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- PDB-3hb2: PrtC methionine mutants: M226I -

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Basic information

Entry
Database: PDB / ID: 3hb2
TitlePrtC methionine mutants: M226I
ComponentsSecreted protease C
KeywordsHYDROLASE / Met-turn / beta roll / zinc / Calcium / Metal-binding / Metalloprotease / Protease / Secreted / Zymogen
Function / homology
Function and homology information


serralysin / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat ...Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsOberholzer, A.E. / Bumann, M. / Hege, T. / Russo, S. / Baumann, U.
CitationJournal: Biol.Chem. / Year: 2009
Title: Metzincin's canonical methionine is responsible for the structural integrity of the zinc-binding site
Authors: Oberholzer, A.E. / Bumann, M. / Hege, T. / Russo, S. / Baumann, U.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.contact_author ..._diffrn_source.pdbx_synchrotron_site / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.version
Revision 1.5Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Secreted protease C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,10711
Polymers49,6901
Non-polymers41710
Water9,872548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.407, 102.407, 121.035
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11P-536-

HOH

21P-561-

HOH

31P-945-

HOH

41P-947-

HOH

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Components

#1: Protein Secreted protease C / ProC


Mass: 49690.090 Da / Num. of mol.: 1 / Mutation: M226I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Gene: prtC / Plasmid: pUC18 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE
References: UniProt: P16317, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 3.69 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M NaCl, 0.1 M phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2003
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Number: 419581 / Rmerge(I) obs: 0.048 / Χ2: 1.04 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 74403 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.755099.810.0290.9929.1
3.774.7510010.0290.9469.4
3.293.7710010.0370.9849.5
2.993.2910010.0521.0739.6
2.782.9910010.0751.0369.6
2.612.7810010.1061.1439.6
2.482.6110010.0771.3154.6
2.382.4810010.0510.9593.9
2.282.3810010.0611.0013.9
2.22.2810010.0691.0283.9
2.142.210010.0781.0083.9
2.072.1410010.0871.0193.9
2.022.0710010.1091.0543.9
1.972.0210010.1250.9823.9
1.931.9710010.1551.0153.9
1.891.9310010.1920.993.9
1.851.8910010.2461.0053.9
1.811.8510010.2880.9793.9
1.781.8110010.3350.9733.9
1.751.7898.510.3291.2883.8
ReflectionResolution: 1.75→50 Å / Num. all: 74320 / Num. obs: 74320 / % possible obs: 100 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 23
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5 / Rsym value: 0.329 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_48refinement
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→35.769 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9 / SU ML: 0.18 / σ(F): 0 / σ(I): -3 / Phase error: 16.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2183 2.94 %random
Rwork0.154 ---
all0.155 74314 --
obs0.155 74314 99.84 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.495 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 133.19 Å2 / Biso mean: 25.481 Å2 / Biso min: 11.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.216 Å20 Å2-0 Å2
2--0.216 Å2-0 Å2
3----0.432 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 10 548 4078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173603
X-RAY DIFFRACTIONf_angle_d1.5624898
X-RAY DIFFRACTIONf_chiral_restr0.136510
X-RAY DIFFRACTIONf_plane_restr0.008661
X-RAY DIFFRACTIONf_dihedral_angle_d18.2671196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.7870.2081240.1864424454898
1.787-1.8290.2051140.1744844598100
1.829-1.8750.2091360.16944274563100
1.875-1.9250.1761250.15544944619100
1.925-1.9820.1751480.14644454593100
1.982-2.0460.1891270.1445014628100
2.046-2.1190.1921360.13944764612100
2.119-2.2040.161400.13544744614100
2.204-2.3040.1811250.14144884613100
2.304-2.4260.1811200.14745194639100
2.426-2.5780.1751500.1545124662100
2.578-2.7760.1711350.15445274662100
2.776-3.0560.1831450.16345024647100
3.056-3.4970.1751570.14445244681100
3.497-4.4050.1421370.13146054742100
4.405-35.7760.1871640.16847294893100
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)
10.8980.0121-0.33620.5115-0.2660.26040.02190.4020.31260.06790.02420.0609-0.2032-0.2864-0.08420.21690.0706-0.0060.31310.08760.274942.98266.006914.1192
20.42570.3076-0.38170.5089-0.27670.48470.0419-0.08860.02030.0698-0.04570.0104-0.0552-0.01610.00320.1360.00330.01430.1927-0.01420.135439.812146.588547.3226
30.16710.1667-0.34080.5316-0.06370.99430.05890.02390.10830.0362-0.01750.1569-0.0527-0.2739-0.04930.12760.01440.03680.2407-0.00050.195437.778453.870235.9797
40.50110.1447-0.47350.3792-0.22890.5041-0.03650.0785-0.0111-0.03150.03660.05560.015-0.12240.00040.1154-0.0114-0.00790.1864-0.00570.140753.863252.323516.2045
50.67330.06650.08340.396-0.44410.5810.00850.37750.1655-0.18510.0507-0.0023-0.028-0.1309-0.0630.1840.0017-0.01530.24880.0570.180562.330467.1861-2.9511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain P and resid 4:41)P4 - 41
2X-RAY DIFFRACTION2(chain P and resid 42:179)P42 - 179
3X-RAY DIFFRACTION3(chain P and resid 180:264)P180 - 264
4X-RAY DIFFRACTION4(chain P and resid 265:410)P265 - 410
5X-RAY DIFFRACTION5(chain P and resid 411:1481)P411 - 1481

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