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- PDB-3qfh: 2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Pe... -

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Entry
Database: PDB / ID: 3qfh
Title2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) from Staphylococcus aureus.
ComponentsEpidermin leader peptide processing serine protease EpiP
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha and beta proteins (a/b) / Subtilisin-like / Rossmann fold / serine-type endopeptidase activity
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Lantibiotic leader peptide-processing serine protease / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 ...Lantibiotic leader peptide-processing serine protease / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Leader peptide-processing serine protease / Leader peptide-processing serine protease
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) from Staphylococcus aureus.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F.
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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_conn.ptnr2_label_atom_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: Epidermin leader peptide processing serine protease EpiP
B: Epidermin leader peptide processing serine protease EpiP
C: Epidermin leader peptide processing serine protease EpiP
D: Epidermin leader peptide processing serine protease EpiP
E: Epidermin leader peptide processing serine protease EpiP
F: Epidermin leader peptide processing serine protease EpiP
G: Epidermin leader peptide processing serine protease EpiP
H: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,93354
Polymers399,7838
Non-polymers4,15046
Water27,2211511
1
A: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6309
Polymers49,9731
Non-polymers6578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7339
Polymers49,9731
Non-polymers7618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3575
Polymers49,9731
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3806
Polymers49,9731
Non-polymers4075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5457
Polymers49,9731
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3575
Polymers49,9731
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3575
Polymers49,9731
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5728
Polymers49,9731
Non-polymers5997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.505, 94.696, 122.999
Angle α, β, γ (deg.)89.98, 90.37, 116.79
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Epidermin leader peptide processing serine protease EpiP


Mass: 49972.879 Da / Num. of mol.: 8 / Fragment: sequence database residues 28-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: epiP, SACOL1874 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q5HEV5, UniProt: A0A0H2WX20*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Non-polymers , 5 types, 1557 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1511 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 7mg/mL, ?M Sodium cloride, Tris-HCl (pH 8.3), Screen: GCSG+ (H9), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 219399 / Num. obs: 219399 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10837 / % possible all: 97

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THM

1thm


Resolution: 2.05→29.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.082 / SU ML: 0.086
Isotropic thermal model: Atomic thermal factors individually refined
Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21596 10599 5 %RANDOM
Rwork0.1695 ---
all0.1718 200752 --
obs0.1718 200752 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.607 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-2.15 Å2-0.19 Å2
2--1.41 Å20.13 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26598 0 221 1511 28330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02227433
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218119
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.94737080
X-RAY DIFFRACTIONr_angle_other_deg0.834344597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.10753421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18925.9511304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.394154907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.991572
X-RAY DIFFRACTIONr_chiral_restr0.0850.24048
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0230643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025093
X-RAY DIFFRACTIONr_mcbond_it1.0181.516941
X-RAY DIFFRACTIONr_mcbond_other0.2971.56976
X-RAY DIFFRACTIONr_mcangle_it1.797227279
X-RAY DIFFRACTIONr_scbond_it2.976310492
X-RAY DIFFRACTIONr_scangle_it4.6684.59801
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 793 -
Rwork0.248 14675 -
obs-10599 96.87 %
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)
11.7482-0.49780.09371.7377-0.53764.98970.04820.08960.1168-0.0645-0.0422-0.1186-0.04180.3702-0.0060.0795-0.0737-0.00370.12390.01390.01414.78371.659458.903
20.97540.10230.00970.50640.13280.8862-0.00990.03290.0259-0.04360.0156-0.0016-0.07570.0382-0.00570.0971-0.0416-0.01670.02090.00140.0241-1.25072.227186.4717
32.7750.348-0.23722.2920.55124.3747-0.02270.1334-0.0862-0.1458-0.00240.08040.0683-0.37330.02510.0393-0.0463-0.00610.1156-0.00010.0068-5.341818.6655-2.2757
40.82680.04570.02480.5419-0.12390.9985-0.00160.0185-0.0055-0.02850.01380.01750.0754-0.0532-0.01220.0669-0.02870.01750.0146-0.00050.036510.222118.066625.011
52.2280.4048-0.09811.7028-0.40065.4697-0.13060.03890.0818-0.07410.0415-0.0892-0.1920.54880.08910.0984-0.00990.06510.1927-0.04010.0969-7.128642.559154.9639
60.8878-0.062-0.2991.18790.49151.8473-0.0470.0747-0.0886-0.1088-0.0264-0.0431-0.03270.02540.07350.01450.00580.00630.0694-0.05360.0908-23.747544.848882.6504
72.64870.0105-0.36061.77190.38695.73660.0868-0.11540.02650.1421-0.02430.16220.2354-0.2669-0.06250.0742-0.04240.00960.05260.02720.0486-21.732-24.26468.6892
80.84710.2438-0.14781.0677-0.07521.38290.0162-0.0260.0352-0.0446-0.00990.03720.0553-0.0447-0.00630.0083-0.0041-0.00890.01360.02070.0537-13.9512-12.383340.8509
92.5345-0.0014-0.223.45590.33088.3504-0.1316-0.3147-0.16260.4565-0.09130.10480.9278-0.09150.22290.21510.01510.08880.10330.0250.056743.203512.006465.5173
100.78170.06630.16190.8627-0.30081.3725-0.09980.003-0.0705-0.04910.0116-0.0420.02250.15650.08820.0289-0.00090.03570.0709-0.01280.059447.01629.694940.3538
113.31280.12530.74523.9893-0.37738.5855-0.1116-0.43380.14390.4317-0.2041-0.0861-0.97520.10270.31570.22990.0313-0.10870.1253-0.04190.0778-34.61118.1249127.005
120.84040.0626-0.14650.90840.35291.3629-0.1353-0.01130.072-0.05150.02840.0584-0.0294-0.18570.10690.041-0.0013-0.04160.07930.00880.0586-38.2307-9.4876101.7782
133.24810.71450.83511.67060.29055.5959-0.19150.02460.0387-0.233-0.03360.12960.1076-0.59040.22510.14090.0138-0.08140.19820.02940.114-26.301962.4413-6.4448
140.9550.02040.35131.2867-0.45031.9528-0.06620.0740.1357-0.1143-0.05330.04450.0109-0.00320.11950.01490.0041-0.00990.06090.0580.1059-10.008160.022221.1289
152.52330.0670.38032.20610.02274.27570.0934-0.1449-0.00890.1333-0.0357-0.1508-0.22850.1495-0.05770.0701-0.0325-0.00210.0578-0.04120.055429.8644.2181130.3764
160.8510.24260.06791.05970.07771.37060.0147-0.0269-0.0242-0.0238-0.0047-0.0359-0.04740.0316-0.010.01620.00390.00760.0187-0.02670.067322.682832.5633102.3778
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 93
2X-RAY DIFFRACTION2A100 - 457
3X-RAY DIFFRACTION3B28 - 94
4X-RAY DIFFRACTION4B100 - 457
5X-RAY DIFFRACTION5C28 - 90
6X-RAY DIFFRACTION6C100 - 457
7X-RAY DIFFRACTION7D28 - 95
8X-RAY DIFFRACTION8D100 - 457
9X-RAY DIFFRACTION9E28 - 95
10X-RAY DIFFRACTION10E100 - 457
11X-RAY DIFFRACTION11F28 - 95
12X-RAY DIFFRACTION12F100 - 457
13X-RAY DIFFRACTION13G28 - 90
14X-RAY DIFFRACTION14G100 - 457
15X-RAY DIFFRACTION15H29 - 95
16X-RAY DIFFRACTION16H100 - 457

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