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- PDB-2x3c: AsaP1 inactive mutant E294Q, an extracellular toxic zinc metalloe... -

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Basic information

Entry
Database: PDB / ID: 2x3c
TitleAsaP1 inactive mutant E294Q, an extracellular toxic zinc metalloendopeptidase
ComponentsTOXIC EXTRACELLULAR ENDOPEPTIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


metalloendopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2970 / Lysine-specific metallo-endopeptidase / Peptidyl-Lys metallopeptidase catalytic domain / Lysine-specific metallo-endopeptidase / Lysine-specific metallo-endopeptidase / : / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Immunoglobulin-like ...Immunoglobulin-like - #2970 / Lysine-specific metallo-endopeptidase / Peptidyl-Lys metallopeptidase catalytic domain / Lysine-specific metallo-endopeptidase / Lysine-specific metallo-endopeptidase / : / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Toxic extracellular endopeptidase
Similarity search - Component
Biological speciesAEROMONAS SALMONICIDA SUBSP. ACHROMOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsBogdanovic, X. / Palm, G.J. / Singh, R.K. / Hinrichs, W.
Citation
Journal: FEBS Lett. / Year: 2016
Title: Structural Evidence of Intramolecular Propeptide Inhibition of the Aspzincin Metalloendopeptidase Asap1.
Authors: Bogdanovic, X. / Palm, G.J. / Schwenteit, J. / Singh, R.K. / Gudmundsdottir, B.K. / Hinrichs, W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Asap1_E294A and Asap1_E294Q, Two Inactive Mutants of the Toxic Zinc Metallopeptidase Asap1 from Aeromonas Salmonicida Subsp. Achromogenes.
Authors: Bogdanovic, X. / Singh, R.K. / Hentschke, J. / Gudmundsdottir, B.K. / Hinrichs, W.
#2: Journal: J.Bacteriol. / Year: 2009
Title: The Asap1 Peptidase of Aeromonas Salmonicida Subsp. Achromogenes is a Highly Conserved Deuterolysin Metalloprotease (Family M35) and a Major Virulence Factor.
Authors: Arnadottir, H. / Hvanndal, I. / Andresdottir, V. / Burr, S.E. / Frey, J. / Gudmundsdottir, B.K.
#3: Journal: Dis.Aquat.Organ. / Year: 1990
Title: Isolation of a New Toxic Protease from a Strain of Aeromonas Salmonicida Subspecies Achromogenes
Authors: Gudmundsdottir, B.K. / Hastingst, S. / Ellis, E.A.
History
DepositionJan 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Oct 12, 2016Group: Database references
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOXIC EXTRACELLULAR ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7677
Polymers37,2861
Non-polymers4816
Water3,621201
1
A: TOXIC EXTRACELLULAR ENDOPEPTIDASE
hetero molecules

A: TOXIC EXTRACELLULAR ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,53314
Polymers74,5712
Non-polymers96212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4600 Å2
ΔGint-192.3 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.958, 72.016, 54.996
Angle α, β, γ (deg.)90.00, 109.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TOXIC EXTRACELLULAR ENDOPEPTIDASE


Mass: 37285.539 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PROPEPTIDE, ASPZINCIN PROTEASE
Source: (gene. exp.) AEROMONAS SALMONICIDA SUBSP. ACHROMOGENES (bacteria)
Strain: KELDUR265-87 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PRI3715 / References: UniProt: Q8GMV9, deuterolysin

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Non-polymers , 5 types, 207 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 294 TO GLN
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: 2.57 Å3/Da / Density % sol: 52.1 % / Description: NONE
Crystal growpH: 8.5 / Details: 1.8 M (NH4)2SO4 0.1 M TRIS/HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97784
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97784 Å / Relative weight: 1
ReflectionResolution: 2→90 Å / Num. obs: 25131 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.61
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.45 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GE6

1ge6


Resolution: 1.99→57.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.231 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21425 1271 5.1 %RANDOM
Rwork0.17191 ---
obs0.17403 23857 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.106 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å21.59 Å2
2--1.22 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.99→57.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 23 201 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222295
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9473129
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80424.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09415349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5431511
X-RAY DIFFRACTIONr_chiral_restr0.1410.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211779
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2011.51431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93622291
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0813864
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5234.5838
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.988→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 61 -
Rwork0.222 1171 -
obs--64.6 %
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)
11.3195-1.3981-0.08931.65550.0630.0146-0.0838-0.01-0.06060.02890.05850.05630.02740.0060.02530.11040.03810.0130.07970.04770.112764.824353.933220.1294
21.4734-0.8135-0.86510.5470.68450.9473-0.2076-0.1821-0.11110.10230.17560.04250.08420.2570.0320.07540.0153-0.00470.0750.00550.060962.351959.965725.6463
33.032-1.4856-0.28672.6327-0.75793.9330.19790.01390.0236-0.0074-0.1135-0.111-0.12880.0742-0.08450.04680.01880.00080.02620.00630.010462.043865.554612.3284
42.0403-0.1013-0.59910.90130.17761.1973-0.04560.05540.0421-0.0870.04370.1151-0.0436-0.0260.00190.0317-0.0003-0.02040.00540.00540.019431.754972.594910.3985
53.98620.2013-0.86432.8562-1.53863.3208-0.12520.2057-0.3012-0.20190.20470.43390.2743-0.5238-0.07950.0534-0.0567-0.04460.09710.01090.130519.156968.10259.1519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 64
2X-RAY DIFFRACTION2A65 - 103
3X-RAY DIFFRACTION3A104 - 155
4X-RAY DIFFRACTION4A175 - 304
5X-RAY DIFFRACTION5A305 - 341

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