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- PDB-5a0s: Apo-structure of metalloprotease Zmp1 variant E143A from Clostrid... -

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Basic information

Entry
Database: PDB / ID: 5a0s
TitleApo-structure of metalloprotease Zmp1 variant E143A from Clostridium difficile
ComponentsZINC METALLOPROTEASE ZMP1
KeywordsHYDROLASE / METALLOPROTEASE / ZMP1 / CLOSTRIDIUM DIFFICILE / PROLINE SPECIFICITY
Function / homology
Function and homology information


Pro-Pro endopeptidase / metallopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Anthrax toxin, lethal/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
Pro-Pro endopeptidase
Similarity search - Component
Biological speciesCLOSTRIDIUM DIFFICILE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsSchacherl, M. / Pichlo, C. / Neundorf, I. / Baumann, U.
CitationJournal: Structure / Year: 2015
Title: Structural Basis of Proline-Proline Peptide Bond Specificity of the Metalloprotease Zmp1 Implicated in Motility of Clostridium Difficile.
Authors: Schacherl, M. / Pichlo, C. / Neundorf, I. / Baumann, U.
History
DepositionApr 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ZINC METALLOPROTEASE ZMP1
B: ZINC METALLOPROTEASE ZMP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9824
Polymers43,8512
Non-polymers1312
Water1,928107
1
A: ZINC METALLOPROTEASE ZMP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9912
Polymers21,9261
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ZINC METALLOPROTEASE ZMP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9912
Polymers21,9261
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.500, 72.390, 118.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.0074, 0.0013), (-0.0075, 0.9994, 0.0324), (-0.0011, -0.0324, 0.9995)
Vector: -0.0004, 35.1901, -2.3689)

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Components

#1: Protein ZINC METALLOPROTEASE ZMP1


Mass: 21925.646 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: WITHOUT SIGNAL PEPTIDE (MISSING AA 1-26), CLEAVED N-TERMINAL HIS-TAG WITH THROMBIN, RESULTING GSH- OVERHANG
Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: 630 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q183R7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.12 Å3/Da / Density % sol: 42.15 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7 / Details: 2.1 M D/L-MALIC ACID, PH 7.0 AT 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→45.9 Å / Num. obs: 12587 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 28.18 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.74
Reflection shellResolution: 2.56→2.71 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.42 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERinphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A0P

5a0p


Resolution: 2.56→45.857 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 629 5 %
Rwork0.1995 --
obs0.2025 12554 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 2.56→45.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 2 107 3163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053114
X-RAY DIFFRACTIONf_angle_d0.6294208
X-RAY DIFFRACTIONf_dihedral_angle_d12.5581138
X-RAY DIFFRACTIONf_chiral_restr0.034460
X-RAY DIFFRACTIONf_plane_restr0.002546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.81760.34141530.26482916X-RAY DIFFRACTION100
2.8176-3.22520.30181550.23432931X-RAY DIFFRACTION99
3.2252-4.06310.23321570.18242974X-RAY DIFFRACTION100
4.0631-45.86450.22481640.16913104X-RAY DIFFRACTION99
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)
12.92990.14930.74411.17780.24951.4798-0.13620.4175-0.2584-0.12630.1912-0.0490.21160.0814-0.02520.23420.01130.01640.3345-0.04860.18446.020269.38973.9513
23.7939-0.76521.58753.3779-1.00080.9312-0.1061-0.12620.5950.1008-0.0808-0.1552-0.11990.06710.15730.4203-0.0585-0.07240.21950.01690.282910.063591.121313.4495
31.541-0.0647-0.2520.5453-0.17371.573-0.02870.05940.04650.05380.04480.1094-0.0068-0.0589-0.03870.2082-0.0187-0.00290.12730.00120.2079-4.685176.523516.1668
42.66990.11310.21411.6409-0.47773.3706-0.14080.2875-0.3924-0.12730.16150.0162-0.11850.0061-0.02950.19890.0294-0.01460.3099-0.04530.25288.666731.6138.7006
52.1811.12020.38061.54680.62220.2888-0.15710.43470.1217-0.11940.2895-0.1168-0.10810.032-0.09960.2465-0.015-0.05110.25750.05570.2225.126147.938112.0809
61.3796-0.46520.18190.91420.13011.44040.01530.0318-0.0190.09130.02060.06820.0515-0.0007-0.03290.2057-0.0379-0.0190.1830.01340.2009-4.937440.731219.8612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 26 THROUGH 82 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 83 THROUGH 109 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 110 THROUGH 220 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 26 THROUGH 63 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 64 THROUGH 109 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 110 THROUGH 220 )

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