[English] 日本語
Yorodumi
- PDB-1bjr: COMPLEX FORMED BETWEEN PROTEOLYTICALLY GENERATED LACTOFERRIN FRAG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bjr
TitleCOMPLEX FORMED BETWEEN PROTEOLYTICALLY GENERATED LACTOFERRIN FRAGMENT AND PROTEINASE K
Components
  • LACTOFERRIN
  • PROTEINASE K
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEINASE K / LACTOFERRIN / IRON TRANSPORT / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEngyodontium album (fungus)
Bubalus bubalis (water buffalo)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsSingh, T.P. / Sharma, S. / Karthikeyan, S. / Betzel, C. / Bhatia, K.L.
Citation
Journal: Proteins / Year: 1998
Title: Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K.
Authors: Singh, T.P. / Sharma, S. / Karthikeyan, S. / Betzel, C. / Bhatia, K.L.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Inhibition of Proteinase K by Methoxysuccinyl-Ala-Ala-Pro-Ala-Chloromethyl Ketone. An X-Ray Study at 2.2-A Resolution
Authors: Wolf, W.M. / Bajorath, J. / Muller, A. / Raghunathan, S. / Singh, T.P. / Hinrichs, W. / Saenger, W.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Synchrotron X-Ray Data Collection and Restrained Least-Squares Refinement of the Crystal Structure of Proteinase K at 1.5 A Resolution
Authors: Betzel, C. / Pal, G.P. / Saenger, W.
History
DepositionJun 27, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_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_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: PROTEINASE K
I: LACTOFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8254
Polymers29,7452
Non-polymers802
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.600, 38.581, 79.220
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTEINASE K


Mass: 28930.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / Strain: LIMBER / References: UniProt: P06873, peptidase K
#2: Protein/peptide LACTOFERRIN


Mass: 813.899 Da / Num. of mol.: 1 / Fragment: FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bubalus bubalis (water buffalo)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.19 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 279 K / Method: microdialysis / pH: 6
Details: 60 MG/ML PROTEIN IN 10MM TRIS.HCL, PH 6.0 WAS MICRODIALYZED AGAINST 10% ETHANOL AT 6 DEGREE CELSIUS, microdialysis, temperature 279K
Crystal
*PLUS
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein11
210 %ethanol12

-
Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: PIN HOLE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→12 Å / Num. obs: 9051 / % possible obs: 92.2 % / Observed criterion σ(I): 3 / Redundancy: 2.42 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 22.2
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 9.7 / Rsym value: 0.168 / % possible all: 80.9
Reflection
*PLUS
Num. measured all: 23005

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PRK

3prk


Resolution: 2.44→12 Å / Cross valid method: A POSTERIORI / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 903 10 %RANDOM
Rwork0.16 ---
obs0.167 9044 92.2 %-
all-9044 --
Displacement parametersBiso mean: 19.3 Å2
Refine analyzeLuzzati d res low obs: 12 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.44→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 2 201 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.01
X-RAY DIFFRACTIONp_angle_d0.0210.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0620.02
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9051
X-RAY DIFFRACTIONp_mcangle_it1.5031.5
X-RAY DIFFRACTIONp_scbond_it1.9411.5
X-RAY DIFFRACTIONp_scangle_it2.862
X-RAY DIFFRACTIONp_plane_restr0.024
X-RAY DIFFRACTIONp_chiral_restr0.1640.12
X-RAY DIFFRACTIONp_singtor_nbd0.1960.3
X-RAY DIFFRACTIONp_multtor_nbd0.320.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor95
X-RAY DIFFRACTIONp_staggered_tor20.84615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.9215
X-RAY DIFFRACTIONp_special_tor05
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.167 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.9 Å / Rfactor obs: 0.214

+
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