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- PDB-1k7q: PrtC from Erwinia chrysanthemi: E189A mutant -

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Basic information

Entry
Database: PDB / ID: 1k7q
TitlePrtC from Erwinia chrysanthemi: E189A mutant
ComponentsSECRETED PROTEASE C
KeywordsHYDROLASE / metalloprotease / protease
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBaumann, U. / Hege, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Protease C of Erwinia chrysanthemi: The Crystal Structure and Role of Amino Acids Y228 and E189
Authors: Hege, T. / Baumann, U.
History
DepositionOct 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_conn.ptnr2_label_seq_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 1.4Feb 7, 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
A: SECRETED PROTEASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9239
Polymers51,5771
Non-polymers3468
Water8,053447
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.396, 102.396, 121.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SECRETED PROTEASE C / PROC


Mass: 51577.211 Da / Num. of mol.: 1 / Mutation: E189A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: prtC / Plasmid: pUC18 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: NaCl, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 M1reservoirNaCl
20.1 M1reservoirNaH2PO4
30.1 M1reservoirKH2PO4
40.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 3, 1998
RadiationMonochromator: Ni Filter, Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→39.18 Å / Num. all: 67901 / Num. obs: 557664 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.7 Å2 / Limit h max: 49 / Limit h min: 0 / Limit k max: 49 / Limit k min: 0 / Limit l max: 67 / Limit l min: 0 / Observed criterion F max: 1960304.07 / Observed criterion F min: 7.2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 25.9
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.27 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Num. obs: 67917 / Num. measured all: 557664 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.91

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.18 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5434 8 %random
Rwork0.197 ---
all0.2 68228 --
obs0.2 67901 99.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 46.1059 Å2 / ksol: 0.390914 e/Å3
Displacement parametersBiso max: 49.55 Å2 / Biso mean: 23.65 Å2 / Biso min: 9.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å21.19 Å20 Å2
2--0.49 Å20 Å2
3----0.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 8 447 3971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg25.6
X-RAY DIFFRACTIONx_torsion_impr_deg0.62
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.860.2934237.60.28351620.0145647558598.9
1.86-1.920.2684518.10.24251200.0135622557199.1
1.92-1.990.23644980.21151480.0115641559799.2
1.99-2.070.2214688.30.19751870.015670565599.7
2.07-2.160.2124307.70.19651780.015626560899.7
2.16-2.270.2114447.80.19652230.015691566799.6
2.27-2.420.234317.60.20152110.0115654564299.8
2.42-2.60.2284818.50.20651970.015686567899.8
2.6-2.860.2144618.10.20252130.015678567499.9
2.86-3.280.2145880.19852520.015721571099.8
3.28-4.130.19845680.17252630.0095773571999.1
4.13-39.180.214828.30.19253130.015953579597.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Rfactor obs: 0.2 / Rfactor Rfree: 0.2183 / Rfactor Rwork: 0.1977
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0042
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.293 / Rfactor Rwork: 0.283

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