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- PDB-9rk9: Fervidolysin B (FerB) from Fervidobacterium pennivorans -

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Basic information

Entry
Database: PDB / ID: 9rk9
TitleFervidolysin B (FerB) from Fervidobacterium pennivorans
Components(Subtilisin-like serine ...) x 2
KeywordsHYDROLASE / Protease / keratinase / Subtilisin-like S8 endopeptidase / FerB
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Thermitase-like, domain / : / Fervidolysin N-terminal prodomain / : / 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. ...Thermitase-like, domain / : / Fervidolysin N-terminal prodomain / : / 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 / Subtilase family / Peptidase S8/S53 domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Subtilisin-like serine protease
Similarity search - Component
Biological speciesFervidobacterium pennivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsOpperman, D.J. / Tolmie, C. / Kruger, M.W.
Funding supportEuropean Union, South Africa, 2items
OrganizationGrant numberCountry
European Union (EU)862555European Union
National Research Foundation in South Africa134126 South Africa
CitationJournal: Enzyme.Microb.Technol. / Year: 2026
Title: Structural characterization of an S8 protease from Fervidobacterium pennivorans reveals a unique tyrosine-rich beta-hairpin.
Authors: Kruger, M.W. / Schroder, G.C. / Javier-Lopez, R. / Tolmie, C. / Ebrecht, A.C. / Littlechild, J.A. / Armengaud, J. / Birkeland, N.K. / Opperman, D.J.
History
DepositionJun 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin-like serine protease
B: Subtilisin-like serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,26110
Polymers47,2072
Non-polymers1,0538
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Chain maturation, cleaved into two chains
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-29 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.574, 71.829, 141.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Subtilisin-like serine ... , 2 types, 2 molecules AB

#1: Protein Subtilisin-like serine protease


Mass: 10853.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium pennivorans (bacteria)
Strain: T / Gene: Ferpe_1165 / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: H9UCM0
#2: Protein Subtilisin-like serine protease


Mass: 36354.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium pennivorans (bacteria)
Strain: T / Gene: Ferpe_1165 / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: H9UCM0

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Non-polymers , 6 types, 335 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.87 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.04 M citric acid, 0.06 M Bis-Tris propane pH 6.5, 24% PEG3350, 6 mg/ml

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.49→64.01 Å / Num. obs: 89725 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.05 / Rrim(I) all: 0.184 / Net I/σ(I): 6.7
Reflection shellResolution: 1.49→1.52 Å / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 2.906 / Num. measured all: 56683 / Num. unique obs: 4424 / CC1/2: 0.383 / Rpim(I) all: 0.843 / Rrim(I) all: 3.028 / Net I/σ(I) obs: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→64.01 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.043 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19491 1970 2.2 %RANDOM
Rwork0.17362 ---
obs0.17409 87606 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.49→64.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 64 327 3536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133294
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172933
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.6474483
X-RAY DIFFRACTIONr_angle_other_deg1.5051.5716792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68722.39159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05815472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0971516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023741
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02707
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8892.0741640
X-RAY DIFFRACTIONr_mcbond_other1.882.071639
X-RAY DIFFRACTIONr_mcangle_it2.5943.0942050
X-RAY DIFFRACTIONr_mcangle_other2.6013.0982051
X-RAY DIFFRACTIONr_scbond_it3.3562.5281654
X-RAY DIFFRACTIONr_scbond_other3.352.5221651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9543.6222434
X-RAY DIFFRACTIONr_long_range_B_refined6.5926.2453784
X-RAY DIFFRACTIONr_long_range_B_other6.5926.2583785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å
RfactorNum. reflection% reflection
Rfree0.387 140 -
Rwork0.387 6353 -
obs--99.11 %

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