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- PDB-1i43: CYSTATHIONINE GAMMA-SYNTHASE IN COMPLEX WITH THE INHIBITOR PPCA -

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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


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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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 %

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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

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