[English] 日本語
Yorodumi
- PDB-1mcv: Crystal Structure Analysis of a Hybrid Squash Inhibitor in Comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mcv
TitleCrystal Structure Analysis of a Hybrid Squash Inhibitor in Complex with Porcine Pancreatic Elastase
Components
  • Elastase 1
  • HEI-TOE I
KeywordsHYDROLASE / elastase-inhibitor complex / hybrid squash inhibitor
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAy, J. / Hilpert, K. / Krauss, N. / Schneider-Mergener, J. / Hoehne, W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of a hybrid squash inhibitor in complex with porcine pancreatic elastase at 1.8 A resolution.
Authors: Ay, J. / Hilpert, K. / Krauss, N. / Schneider-Mergener, J. / Hohne, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Atomic Resolution Structure of native porcine pancreatic elastase at 1.1 A
Authors: Wurtele, M. / Hahn, M. / Hilpert, K. / Hohne, W.
#2: Journal: Embo J. / Year: 1986
Title: X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third DOMAIN OF the turkey ovomucoid inhibitor
Authors: Bode, W. / Wei, A.Z. / Huber, R. / Meyer, E. / Travis, J. / Neumann, S.
#3: Journal: FEBS Lett. / Year: 1989
Title: THE REFINED 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPSIN AND CMTI-I, A TRYPSIN INHIBITOR FROM SQUASH SEEDS (CUCURBITA MAXIMA). TOPOLOGICAL SIMILARITY ...Title: THE REFINED 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPSIN AND CMTI-I, A TRYPSIN INHIBITOR FROM SQUASH SEEDS (CUCURBITA MAXIMA). TOPOLOGICAL SIMILARITY OF THE SQUASH SEED INHIBITORS WITH THE CARBOXYPEPTIDASE A INHIBITOR FROM POTATOES
Authors: Bode, W. / Greyling, H.J. / Huber, R. / Otlewski, J. / Wilusz, T.
History
DepositionAug 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 400COMPOUND RESIDUE NUMBERING FOR ELASTASE FOLLOWS THE NUMBERING OF BOVINE CHYMOTRYPSINOGEN A.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elastase 1
I: HEI-TOE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0394
Polymers28,9022
Non-polymers1362
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-36 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.330, 56.440, 72.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Elastase 1 /


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Protein/peptide HEI-TOE I / Hybrid squash inhibitor HEI-TOE 1


Mass: 2973.452 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized using solid phase peptide synthesis. It was constructed using the trypsin binding loop of squash inhibitor EETI II, substituted by the sequence of a ...Details: The peptide was chemically synthesized using solid phase peptide synthesis. It was constructed using the trypsin binding loop of squash inhibitor EETI II, substituted by the sequence of a peptide that was derived from the third domain of the turkey ovomucoid inhibitor.
Keywords: trypsin binding loop of squash inhibitor EETI II, substituted by the sequence of a peptide that was derived from the third domain of the turkey ovomucoid inhibitor
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium citrate, ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
Conc.: 0.02 M / Common name: citrate / Details: pH6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9073 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2002
RadiationMonochromator: triangular monochromator, bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9073 Å / Relative weight: 1
ReflectionResolution: 1.8→14 Å / Num. all: 22112 / Num. obs: 21938 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.037 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 1941 / Rsym value: 0.116 / % possible all: 87.8
Reflection
*PLUS
Num. obs: 22112 / Num. measured all: 79096 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 87.8 % / Num. unique obs: 1941 / Rmerge(I) obs: 0.116

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNJ

1qnj


Resolution: 1.8→14 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 1103 RANDOM
Rwork0.182 --
all0.184 21938 -
obs0.184 21938 -
Solvent computationSolvent model: bulk solvent / Bsol: 40.2 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å20 Å2
2---3.1 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 6 353 2457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0046
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d25.56
X-RAY DIFFRACTIONc_improper_angle_d0.676
X-RAY DIFFRACTIONc_mcbond_it0.584
X-RAY DIFFRACTIONc_mcangle_it0.979
X-RAY DIFFRACTIONc_scbond_it0.867
X-RAY DIFFRACTIONc_scangle_it1.322
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.247 100 -
Rwork0.21 --
obs-2138 99 %
Refinement
*PLUS
Lowest resolution: 14 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.56
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.676

+
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