[English] 日本語
Yorodumi
- PDB-1e36: PORCINE PANCREATIC ELASTASE COMPLEXED WITH (3S, 4S)N-PARA-NITROBE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1.0E+36
TitlePORCINE PANCREATIC ELASTASE COMPLEXED WITH (3S, 4S)N-PARA-NITROBENZENESULPHONYL -3-ETHYL-4-(CARBOXYLIC ACID)PYRROLIDIN-2-ONE
ComponentsELASTASE
KeywordsHYDROLASE(SERINE PROTEASE) / SERINE PROTEASE / HYDROLASE / SERINE PROTEINASE
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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Chem-TPY / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWright, P.A. / Wilmouth, R.C. / Clifton, I.J. / Schofield, C.J.
Citation
Journal: Biochem.J. / Year: 2000
Title: 'Ph-Jump' Crystallographic Analyses of Gamma-Lactam-Porcine Pancreatic Elastase Complexes
Authors: Wright, P.A. / Wilmouth, R.C. / Clifton, I.J. / Schofield, C.J.
#1: Journal: Biochemistry / Year: 1999
Title: Mechanistic Insights Into the Inhibition of Serine Proteases by Monocyclic Lactams
Authors: Wilmouth, R.C. / Kassamally, S. / Westwood, N.J. / Sheppard, R.J. / Claridge, T.D.W. / Aplin, R.T. / Wright, P.A. / Pritchard, G.J. / Schofield, C.J.
#2: Journal: Biochemistry / Year: 1998
Title: Inhibition of Elastase by N-Sulfonylaryl Beta-Lactams: Anatomy of a Stable Acyl-Enzyme Complex
Authors: Wilmouth, R.C. / Westwood, N.J. / Anderson, K. / Brownlee, W. / Claridge, T.D.W. / Clifton, I.J. / Pritchard, G.J. / Aplin, R.T. / Schofield, C.J.
#3: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a Specific Acyl-Enzyme Complex Formed between Beta-Casomorphin-7 and Porcine Pancreatic Elastase
Authors: Wilmouth, R.C. / Clifton, I.J. / Robinson, C.V. / Roach, P.L. / Aplin, R.T. / Westwood, N.J. / Hajdu, J. / Schofield, C.J.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65 A Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
History
DepositionJun 6, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 6, 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_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_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.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_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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4094
Polymers25,9281
Non-polymers4803
Water3,351186
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.170, 57.560, 74.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ELASTASE / PPE (PORCINE PANCREATIC ELASTASE)


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TPY / (2S,3S)-3-FORMYL-2-({[(4-NITROPHENYL)SULFONYL]AMINO}METHYL)PENTANOIC ACID


Mass: 344.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O7S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE USED FOR THIS STRUCTURE IS THE SAME AS THAT OF NATIVE PORCINE PANCREATIC ELASTASE (3EST).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 30.1 %
Crystal growpH: 5
Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE, PH 5.0; THEN SOAKED IN 25 MM SODIUM SULPHATE, 50MM SODIUM ACETATE, 20 MG/ML GAMMA-LACTAM, 10% (V/V) DMSO, PH 5.0 FOR 24 HOURS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
250 mMsodium acetate11
325 mMsodium sulfate11
425 mg/mlPPE11
510 %(v/v)DMSO11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: YALE-TYPE MIRRORS
RadiationMonochromator: NICKEL FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→18.3 Å / Num. obs: 24440 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 5.74 / % possible all: 95.4
Reflection
*PLUS
Num. measured all: 188087
Reflection shell
*PLUS
% possible obs: 95.4 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EST

3est


Resolution: 1.7→18.3 Å / SU B: 2.02 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114 / Details: SHELX ALSO USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1011 4 %RANDOM
Rwork0.183 ---
obs-24440 98.5 %-
Displacement parametersBiso mean: 18.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.169 Å20.368 Å20 Å2
2--0 Å2-0.533 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 29 186 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2522
X-RAY DIFFRACTIONp_mcangle_it1.76983
X-RAY DIFFRACTIONp_scbond_it1.7052
X-RAY DIFFRACTIONp_scangle_it2.6163
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1210.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2470.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1290.3
X-RAY DIFFRACTIONp_planar_tor3.67
X-RAY DIFFRACTIONp_staggered_tor13.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.720
X-RAY DIFFRACTIONp_special_tor015

+
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