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- PDB-5a0r: Product peptide-bound structure of metalloprotease Zmp1 variant E... -

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Basic information

Entry
Database: PDB / ID: 5a0r
TitleProduct peptide-bound structure of metalloprotease Zmp1 variant E143A from Clostridium difficile
Components
  • PRODUCT PEPTIDE
  • ZINC METALLOPROTEASE ZMP1
KeywordsHYDROLASE / METALLOPROTEASE / ZMP1 / 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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.251 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 / 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
D: PRODUCT PEPTIDE
E: PRODUCT PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,31810
Polymers44,8184
Non-polymers4996
Water8,179454
1
A: ZINC METALLOPROTEASE ZMP1
D: PRODUCT PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7516
Polymers22,4092
Non-polymers3424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-42.2 kcal/mol
Surface area9250 Å2
MethodPISA
2
B: ZINC METALLOPROTEASE ZMP1
E: PRODUCT PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5674
Polymers22,4092
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-42 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.060, 42.960, 119.210
Angle α, β, γ (deg.)90.00, 92.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.864, 0.1518, -0.4801), (0.1323, -0.9884, -0.0744), (-0.4858, 0.0008, -0.8741)
Vector: 124.5911, 9.1758, 483.6919)

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Components

#1: Protein ZINC METALLOPROTEASE ZMP1 / 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): STAR
References: UniProt: Q183R7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide PRODUCT PEPTIDE


Mass: 483.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACETYLATION (ACE): ACETYLATION AT THE N-TERMINUS OF PRODUCT PEPTIDE GLYCEROL (GOL): ORIGINATES FROM ...ACETYLATION (ACE): ACETYLATION AT THE N-TERMINUS OF PRODUCT PEPTIDE GLYCEROL (GOL): ORIGINATES FROM CRYO-SOLUTION

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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: 2.37 Å3/Da / Density % sol: 48.14 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7
Details: 1.8 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M TRIS PH 8.5 GROWN 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: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→40.4 Å / Num. obs: 102218 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 12.32 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.82
Reflection shellResolution: 1.25→1.33 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.67 / % possible all: 93.7

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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: 1.251→40.411 Å / SU ML: 0.1 / σ(F): 1.36 / Phase error: 15.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.162 5111 5 %
Rwork0.1415 --
obs0.1425 102215 98.55 %
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: 1.251→40.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 26 454 3560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153237
X-RAY DIFFRACTIONf_angle_d1.4894387
X-RAY DIFFRACTIONf_dihedral_angle_d12.8251191
X-RAY DIFFRACTIONf_chiral_restr0.069476
X-RAY DIFFRACTIONf_plane_restr0.009574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2508-1.2650.26571430.24282726X-RAY DIFFRACTION81
1.265-1.27990.23751650.21793127X-RAY DIFFRACTION97
1.2799-1.29550.21111640.21853131X-RAY DIFFRACTION96
1.2955-1.31190.22011660.20473147X-RAY DIFFRACTION97
1.3119-1.32920.2151680.20213197X-RAY DIFFRACTION98
1.3292-1.34740.18681690.18863203X-RAY DIFFRACTION98
1.3474-1.36670.22061700.18843229X-RAY DIFFRACTION100
1.3667-1.38710.20091730.18453292X-RAY DIFFRACTION99
1.3871-1.40870.19491680.18023194X-RAY DIFFRACTION100
1.4087-1.43180.21271760.17113340X-RAY DIFFRACTION100
1.4318-1.45650.17071690.16713217X-RAY DIFFRACTION100
1.4565-1.4830.17541740.16143289X-RAY DIFFRACTION100
1.483-1.51150.15981680.15453200X-RAY DIFFRACTION100
1.5115-1.54240.16441750.1463317X-RAY DIFFRACTION100
1.5424-1.57590.16941690.14513230X-RAY DIFFRACTION100
1.5759-1.61260.1661740.14163302X-RAY DIFFRACTION100
1.6126-1.65290.15561710.14333238X-RAY DIFFRACTION100
1.6529-1.69760.1591710.14663248X-RAY DIFFRACTION100
1.6976-1.74760.1651710.14823255X-RAY DIFFRACTION100
1.7476-1.8040.18251710.14183250X-RAY DIFFRACTION99
1.804-1.86840.1641730.1413292X-RAY DIFFRACTION99
1.8684-1.94320.15151720.13813258X-RAY DIFFRACTION99
1.9432-2.03170.15391720.13273264X-RAY DIFFRACTION99
2.0317-2.13880.12521710.12673255X-RAY DIFFRACTION99
2.1388-2.27280.131730.12443282X-RAY DIFFRACTION99
2.2728-2.44820.13741730.12523286X-RAY DIFFRACTION100
2.4482-2.69460.16221740.13143313X-RAY DIFFRACTION100
2.6946-3.08440.16471740.13523307X-RAY DIFFRACTION100
3.0844-3.88550.15771730.1263291X-RAY DIFFRACTION99
3.8855-40.43220.15831810.13263424X-RAY DIFFRACTION100
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)
10.9090.430.2733.29481.01641.5215-0.04020.0965-0.0269-0.2440.0196-0.09-0.05360.05080.02110.1176-0.00890.0220.07060.00820.0633-44.064-1.8462242.7659
27.75924.5164-2.49862.6752-1.21942.7351-0.02780.10410.4427-0.05430.15810.3292-0.2427-0.252-0.09980.11610.0326-0.00520.13740.00950.1965-60.30772.3506253.8047
37.05-0.5642.10325.5859-0.30757.0672-0.1787-0.70980.11780.54790.05610.0253-0.196-0.03370.13630.13970.03840.02930.2740.00410.1328-57.8572-4.7919265.9928
41.61960.11440.36061.9472-0.09211.8226-0.0555-0.09540.05050.0254-0.01240.016-0.0773-0.04820.06310.08230.00530.00390.08320.00230.0695-48.6351-4.273255.4074
52.18490.85063.38340.9488-0.04278.30790.0906-0.103-0.083-0.0704-0.0608-0.07870.4092-0.1811-0.05660.15410.00970.02310.0711-0.00170.1045-47.2046-23.7222255.9894
63.51260.5038-1.27162.4097-0.21163.62290.0089-0.1751-0.01320.2094-0.0392-0.0990.0378-0.0330.03690.09150.0054-0.01360.08720.01010.0967-43.9029-14.8621260.7772
73.00751.1280.57944.057-0.60011.2639-0.0596-0.0027-0.3318-0.0464-0.0075-0.50890.170.24350.04320.08620.0340.03840.11480.01790.1882-34.197-17.9199254.4646
82.34442.11990.36315.75971.95782.53640.1158-0.07660.02940.0871-0.1405-0.09830.00670.01390.02670.06780.0218-0.0220.12030.02810.1047-28.9098-18.555293.9321
90.8842-0.1014-0.09093.96722.19082.38630.0292-0.0354-0.01570.0109-0.0442-0.0969-0.02990.08260.01740.0564-0.0011-0.0120.11320.01320.0801-31.5729-12.8923291.533
108.8317-5.0475-1.4777.16731.98962.95380.0686-0.3973-0.38850.17240.11190.22480.2899-0.2635-0.16260.1009-0.0305-0.02290.14250.06230.1923-48.8537-21.3849290.3352
115.8521.02942.32711.79341.5573.50790.03980.2885-0.0858-0.1106-0.01810.2378-0.0956-0.1066-0.01710.10380.0138-0.00170.1120.02070.1273-49.3095-15.2209282.7633
121.41320.33310.91663.53130.31081.91430.0050.1066-0.0513-0.2358-0.0044-0.0397-0.07660.11380.00020.07860.00250.00290.10940.00440.0754-38.2141-11.7572282.2401
132.6793-0.62750.97483.6178-1.06647.9595-0.0620.06390.19080.06340.0260.176-0.4206-0.2171-0.00150.1527-0.0019-0.030.0868-0.00730.1433-42.01016.4708283.9466
143.59650.41091.04781.37580.51512.3046-0.13280.16270.0848-0.2051-0.01810.0374-0.11620.05970.14820.15180.0009-0.00190.120.02080.0999-40.5928-1.9201277.4982
152.3361-1.6886-1.36056.55311.55053.59150.00460.03220.1046-0.32890.1251-0.4195-0.30880.3108-0.12280.1333-0.04020.01240.17030.02420.1403-29.47432.674278.38
165.4882-0.71054.51292.0757-1.02433.81470.2019-0.39750.28420.02570.00270.24770.0699-0.6008-0.18720.15020.00180.01340.2105-0.0080.1743-54.6572-9.0777257.1555
179.06123.8719-1.77619.7523-4.4322.04710.2129-0.1841-0.01470.19670.03220.2292-0.35890.1401-0.23110.3299-0.03810.03610.2837-0.04330.231-47.2121-9.4036285.2446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 29 THROUGH 82 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 83 THROUGH 95 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 96 THROUGH 109 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 110 THROUGH 151 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 152 THROUGH 169 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 170 THROUGH 195 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 196 THROUGH 220 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 30 THROUGH 50 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 51 THROUGH 82 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 83 THROUGH 95 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 96 THROUGH 124 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 125 THROUGH 151 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 152 THROUGH 169 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 170 THROUGH 195 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 196 THROUGH 220 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 2 THROUGH 5 )
17X-RAY DIFFRACTION17CHAIN 'E' AND (RESID 2 THROUGH 5 )

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