[English] 日本語
Yorodumi
- PDB-1ga4: CRYSTAL STRUCTURE ANALYSIS OF PSCP (PSEUDOMONAS SERINE-CARBOXYL P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ga4
TitleCRYSTAL STRUCTURE ANALYSIS OF PSCP (PSEUDOMONAS SERINE-CARBOXYL PROTEINASE) COMPLEXED WITH INHIBITOR PSEUDOIODOTYROSTATIN (THIS ENZYME RENAMED "SEDOLISIN" IN 2003)
Components
  • PSEUDOIODOTYROSTATIN
  • SERINE-CARBOXYL PROTEINASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE-CARBOXYL PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


sedolisin / tripeptidyl-peptidase activity / periplasmic space / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Subtilase family ...Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PSEUDO-IODOTYROSTATIN / Pseudomonalisin
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH 1GA1 / Resolution: 1.4 Å
AuthorsWlodawer, A. / Li, M. / Dauter, Z. / Gustchina, A. / Uchida, K.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes.
Authors: Wlodawer, A. / Li, M. / Dauter, Z. / Gustchina, A. / Uchida, K. / Oyama, H. / Dunn, B.M. / Oda, K.
History
DepositionNov 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Aug 9, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_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: SERINE-CARBOXYL PROTEINASE
I: PSEUDOIODOTYROSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1014
Polymers38,9692
Non-polymers1322
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-19 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.630, 97.630, 83.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

21A-596-

HOH

-
Components

#1: Protein SERINE-CARBOXYL PROTEINASE / PSCP / PSEUDOMONAPEPSIN / PEPSTATIN-INSENSITIVE CARBOXYL PROTEINASE


Mass: 38446.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Plasmid: PUKCP2212 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P42790, EC: 3.4.23.37
#2: Protein/peptide PSEUDOIODOTYROSTATIN


Type: Peptide-like / Class: Inhibitor / Mass: 522.377 Da / Num. of mol.: 1 / Mutation: Y2(PHI) / Source method: obtained synthetically / Details: THE INHIBITOR WAS CHEMICALLY SYNTHESIZED. / References: PSEUDO-IODOTYROSTATIN
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTYROSTATIN IS A NATURAL INHIBITOR, COMPOSED OF ISOVALERYL-TYROSYL-LEUSYL-TYROSINAL. IN 1GA1 AND ...TYROSTATIN IS A NATURAL INHIBITOR, COMPOSED OF ISOVALERYL-TYROSYL-LEUSYL-TYROSINAL. IN 1GA1 AND 1GA4, THE PROTEIN WAS CRYSTALLIZED WITH THE VARIANT OF THIS INHIBITOR, WHERE THE SECOND TYR HAD IODINE INSTEAD OF HYDROXYL, SO IN FACT IT IS P-IODOPHENYLALANINE. IN 1GA6, TYR WAS USED. WHAT THE AUTHORS OBSERVED IN 1GA4, WAS THE TRIPEPTIDE NOT TETRAPEPTIDE, LACKING THE LEU RESIDUE BETWEEN TWO AROMATIC RESIDUES. THIS IS CERTAIN, BUT IT IS NOT CLEAR HOW SUCH A MODIFIED ENTITY ENDED UP IN THE STRUCTURE, AS DISCUSSED IN THE PRIMARY REFERENCE. IN 1GA1 AND 1GA6 ONLY PARTS OF THE INHIBITOR (PARTIALLY OCCUPIED AS WELL) ARE VISIBLE IN THE ELECTRON DENSITY AND ARE MODELED AS A TYROSINE IN 1GA6 AND IODOPHENYLALANINE IN 1GA1 ACCOMPANIED BY JUST MAIN CHAIN PARTS OF ADJOINING RESIDUES, THEREFORE REPRESENTED AS UNK, UNKNOWNS. IN 1GA6 THERE WAS NO DENSITY FOR THE RESIDUE EXPECTED TO BIND TO THE N-TERMINUS OF THE AROMATIC. THE IDENTIFICATION OF IODINE IN 1GA1 WAS CONFIRMED UNEQUIVOCALLY BY ITS ANOMALOUS SCATTERING SIGNAL IN THE ANOMALOUS FOURIER MAP. THEREFORE IN 1GA4 THE AUTHORS CALLED THE MODIFIED INHIBITOR, LACKING LEU IN THE MIDDLE, AS "PSEUDOIODOTYROSTATIN". IN TWO OTHER STRUCTURES THE AUTHORS ARE NOT SURE WHAT IS REALLY THERE, SO THE INHIBITOR IS DESCRIBED AS "FRAGMENTS OF IODOTYROSTATIN" IN 1GA1 AND "FRAGMENTS OF TYROSTATIN" IN 1GA6.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 5% guanidine, 7% glycerol, 5% methanol, 1 M ammoniumm sulfate, 0.1 M sodium citrate buffer pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Msodium chloride1drop
35 mMcalcium chloride1drop
450 mMsodium acetate1drop
51.4 Mlithium sulfate1reservoir
60.1 MTris1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 3, 2000 / Details: focussing mirror
RadiationMonochromator: Si(111) double crystal, sagitally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. all: 88568 / Num. obs: 88568 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8779 / % possible all: 10
Reflection
*PLUS
Num. measured all: 529714
Reflection shell
*PLUS
% possible obs: 99.3 %

-
Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: ISOMORPHOUS WITH 1GA1
Starting model: PDB ENTRY 1GA1

1ga1


Resolution: 1.4→25 Å / Cross valid method: R-FREE / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: Anisotropic refinement of individual atoms. Parameter errors estimated from least-squares blocked full-matrix inversion
RfactorNum. reflection% reflectionSelection details
Rfree0.1554 1305 -RANDOM
Rwork0.1184 ---
all0.1222 88568 --
obs0.103 69896 79 %-
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 7 450 3182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_approx_iso_adps0.098
LS refinement shellResolution: 1.4→25 Å
RfactorNum. reflection% reflection
Rfree0.1554 1305 -
Rwork0.1222 --
obs-88568 79 %

+
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