[English] 日本語
Yorodumi
- PDB-1k7g: PrtC from Erwinia chrysanthemi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k7g
TitlePrtC from Erwinia chrysanthemi
Componentssecreted protease C
KeywordsHYDROLASE / protease / metalloprotease
Function / homology
Function and homology information


serralysin / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / 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 M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / 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
PHOSPHATE ION / Serralysin C
Similarity search - Component
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHege, T. / Baumann, U.
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 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: secreted protease C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,07610
Polymers51,6351
Non-polymers4419
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.892, 101.892, 122.009
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein secreted protease C / PROC


Mass: 51635.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: prtC / Plasmid: pUC18 / 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.26 %
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

-
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: Mar 1, 1999 / Details: Yale mirrors
RadiationMonochromator: yale mirrors, Ni/filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→39.1 Å / Num. all: 49161 / Num. obs: 292821 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17 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: 2168733.99 / Observed criterion F min: 15.7 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. obs: 49161 / Num. measured all: 292821 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 3.01

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KAP

1kap


Resolution: 2→40 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3917 8 %random
Rwork0.195 ---
all0.199 49962 --
obs0.199 49123 98.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 45.524 Å2 / ksol: 0.404771 e/Å3
Displacement parametersBiso max: 82.96 Å2 / Biso mean: 24.68 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å21.82 Å20 Å2
2--1.69 Å20 Å2
3----3.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 13 386 3870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONx_torsion_deg25.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.59
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 (%)
2-2.060.24428180.23632300.0154101351185.6
2.06-2.130.2493187.70.21738260.0144155414499.7
2.13-2.20.2263207.80.20737600.0134090408099.8
2.2-2.290.223117.60.20338000.0124120411199.8
2.29-2.390.2333157.60.20838200.0134146413599.7
2.39-2.520.2313508.50.20537890.01241404139100
2.52-2.680.2243498.40.20437850.0124145413499.7
2.68-2.880.2283297.90.19938110.01341404140100
2.88-3.170.223237.70.20138620.0124189418599.9
3.17-3.630.1983618.60.17838160.014182417799.9
3.63-4.580.1863137.50.16438650.0114223417898.9
4.58-39.10.2083478.30.20538420.0114384418995.6
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
Lowest resolution: 40 Å / Rfactor obs: 0.199 / Rfactor Rfree: 0.2146 / Rfactor Rwork: 0.1949
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0045
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.25
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / Rfactor Rwork: 0.236

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more