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- PDB-3lpd: Crystal structure of a subtilisin-like protease -

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Basic information

Entry
Database: PDB / ID: 3lpd
TitleCrystal structure of a subtilisin-like protease
ComponentsAcidic extracellular subtilisin-like protease AprV2
KeywordsHYDROLASE / protease / subtilase / virulence factor / Serine protease
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase MprA-like catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / : / 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 ...Peptidase MprA-like catalytic domain / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / Peptidase S8/S53 domain / : / 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 / Subtilase family / Peptidase S8/S53 domain / Galactose-binding-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acidic extracellular subtilisin-like protease AprV2
Similarity search - Component
Biological speciesDichelobacter nodosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsPorter, C.J. / Wong, W. / Whisstock, J.C. / Rood, J.I. / Kennan, R.M.
CitationJournal: Plos Pathog. / Year: 2010
Title: The Subtilisin-Like Protease AprV2 Is Required for Virulence and Uses a Novel Disulphide-Tethered Exosite to Bind Substrates
Authors: Kennan, R.M. / Wong, W. / Dhungyel, O.P. / Han, X. / Wong, D. / Parker, D. / Rosado, C.J. / Law, R.H.P. / McGowan, S. / Reeve, S.B. / Levina, V. / Powers, G.A. / Pike, R.N. / Bottomley, S.P. ...Authors: Kennan, R.M. / Wong, W. / Dhungyel, O.P. / Han, X. / Wong, D. / Parker, D. / Rosado, C.J. / Law, R.H.P. / McGowan, S. / Reeve, S.B. / Levina, V. / Powers, G.A. / Pike, R.N. / Bottomley, S.P. / Smith, A.I. / Marsh, I. / Whittington, R.J. / Whisstock, J.C. / Porter, C.J. / Rood, J.I.
History
DepositionFeb 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acidic extracellular subtilisin-like protease AprV2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9514
Polymers35,8301
Non-polymers1203
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.936, 45.655, 47.248
Angle α, β, γ (deg.)98.00, 115.13, 113.41
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Acidic extracellular subtilisin-like protease AprV2


Mass: 35830.340 Da / Num. of mol.: 1 / Fragment: UNP residues 131-469 / Mutation: C141S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dichelobacter nodosus (bacteria) / Strain: VCS1703A / Gene: aprV2, DNO_1167 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami(DE3)LysS
References: UniProt: A5EXI3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.34 % / Mosaicity: 0.94 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Acetate, Sodium Cacodylate, PEG 8000, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 7, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.1→24.108 Å / Num. all: 15131 / Num. obs: 15131 / % possible obs: 93.6 % / Redundancy: 3.8 % / Rsym value: 0.092
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2152

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.92 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å24.11 Å
Translation2.1 Å24.11 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LPC

3lpc


Resolution: 2.1→24.108 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.837 / SU B: 13.966 / SU ML: 0.164 / SU R Cruickshank DPI: 0.312 / SU Rfree: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 769 5.1 %RANDOM
Rwork0.182 ---
obs0.185 15129 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.79 Å2 / Biso mean: 30.249 Å2 / Biso min: 3.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.17 Å20.03 Å2
2--0.1 Å20.19 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 3 78 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212522
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9243450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66424.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39915341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1981512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211984
X-RAY DIFFRACTIONr_mcbond_it0.5151.51672
X-RAY DIFFRACTIONr_mcangle_it0.91822661
X-RAY DIFFRACTIONr_scbond_it1.4443850
X-RAY DIFFRACTIONr_scangle_it2.2914.5789
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 53 -
Rwork0.265 1037 -
all-1090 -
obs--90.31 %
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)
12.67410.62690.03371.16790.4580.7173-0.10320.29720.2578-0.06490.1040.0606-0.0368-0.0675-0.00080.10590.009-0.01130.06380.04810.055912.4648-5.015-17.8008
21.15013.334-1.300132.9058-8.09482.2778-0.2259-0.05-0.1889-0.36530.13340.00770.2043-0.01090.09250.097-0.02810.01140.0847-0.00690.09688.2089-30.5942-19.7678
33.06270.7856-0.03531.06950.00860.6791-0.00810.0315-0.1996-0.01540.0017-0.10670.05570.07480.00640.12270.0207-0.00210.04750.02530.067821.9577-10.7301-12.9969
42.64441.05620.11131.47180.3751.04830.1646-0.35030.22990.1419-0.13510.0752-0.0354-0.0409-0.02950.10910.01040.01780.1195-0.01480.082212.3753-5.7192-4.3294
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 81
2X-RAY DIFFRACTION2A82 - 103
3X-RAY DIFFRACTION3A104 - 221
4X-RAY DIFFRACTION4A222 - 340

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