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- PDB-5a0x: Substrate peptide-bound structure of metalloprotease Zmp1 variant... -

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Basic information

Entry
Database: PDB / ID: 5a0x
TitleSubstrate peptide-bound structure of metalloprotease Zmp1 variant E143AY178F from Clostridium difficile
Components
  • SUBSTRATE PEPTIDE
  • ZINC METALLOPROTEASE ZMP1
KeywordsHYDROLASE / METALLOPROTEASE / 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 factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / 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: 1.7 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 23, 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: 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_conn_type / 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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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
C: SUBSTRATE PEPTIDE
D: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5006
Polymers45,3694
Non-polymers1312
Water7,710428
1
A: ZINC METALLOPROTEASE ZMP1
C: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7503
Polymers22,6852
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-8.8 kcal/mol
Surface area11180 Å2
MethodPQS
2
B: ZINC METALLOPROTEASE ZMP1
D: SUBSTRATE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7503
Polymers22,6852
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-8.3 kcal/mol
Surface area10990 Å2
MethodPQS
Unit cell
Length a, b, c (Å)37.435, 42.941, 123.244
Angle α, β, γ (deg.)90.00, 96.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8775, -0.0958, -0.47), (-0.0983, 0.995, -0.0191), (0.4694, 0.0294, -0.8825)
Vector: 104.7987, 8.8916, 522.6555)

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Components

#1: Protein ZINC METALLOPROTEASE ZMP1


Mass: 21909.646 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): STAR
References: UniProt: Q183R7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide SUBSTRATE PEPTIDE


Mass: 774.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) CLOSTRIDIUM DIFFICILE (bacteria)
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAMIDATION (NH2): AMIDATION AT THE C-TERMINUS OF THE SUBSTRATE PEPTIDE ACETYLATION (ACE): ...AMIDATION (NH2): AMIDATION AT THE C-TERMINUS OF THE SUBSTRATE PEPTIDE ACETYLATION (ACE): ACETYLATION T THE N-TERMINUS OF THE SUBSTRATE PEPTIDE

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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: 2.46 Å3/Da / Density % sol: 50.08 % / Description: NONE
Crystal growTemperature: 293 K / pH: 9
Details: 2.25 AMMONIUM PHOSPHATE DIBASIC, 0.1 M TRIS PH 9.0 GROWN AT 293K

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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: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40.9 Å / Num. obs: 43083 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 16.49 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.58
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.78 / % possible all: 87.8

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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: 1.7→40.85 Å / SU ML: 0.18 / σ(F): 1.38 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 2152 5 %
Rwork0.1796 --
obs0.181 43067 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 2 428 3557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063212
X-RAY DIFFRACTIONf_angle_d0.9324352
X-RAY DIFFRACTIONf_dihedral_angle_d11.711178
X-RAY DIFFRACTIONf_chiral_restr0.038475
X-RAY DIFFRACTIONf_plane_restr0.005570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73960.24991410.21342677X-RAY DIFFRACTION100
1.7396-1.78310.26411430.2112735X-RAY DIFFRACTION99
1.7831-1.83130.23361420.20692686X-RAY DIFFRACTION100
1.8313-1.88520.21451430.20862722X-RAY DIFFRACTION100
1.8852-1.9460.21191420.20222721X-RAY DIFFRACTION100
1.946-2.01560.25341420.20262686X-RAY DIFFRACTION100
2.0156-2.09630.25421430.19112724X-RAY DIFFRACTION99
2.0963-2.19160.2021440.18432737X-RAY DIFFRACTION100
2.1916-2.30720.22221410.1732681X-RAY DIFFRACTION100
2.3072-2.45170.21251450.17822749X-RAY DIFFRACTION100
2.4517-2.6410.19981430.17852722X-RAY DIFFRACTION100
2.641-2.90670.21440.18382728X-RAY DIFFRACTION99
2.9067-3.32710.20541450.18532755X-RAY DIFFRACTION100
3.3271-4.19120.20721440.15972760X-RAY DIFFRACTION99
4.1912-40.86150.16721500.15812832X-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)
17.694-1.2576-2.08687.96280.73666.80360.06360.42010.3213-0.4641-0.0379-0.75980.13250.2785-0.09140.2366-0.00620.06320.1663-0.00460.163-16.1066-1.2653244.5886
21.2896-0.6828-0.35214.75170.41191.86510.01880.16050.1051-0.0503-0.0355-0.1416-0.13350.07580.00040.1335-0.01320.02940.13320.01930.0845-22.55097.9821253.4372
31.13051.02790.53493.19232.02813.77350.14920.0884-0.0846-0.425-0.142-0.08610.1735-0.12820.02720.1737-0.01110.01710.13430.01010.1051-26.5716-4.9608248.9928
46.32394.0418-2.13837.6322-1.21433.21550.02180.22710.1661-0.09050.21760.1662-0.3315-0.1448-0.11870.09240.02190.0040.14070.02270.179-39.22785.5288260.6143
54.0651-1.27850.18271.48950.75193.72-0.0585-0.12910.12290.29780.09770.1394-0.1259-0.052700.1482-0.01510.03970.17810.01640.1129-36.5731-1.0706272.91
61.4798-0.0943-0.18842.43220.25431.56420.0534-0.1140.0540.0543-0.0546-0.0011-0.04250.0314-0.01730.0797-0.00420.00830.09010.01080.0799-27.4779-0.6901262.6846
72.26780.81241.24351.8597-0.45465.25790.1741-0.0731-0.19280.2875-0.0459-0.00330.5103-0.0693-0.15990.2162-0.01990.00330.0884-0.01150.1267-26.2357-20.5394262.9014
85.1251-0.98852.79942.25750.44552.4165-0.1217-0.0778-0.00230.37680.0901-0.1018-0.02830.03860.03840.2507-0.0146-0.0210.14790.0150.0895-24.8214-12.5136273.7324
92.76820.6933-0.38012.0539-0.29021.6305-0.0362-0.0182-0.05820.0555-0.0028-0.33280.35930.21220.02080.13950.0347-0.00810.09710.00670.1317-16.1894-13.2564262.4751
102.1940.11190.27772.5013-0.03623.47120.01230.00590.01320.0421-0.00370.1499-0.3894-0.1253-0.00350.09990.02220.01720.11330.00620.1208-16.93170.1058299.2455
111.26130.0442-0.47853.4192-2.51783.37510.1684-0.276-0.10450.2369-0.20190.06510.1950.09850.03350.08960.00210.0140.12030.02350.099-11.6861-9.347303.5696
128.2536-5.25591.00637.1313-1.79942.73870.1264-0.21470.25860.2417-0.0091-0.1053-0.30430.4233-0.12950.1678-0.06260.01670.1668-0.02630.13683.49333.0237299.0087
132.09140.3251-0.21131.5753-0.16051.05410.02460.09280.0365-0.0921-0.0061-0.0523-0.00080.1467-0.01030.13270.00250.01870.13450.00070.096-1.7759-4.3658290.8847
142.4517-0.2506-0.22360.9061-0.63861.51630.10470.091-0.2377-0.1225-0.0766-0.04070.03190.0874-0.02360.22480.0082-0.00960.1098-0.00930.1398-4.9775-19.2387287.665
153.0671-2.4023-0.41623.53932.71774.47570.14620.2507-0.0288-0.4286-0.3430.2496-0.1224-0.23730.07830.2661-0.0087-0.04380.1449-0.00370.126-18.0527-15.0768281.6547
163.29220.3292-0.88332.9949-0.81029.00950.0743-0.1239-0.32080.1956-0.09070.08980.2666-0.24130.0240.2737-0.0275-0.05490.11090.01290.1689-15.2237-23.8152289.5464
176.15940.90194.82132.76490.45665.6558-0.05820.194-0.28060.22420.22520.1523-0.3269-0.1382-0.08430.10720.02110.03390.1410.01270.1315-30.5829-4.4109267.3745
184.6568-1.02533.03733.9474-5.24757.64440.0764-0.0366-0.0397-0.21820.1024-0.15680.09850.2817-0.06780.27920.03290.06690.1156-0.00570.130.3257-7.8124289.2475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 27 THROUGH 40 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 41 THROUGH 63 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 64 THROUGH 82 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 83 THROUGH 95 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 96 THROUGH 109 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 110 THROUGH 151 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 152 THROUGH 169 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 170 THROUGH 182 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 183 THROUGH 220 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 30 THROUGH 63 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 64 THROUGH 82 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 83 THROUGH 95 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 96 THROUGH 151 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 152 THROUGH 195 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 196 THROUGH 207 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 208 THROUGH 220 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 2 THROUGH 8 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 2 THROUGH 8 )

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