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- PDB-2x3a: AsaP1 inactive mutant E294Q, an extracellular toxic zinc metalloe... -

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Basic information

Entry
Database: PDB / ID: 2x3a
TitleAsaP1 inactive mutant E294Q, an extracellular toxic zinc metalloendopeptidase
ComponentsTOXIC EXTRACELLULAR ENDOPEPTIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


metalloendopeptidase activity / 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: 2 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 / 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 / _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

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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)38,0198
Polymers37,2861
Non-polymers7337
Water3,585199
1
A: TOXIC EXTRACELLULAR ENDOPEPTIDASE
hetero molecules

A: TOXIC EXTRACELLULAR ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,03716
Polymers74,5712
Non-polymers1,46614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5480 Å2
ΔGint-152.6 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.249, 74.468, 54.703
Angle α, β, γ (deg.)90.00, 112.35, 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
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, 206 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 294 TO GLN

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2 M MES PH 7.5, 1.6 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.95369
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: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. obs: 24682 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.17
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / % possible all: 86.3

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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 2X3C

2x3c


Resolution: 2→57.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.686 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20461 1258 5.1 %RANDOM
Rwork0.17014 ---
obs0.17203 23411 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å22.82 Å2
2---0.43 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→57.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 40 199 2492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222370
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9593227
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02924.732112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66215362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9871513
X-RAY DIFFRACTIONr_chiral_restr0.1490.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211819
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_it1.1041.51474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85622361
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1953896
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7824.5865
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: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 73 -
Rwork0.272 1632 -
obs--93.07 %
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)
11.32791.2519-0.10281.8945-0.35020.1005-0.0268-0.035-0.04640.04680.0005-0.0871-0.0093-0.02220.02620.0914-0.06120.01820.0671-0.04040.047715.8155.728930.2605
21.74551.1725-0.50030.7913-0.36270.6832-0.08520.1689-0.1559-0.04510.1228-0.10190.0658-0.2285-0.03760.0776-0.0105-0.00430.0790.01010.027118.386662.153224.7162
31.85551.4275-0.53382.06490.81882.48370.067-0.0248-0.04810.0579-0.04730.06860.0377-0.1437-0.01970.0756-0.0125-0.01530.0709-0.00360.063216.646366.461336.0543
41.6017-0.0855-0.09821.07150.08861.1159-0.04070.1333-0.0204-0.0960.03560.1567-0.0861-0.11550.00510.06190.0017-0.02540.03060.00670.026629.85174.97710.5118
58.0463-1.9723-1.65673.2137-1.0712.7786-0.21550.2542-0.7202-0.13870.0530.70150.3279-0.43590.16250.1197-0.0594-0.04590.1348-0.02260.280916.743671.12999.6438
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 - 340

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