolysin from Fervidobacterium pennivorans, a keratinolytic enzyme related to subtilisin.
Authors: Kim, J.S. / Kluskens, L.D. / de Vos, W.M. / Huber, R. / van der Oost, J.
History
DepositionOct 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: subtilisin-like serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0392
Polymers71,9981
Non-polymers401
Water10,233568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.558, 51.031, 79.101
Angle α, β, γ (deg.)93.90, 104.72, 115.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein subtilisin-like serine protease


Mass: 71998.453 Da / Num. of mol.: 1 / Fragment: peptidase / Mutation: H208A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium pennivorans (bacteria)
Plasmid: pET9D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93LQ6
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, Isopropanol, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9794,0.9790,0.97855
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.9791
30.978551
ReflectionResolution: 1.7→20 Å / Num. all: 72230 / Num. obs: 68665 / % possible obs: 94.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.432 / % possible all: 91.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEmodel building
CNS1refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.214 6703 RANDOM
Rwork0.186 --
all0.186 72230 -
obs0.186 67227 -
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 1 568 5573
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 1.7→1.71 Å
RfactorNum. reflection
Rfree0.251 129
Rwork0.248 -
obs-1059

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