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- PDB-2pqm: Crystal structure of Cysteine Synthase (OASS) from Entamoeba hist... -

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Basic information

Entry
Database: PDB / ID: 2pqm
TitleCrystal structure of Cysteine Synthase (OASS) from Entamoeba histolytica at 1.86 A resolution
ComponentsCysteine synthase
KeywordsLYASE / OASS / Cysteine synthase / PLP
Function / homology
Function and homology information


cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsChinthalapudi, K. / Alam, N. / Gourinath, S.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of native O-acetyl-serine sulfhydrylase from Entamoeba histolytica and its complex with cysteine: structural evidence for cysteine binding and lack of interactions with serine acetyl transferase.
Authors: Chinthalapudi, K. / Kumar, M. / Kumar, S. / Jain, S. / Alam, N. / Gourinath, S.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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_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
Remark 600 HETEROGEN THE OXYGEN ATOM (O4) ON PLP IS DISPLACED BY THE NZ OF LYS58 TO FORM A COVALENT SCHIFF ... HETEROGEN THE OXYGEN ATOM (O4) ON PLP IS DISPLACED BY THE NZ OF LYS58 TO FORM A COVALENT SCHIFF BASE LINKAGE BETWEEN THE COFACTOR (PLP) AND THE ENZYME.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8856
Polymers75,1992
Non-polymers6864
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.316, 80.316, 112.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Cysteine synthase


Mass: 37599.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: OASS / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O15570
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5 Ammonium sulfate, 100mM Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 3, 2007
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 59571 / Num. obs: 59571 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 45.5
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 5820 / Rsym value: 0.336 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OAS

1oas


Resolution: 1.86→32.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.502 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3006 5 %RANDOM
Rwork0.18 ---
obs0.182 59528 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.186 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.86→32.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5117 0 40 356 5513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225241
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9857067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5615670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73725.35200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87515975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9341520
X-RAY DIFFRACTIONr_chiral_restr0.10.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023812
X-RAY DIFFRACTIONr_nbd_refined0.220.22618
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23618
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2374
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.214
X-RAY DIFFRACTIONr_mcbond_it1.011.53454
X-RAY DIFFRACTIONr_mcangle_it1.48325354
X-RAY DIFFRACTIONr_scbond_it2.55832053
X-RAY DIFFRACTIONr_scangle_it3.8074.51713
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 215 -
Rwork0.227 4066 -
obs-4281 98.08 %

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