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- PDB-4mmo: The crystal structure of a M20 family metallo-carboxypeptidase Ss... -

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Basic information

Entry
Database: PDB / ID: 4mmo
TitleThe crystal structure of a M20 family metallo-carboxypeptidase Sso-CP2 from Sulfolobus solfataricus
ComponentsSso-CP2 metallo-carboxypetidase
KeywordsHYDROLASE / M20 family peptidase / metallo protein / protease / metalloprotease / metal-binding hydrolase / carboxypeptidase
Function / homology
Function and homology information


peptidase activity / proteolysis / metal ion binding
Similarity search - Function
: / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich ...: / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Deacetylase, putative
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3363 Å
AuthorsDupuy, J. / Dutoit, R. / Durisotti, V. / Demarez, M. / Borel, F. / Van Elder, D. / Legrain, C. / Bauvois, C.
Citation
Journal: To be Published
Title: Biochemical characterization of a novel thermostable dinuclear carboxypeptidase from the thermoacidophilic archaeum Sulfolobus solfataricus.
Authors: Bauvois, C. / Demarez, M. / Durisotti, V. / Roovers, M. / Dutoit, R. / Gigot, D. / Dupuy, J. / Wattiez, R. / Legrain, C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The complete genome of the crenarchaeon Sulfolobus solfataricus P2.
Authors: She, Q. / Singh, R.K. / Confalonieri, F. / Zivanovic, Y. / Allard, G. / Awayez, M.J. / Chan-Weiher, C.C. / Clausen, I.G. / Curtis, B.A. / De Moors, A. / Erauso, G. / Fletcher, C. / Gordon, P. ...Authors: She, Q. / Singh, R.K. / Confalonieri, F. / Zivanovic, Y. / Allard, G. / Awayez, M.J. / Chan-Weiher, C.C. / Clausen, I.G. / Curtis, B.A. / De Moors, A. / Erauso, G. / Fletcher, C. / Gordon, P.M. / Heikamp-de Jong, I. / Jeffries, A.C. / Kozera, C.J. / Medina, N. / Peng, X. / Thi-Ngoc, H.P. / Redder, P. / Schenk, M.E. / Theriault, C. / Tolstrup, N. / Charlebois, R.L. / Doolittle, W.F. / Duguet, M. / Gaasterland, T. / Garrett, R.A. / Ragan, M.A. / Sensen, C.W. / Van der Oost, J.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Sep 20, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sso-CP2 metallo-carboxypetidase
B: Sso-CP2 metallo-carboxypetidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6929
Polymers98,0542
Non-polymers6387
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-161 kcal/mol
Surface area33620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.070, 89.370, 161.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sso-CP2 metallo-carboxypetidase


Mass: 49027.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO2737 / Plasmid: pET-30b(SSO2737) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q97V97
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: SsoCP2 (120 uM) was mixed 2:2 with well buffer (100 mM acetate HCl pH 4.3 with 12% PEG 8000,(NH4)2SO4 500 mM and 20 % glycerol) with 500 uL well buffer., VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979798 Å / Relative weight: 1
ReflectionResolution: 2.336→50 Å / Num. all: 53510 / Num. obs: 53076 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 46.91 Å2 / Rmerge(I) obs: 0.06374 / Net I/σ(I): 22.33
Reflection shellResolution: 2.336→2.42 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.7355 / Mean I/σ(I) obs: 3.04 / Num. unique all: 3877 / % possible all: 96.4

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Processing

Software
NameVersionClassification
MAR345data collection
BALBESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DLJ

3dlj


Resolution: 2.3363→46.097 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 27.25 / Stereochemistry target values: ML
Details: DUE TO INCOMPLETE ELECTRON DENSITY, SEVERAL LOOPS (FORMED BY RESIDUES 1-7, 18-19, 73-86, 92-102, 135-139, 369 and 400-414) OF THE MONOMER B CATALYTIC DOMAIN ARE MISSING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 2651 5 %RANDOM
Rwork0.206 ---
obs0.2084 53035 99.13 %-
all-53076 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3363→46.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6254 0 32 318 6604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046409
X-RAY DIFFRACTIONf_angle_d0.8368691
X-RAY DIFFRACTIONf_dihedral_angle_d12.2252340
X-RAY DIFFRACTIONf_chiral_restr0.0451002
X-RAY DIFFRACTIONf_plane_restr0.0031099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3363-2.37880.2861280.24712423X-RAY DIFFRACTION93
2.3788-2.42450.31521390.25332651X-RAY DIFFRACTION100
2.4245-2.4740.34431380.25042626X-RAY DIFFRACTION100
2.474-2.52780.3281380.25042625X-RAY DIFFRACTION100
2.5278-2.58660.3211370.23552623X-RAY DIFFRACTION100
2.5866-2.65130.27481390.23372636X-RAY DIFFRACTION100
2.6513-2.7230.27491380.22312634X-RAY DIFFRACTION100
2.723-2.80310.26111400.2232660X-RAY DIFFRACTION100
2.8031-2.89350.26741400.22882646X-RAY DIFFRACTION100
2.8935-2.99690.30021390.21972659X-RAY DIFFRACTION100
2.9969-3.11690.28911400.22922653X-RAY DIFFRACTION100
3.1169-3.25870.28771400.21422657X-RAY DIFFRACTION100
3.2587-3.43050.2541410.20852684X-RAY DIFFRACTION100
3.4305-3.64530.25261410.19522665X-RAY DIFFRACTION100
3.6453-3.92660.21191410.192691X-RAY DIFFRACTION100
3.9266-4.32150.20631420.17242690X-RAY DIFFRACTION100
4.3215-4.94620.19071430.16552716X-RAY DIFFRACTION100
4.9462-6.22930.26721440.20422745X-RAY DIFFRACTION100
6.2293-46.10570.27041430.22782700X-RAY DIFFRACTION94
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)
10.72010.1906-0.4490.4956-0.1755-0.12820.03740.10850.0288-0.0363-0.0467-0.0938-0.09660.1455-00.1208-0.0257-0.01520.3366-0.05820.117-8.915226.09670.2602
20.1623-0.1950.38650.2384-0.30860.7817-0.05360.0754-0.01420.0992-0.0075-0.0279-0.0233-0.085400.237-0.0265-0.02140.1693-0.01220.2145-11.940119.258225.578
30.19170.4159-0.22680.2418-0.75050.0632-0.0323-0.0539-0.20670.00650.04660.13530.0374-0.099800.18320.0072-0.04180.3559-0.07810.2176-19.367919.12392.1403
40.00530.01130.02320.00440.0023-0.0389-0.4796-0.0396-0.0285-0.2827-0.24690.01320.03870.233800.80260.14350.33311.08590.0770.681645.952-1.954234.2443
50.07480.0020.0018-0.00170.0117-0.015-0.1454-0.0084-0.1341-0.2703-0.0087-0.34480.07470.142100.6344-0.02650.06620.47860.06730.631642.0667-5.825243.3745
60.04020.0279-0.09390.09390.03730.0872-0.03830.35180.00250.2262-0.20460.25840.04470.360800.56070.0003-0.07970.81210.04691.071141.2214-7.356748.9356
70.2335-0.3861-0.00190.1091-0.1099-0.0949-0.08490.01470.12950.0180.0178-0.066-0.05070.012900.3171-0.0174-0.06510.14170.03370.28378.87647.948540.7884
80.13540.11360.16820.07470.12490.2192-0.1867-0.08890.18090.12360.01690.05590.01240.0224-00.2884-0.0743-0.12620.19630.0630.313920.149115.20557.9263
90.21410.0720.0054-0.08060.0181-0.0389-0.1550.11330.42350.078-0.20930.05770.27480.192300.2402-0.0258-0.11660.22110.09880.25865.4212.673532.6971
100.1813-0.1287-0.12550.16430.02030.3932-0.06910.0863-0.04830.02520.0026-0.03930.03280.029900.3290.0154-0.06430.18230.05170.32112.0195-0.717347.2174
11-0.04420.05310.03870.0168-0.05780.01240.48830.17530.4677-0.4131.1235-0.3723-0.0226-0.635700.23190.02010.0477-0.0016-0.54950.846537.20167.936658.8363
120.00980.03080.0734-0.0287-0.1057-0.04720.0721-0.17490.10390.21560.3375-0.24460.48760.4001-00.50140.0281-0.08830.47660.01180.522131.8678-3.52152.8371
13-0.0277-0.0242-0.0509-0.0327-0.0488-0.03210.8807-0.02030.0188-0.09120.6914-0.40250.2429-0.000900.4802-0.1166-0.25320.5093-0.03820.815248.00474.669755.5822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 388 )
3X-RAY DIFFRACTION3chain 'A' and (resid 389 through 437 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 39 )
5X-RAY DIFFRACTION5chain 'B' and (resid 40 through 107 )
6X-RAY DIFFRACTION6chain 'B' and (resid 108 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 227 )
8X-RAY DIFFRACTION8chain 'B' and (resid 228 through 278 )
9X-RAY DIFFRACTION9chain 'B' and (resid 279 through 302 )
10X-RAY DIFFRACTION10chain 'B' and (resid 303 through 353 )
11X-RAY DIFFRACTION11chain 'B' and (resid 354 through 381 )
12X-RAY DIFFRACTION12chain 'B' and (resid 382 through 416 )
13X-RAY DIFFRACTION13chain 'B' and (resid 417 through 437 )

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