[English] 日本語
Yorodumi
- PDB-1i43: CYSTATHIONINE GAMMA-SYNTHASE IN COMPLEX WITH THE INHIBITOR PPCA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i43
TitleCYSTATHIONINE GAMMA-SYNTHASE IN COMPLEX WITH THE INHIBITOR PPCA
ComponentsCYSTATHIONINE GAMMA-SYNTHASE
KeywordsLYASE / PLP-dependent enzyme / homotetramer / inhibitor complex / PPCA
Function / homology
Function and homology information


plant cystathionine gamma-synthase / cystathionine gamma-synthase activity / transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Cystathionine gamma-synthase 1/2 / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Cystathionine gamma-synthase 1/2 / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 3-(PHOSPHONOMETHYL)PYRIDINE-2-CARBOXYLIC ACID / Cystathionine gamma-synthase 1, chloroplastic
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSteegborn, C. / Laber, B. / Messerschmidt, A. / Huber, R. / Clausen, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structures of cystathionine gamma-synthase inhibitor complexes rationalize the increased affinity of a novel inhibitor.
Authors: Steegborn, C. / Laber, B. / Messerschmidt, A. / Huber, R. / Clausen, T.
History
DepositionFeb 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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: CYSTATHIONINE GAMMA-SYNTHASE
B: CYSTATHIONINE GAMMA-SYNTHASE
C: CYSTATHIONINE GAMMA-SYNTHASE
D: CYSTATHIONINE GAMMA-SYNTHASE
E: CYSTATHIONINE GAMMA-SYNTHASE
F: CYSTATHIONINE GAMMA-SYNTHASE
G: CYSTATHIONINE GAMMA-SYNTHASE
H: CYSTATHIONINE GAMMA-SYNTHASE
I: CYSTATHIONINE GAMMA-SYNTHASE
J: CYSTATHIONINE GAMMA-SYNTHASE
K: CYSTATHIONINE GAMMA-SYNTHASE
L: CYSTATHIONINE GAMMA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)582,38736
Polymers576,81612
Non-polymers5,57124
Water00
1
A: CYSTATHIONINE GAMMA-SYNTHASE
B: CYSTATHIONINE GAMMA-SYNTHASE
C: CYSTATHIONINE GAMMA-SYNTHASE
D: CYSTATHIONINE GAMMA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,12912
Polymers192,2724
Non-polymers1,8578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25040 Å2
ΔGint-97 kcal/mol
Surface area46460 Å2
MethodPISA
2
E: CYSTATHIONINE GAMMA-SYNTHASE
F: CYSTATHIONINE GAMMA-SYNTHASE
G: CYSTATHIONINE GAMMA-SYNTHASE
H: CYSTATHIONINE GAMMA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,12912
Polymers192,2724
Non-polymers1,8578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24990 Å2
ΔGint-97 kcal/mol
Surface area46470 Å2
MethodPISA
3
I: CYSTATHIONINE GAMMA-SYNTHASE
J: CYSTATHIONINE GAMMA-SYNTHASE
K: CYSTATHIONINE GAMMA-SYNTHASE
L: CYSTATHIONINE GAMMA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,12912
Polymers192,2724
Non-polymers1,8578
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25000 Å2
ΔGint-96 kcal/mol
Surface area46560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)309.600, 170.100, 162.100
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
CYSTATHIONINE GAMMA-SYNTHASE


Mass: 48067.973 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: METB / Plasmid: PENCN1117 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZPL5, EC: 4.2.99.9
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-PMC / 3-(PHOSPHONOMETHYL)PYRIDINE-2-CARBOXYLIC ACID


Mass: 217.116 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H8NO5P

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: MES, magnesium acetate, PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 291K
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, sitting drop / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMES-NaOH1reservoir
2200 mMmagnesium acetate1reservoir
310 %(w/v)PEG80001reservoir
410 mMTris-HCl1drop
50.010 mMPLP1drop

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12911
22911
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEApr 19, 1999
MARRESEARCH2IMAGE PLATEApr 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 117473 / Num. obs: 117473 / % possible obs: 78 % / Observed criterion σ(I): -100 / Redundancy: 2.1 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 5.9
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.327 / % possible all: 64
Reflection
*PLUS
% possible obs: 78 %
Reflection shell
*PLUS
% possible obs: 64 %

-
Processing

Software
NameClassification
MOLREPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGN

1qgn


Resolution: 3.1→20 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 5930 RANDOM
Rwork0.236 --
all-117473 -
obs-117451 -
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36276 0 348 0 36624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_d1
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.5

+
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