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- PDB-3t41: 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Pe... -

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Entry
Database: PDB / ID: 3t41
Title1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) S393A Mutant 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Kuhn, M. / Ruan, J. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. ...Minasov, G. / Kuhn, M. / Ruan, J. / 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: 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) S393A Mutant from Staphylococcus aureus.
Authors: Minasov, G. / Kuhn, M. / Ruan, J. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural ...Authors: Minasov, G. / Kuhn, M. / Ruan, J. / 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)
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_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.value / _struct_conn.pdbx_dist_value / _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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6779
Polymers105,4022
Non-polymers2767
Water8,773487
1
A: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8214
Polymers52,7011
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Epidermin leader peptide processing serine protease EpiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8565
Polymers52,7011
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.234, 68.473, 97.723
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Epidermin leader peptide processing serine protease EpiP


Mass: 52700.789 Da / Num. of mol.: 2 / Fragment: sequence database residues 28-457 / Mutation: S393A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus 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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein solution: 7.8 mG/mL, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen solution: PACT (D11), 0.2M Calcium chloride, 0.1M Tris (pH 8.0), 20% w/v PEG 6000, VAPOR DIFFUSION, ...Details: Protein solution: 7.8 mG/mL, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen solution: PACT (D11), 0.2M Calcium chloride, 0.1M Tris (pH 8.0), 20% w/v PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 67885 / Num. obs: 67885 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3 / Num. unique all: 3419 / % possible all: 97.8

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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: 3QFH

3qfh


Resolution: 1.95→29.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.083 / SU ML: 0.092
Isotropic thermal model: Atomic Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19477 3416 5.1 %RANDOM
Rwork0.16597 ---
all0.16749 63887 --
obs0.16749 63887 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.031 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å2-0 Å21.88 Å2
2--0.52 Å2-0 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 7 487 7100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227006
X-RAY DIFFRACTIONr_bond_other_d0.0010.024639
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9389500
X-RAY DIFFRACTIONr_angle_other_deg0.851311433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5775892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03125.953341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.445151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.4811518
X-RAY DIFFRACTIONr_chiral_restr0.0870.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021335
X-RAY DIFFRACTIONr_mcbond_it1.1121.54334
X-RAY DIFFRACTIONr_mcbond_other0.3661.51776
X-RAY DIFFRACTIONr_mcangle_it1.8827007
X-RAY DIFFRACTIONr_scbond_it3.06532672
X-RAY DIFFRACTIONr_scangle_it4.7924.52493
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 231 -
Rwork0.226 4694 -
obs-4694 98.42 %
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)
11.9018-0.1377-1.65661.7045-0.6193.9326-0.1071-0.55890.13710.71790.14830.1593-0.194-0.0784-0.04120.43210.12150.05640.5343-0.02710.1066-33.6875-12.0623-13.2282
21.4849-0.1598-0.3631.8402-0.06021.6208-0.0975-0.23860.10.33760.17610.016-0.0781-0.3938-0.07870.0760.0668-0.01030.1826-0.00250.0371-26.8881-12.4259-33.6688
31.3284-0.21650.06371.9275-0.53321.8964-0.1051-0.09670.10040.1160.1259-0.3341-0.0782-0.1674-0.02080.02230.0215-0.0310.0296-0.03130.1009-14.3274-13.3682-41.7981
44.0204-0.635-0.88412.8467-0.95393.5540.1158-0.51390.19470.66440.05840.3251-0.1552-0.1503-0.17420.45910.02520.17760.4936-0.04030.1902-10.5777-37.25442.2917
51.37780.2971-0.24251.5017-0.2431.94160.032-0.4358-0.00210.4029-0.0253-0.03650.06410.1133-0.00670.15660.0281-0.00710.15050.01060.08196.541-37.7503-15.148
61.8645-0.1978-0.26761.92860.18471.5431-0.0566-0.1357-0.08310.1040.01290.13330.0784-0.07380.04370.05180.01530.02140.02140.01410.10341.0342-37.4432-29.1846
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 106
2X-RAY DIFFRACTION2A107 - 310
3X-RAY DIFFRACTION3A311 - 454
4X-RAY DIFFRACTION4B28 - 100
5X-RAY DIFFRACTION5B107 - 278
6X-RAY DIFFRACTION6B279 - 452

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