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- PDB-1qgn: CYSTATHIONINE GAMMA-SYNTHASE FROM NICOTIANA TABACUM -

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Basic information

Entry
Database: PDB / ID: 1qgn
TitleCYSTATHIONINE GAMMA-SYNTHASE FROM NICOTIANA TABACUM
ComponentsPROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
KeywordsLYASE / METHIONINE BIOSYNTHESIS / PYRIDOXAL 5'-PHOSPHATE / GAMMA-FAMILY
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 / Pyridoxal phosphate-dependent transferase, major 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 / Cystathionine gamma-synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSteegborn, C. / Messerschmidt, A. / Laber, B. / Streber, W. / Huber, R. / Clausen, T.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.
Authors: Steegborn, C. / Messerschmidt, A. / Laber, B. / Streber, W. / Huber, R. / Clausen, T.
History
DepositionMay 2, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Aug 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_source.pdbx_wavelength_list
Revision 1.4Aug 16, 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_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
B: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
C: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
D: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
E: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
F: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
G: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
H: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,52116
Polymers384,5448
Non-polymers1,9778
Water5,873326
1
A: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
B: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
C: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
D: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,2608
Polymers192,2724
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22550 Å2
ΔGint-129 kcal/mol
Surface area47770 Å2
MethodPISA
2
E: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
F: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
G: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
H: PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,2608
Polymers192,2724
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22610 Å2
ΔGint-128 kcal/mol
Surface area47630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.000, 129.500, 309.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.638161, -0.753666, -0.157282), (-0.753206, -0.653469, 0.075223), (-0.159472, 0.070462, -0.984685)23.9315, 39.8878, 58.5169
2given(-0.64551, 0.763684, 0.01022), (0.763658, 0.645163, 0.024293), (0.011958, 0.023486, -0.999653)54.6107, -26.1385, 52.9122
3given(-0.989182, -0.014049, 0.146021), (3.8E-5, -0.995428, -0.095511), (0.146695, -0.094473, 0.98466)70.2576, 19.1497, -4.3414
4given(-0.06148, -0.997951, 0.017701), (0.997999, -0.061726, -0.013689), (0.014754, 0.016824, 0.99975)33.9057, -31.8787, 77.0395
5given(-0.794814, -0.591162, -0.137108), (-0.602937, 0.794892, 0.067924), (0.068832, 0.136654, -0.988225)57.571, 40.7738, -25.2196
6given(0.802258, 0.596946, -0.006203), (0.596828, -0.801779, 0.030775), (0.013397, -0.028391, -0.999507)9.4804, -18.8983, -24.6871
7given(0.054148, 0.990222, 0.128562), (-0.99413, 0.065538, -0.086086), (-0.09367, -0.123146, 0.987958)48.3061, 43.4776, 79.7609

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Components

#1: Protein
PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)


Mass: 48067.973 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: ALDIMINE LINKAGE BETWEEN PYRIDOXAL 5'-PHOSPHATE C4A AND LYS261 NZ
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: METB / Organelle: CHLOROPLAST / Plasmid: PET23C(+) / 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.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61 %
Crystal growpH: 6.5
Details: 100 MM MES/NAOH, PH6.5, 200 MM MGAC2, 12 % (W/V) PEG8000
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMMES-NaOH1reservoir
2200 mM1reservoirMgAc2
312 %(w/v)PEG80001reservoir
410 mMTris-HCl1drop
50.010 mMPLP1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→8 Å / Num. obs: 95418 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 6.9
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / % possible all: 86
Reflection
*PLUS
% possible obs: 88.2 % / Num. measured all: 473805
Reflection shell
*PLUS
% possible obs: 86.4 % / Rmerge(I) obs: 0.554

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CS1

1cs1


Resolution: 2.9→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.25 -5 %
Rwork0.201 --
obs-95418 88.2 %
Displacement parametersBiso mean: 33 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24256 0 120 326 24702
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PARAM19.SOL / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.201 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

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