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- PDB-3pc2: Full length structure of cystathionine beta-synthase from Drosophila -

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Basic information

Entry
Database: PDB / ID: 3pc2
TitleFull length structure of cystathionine beta-synthase from Drosophila
ComponentsCG1753, isoform A
KeywordsLYASE / CBS / synthase / PLP / Heme
Function / homology
Function and homology information


Cysteine formation from homocysteine / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / homocysteine metabolic process / cysteine biosynthetic process from serine / nitrite reductase (NO-forming) activity / response to endoplasmic reticulum stress / determination of adult lifespan / transferase activity ...Cysteine formation from homocysteine / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / homocysteine metabolic process / cysteine biosynthetic process from serine / nitrite reductase (NO-forming) activity / response to endoplasmic reticulum stress / determination of adult lifespan / transferase activity / metal ion binding / cytoplasm
Similarity search - Function
Cystathionine beta-synthase / CBS-domain / CBS-domain / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme ...Cystathionine beta-synthase / CBS-domain / CBS-domain / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-synthase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKoutmos, M. / Smith, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for substrate activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine {beta}-synthase.
Authors: Koutmos, M. / Kabil, O. / Smith, J.L. / Banerjee, R.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id / _struct_ref_seq_dif.details / _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: CG1753, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3333
Polymers57,4701
Non-polymers8642
Water7,837435
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CG1753, isoform A
hetero molecules

A: CG1753, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6676
Polymers114,9402
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9690 Å2
ΔGint-75 kcal/mol
Surface area38270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.914, 138.157, 75.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-836-

HOH

21A-842-

HOH

31A-845-

HOH

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Components

#1: Protein CG1753, isoform A / CG1753 / isoform B / LD21426p


Mass: 57469.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG1753, Dmel_CG1753 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9VRD9, cystathionine beta-synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 23% PEG 3350, 0.2 Li2SO4, 100 mM BIS-TRIS 6.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2009
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 44821 / Num. obs: 42962 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.08 / Χ2: 0.892 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.865.80.40332091.0472.2
1.86-1.946.90.31139701.01589.8
1.94-2.038.20.24243841.06498.8
2.03-2.138.30.17343901.0299.4
2.13-2.278.30.13444090.98399.3
2.27-2.448.30.10944520.91599.5
2.44-2.698.30.09644400.93399.6
2.69-3.088.30.06944950.79399.8
3.08-3.888.30.05445210.70699.9
3.88-5080.04446920.57899.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-IceEpicsdata collection
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M54

1m54


Resolution: 1.8→41.26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.1932 / WRfactor Rwork: 0.1595 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.894 / SU B: 2.138 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1268 / SU Rfree: 0.1167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 2186 5.1 %RANDOM
Rwork0.1595 ---
obs0.1612 41020 95.66 %-
all-44821 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 62.21 Å2 / Biso mean: 20.0323 Å2 / Biso min: 6.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.166 Å
Refinement stepCycle: LAST / Resolution: 1.8→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 58 435 4319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223986
X-RAY DIFFRACTIONr_bond_other_d00.023687
X-RAY DIFFRACTIONr_angle_refined_deg1.3482.0125429
X-RAY DIFFRACTIONr_angle_other_deg0.70638612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11824.843159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64215694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1641522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214399
X-RAY DIFFRACTIONr_gen_planes_other00.02710
X-RAY DIFFRACTIONr_mcbond_it0.8421.52498
X-RAY DIFFRACTIONr_mcbond_other0.2191.51019
X-RAY DIFFRACTIONr_mcangle_it1.5524045
X-RAY DIFFRACTIONr_scbond_it2.34131488
X-RAY DIFFRACTIONr_scangle_it3.8644.51380
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 138 -
Rwork0.212 2147 -
all-2285 -
obs--69.33 %

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