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- PDB-1cs1: CYSTATHIONINE GAMMA-SYNTHASE (CGS) FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1cs1
TitleCYSTATHIONINE GAMMA-SYNTHASE (CGS) FROM ESCHERICHIA COLI
ComponentsPROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
KeywordsLYASE / LLP-DEPENDENT ENZYMES / METHIONINE BIOSYNTHESIS
Function / homology
Function and homology information


cystathionine gamma-synthase / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
O-succinylhomoserine (thiol)-lyase / : / 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 ...O-succinylhomoserine (thiol)-lyase / : / 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
2,4-DIOXO-PENTANEDIOIC ACID / Cystathionine gamma-synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsClausen, T. / Messerschmidt, A.
Citation
Journal: EMBO J. / Year: 1998
Title: Crystal structure of Escherichia coli cystathionine gamma-synthase at 1.5 A resolution.
Authors: Clausen, T. / Huber, R. / Prade, L. / Wahl, M.C. / Messerschmidt, A.
#1: Journal: FEBS Lett. / Year: 1997
Title: Cloning, Purification, Crystallization and Preliminary Xray-Diffraction Analysis of Cystathionine Gamma-Synthase from Escherichia Coli
Authors: Wahl, M.C. / Huber, R. / Prade, L. / Marinkovic, S. / Messerschmidt, A. / Clausen, T.
History
DepositionSep 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,4625
Polymers167,3024
Non-polymers1601
Water23,4381301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20600 Å2
ΔGint-96 kcal/mol
Surface area45050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.040, 61.300, 153.840
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-1501-

DHD

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Components

#1: Protein
PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE) / E.C.4.2.99.9 LYASE / CGS


Mass: 41825.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PLP BOUND AS COFACTOR TO LYS 198 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 / Gene: METB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P00935, EC: 4.2.99.9
#2: Chemical ChemComp-DHD / 2,4-DIOXO-PENTANEDIOIC ACID


Mass: 160.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1301 / 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: 2.3 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.45 / Details: 17% PEG400, 10% MPD, 0.1 M MES/NAOH (PH 7.45)
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop / Details: Wahl, M.C., (1997) FEBS Lett., 414, 492.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
233 mMHEPES-NaOH1drop
36.7 %(w/v)PEG40001drop
43.3 %(v/v)2-propanol1drop
5100 mMHEPES-NaOH1reservoir
620 %(w/v)PEG40001reservoir
710 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→8 Å / Num. obs: 200884 / % possible obs: 86.9 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.058 / Net I/σ(I): 23.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 7.2 / Rsym value: 0.214 / % possible all: 70.1
Reflection shell
*PLUS
% possible obs: 70.1 % / Num. unique obs: 16087

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Processing

Software
NameVersionClassification
AMoRE(STAND ALONE)phasing
X-PLOR3.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CL1

1cl1


Resolution: 1.5→8 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.255 -10 %RANDOM
Rwork0.2 ---
obs0.2 200884 86.9 %-
Displacement parametersBiso mean: 30.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11680 0 11 1301 12992
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.02
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.76
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
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.02
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.76

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