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- PDB-6c2q: Crystal Structures of Cystathionine beta-Synthase from Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 6c2q
TitleCrystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-L-Serine Intermediate
ComponentsCystathionine beta-synthaseCystathionine beta synthase
KeywordsLYASE / CBS / synthase / PLP
Function / homology
Function and homology information


Cysteine formation from homocysteine / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / hydrogen sulfide biosynthetic process / cysteine biosynthetic process from serine / traversing start control point of mitotic cell cycle / transsulfuration / cytoplasmic stress granule / pyridoxal phosphate binding ...Cysteine formation from homocysteine / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / hydrogen sulfide biosynthetic process / cysteine biosynthetic process from serine / traversing start control point of mitotic cell cycle / transsulfuration / cytoplasmic stress granule / pyridoxal phosphate binding / mRNA binding / mitochondrion / cytoplasm
Similarity search - Function
Cystathionine beta-synthase / 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 / CBS domain ...Cystathionine beta-synthase / 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 / CBS domain / CBS domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EVM / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cystathionine beta-synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsKreinbring, C.A. / Tu, Y. / Liu, D. / Petsko, G.A. / Ringe, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32415 United States
CitationJournal: Biochemistry / Year: 2018
Title: Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time.
Authors: Tu, Y. / Kreinbring, C.A. / Hill, M. / Liu, C. / Petsko, G.A. / McCune, C.D. / Berkowitz, D.B. / Liu, D. / Ringe, D.
History
DepositionJan 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,41712
Polymers41,2871
Non-polymers1,13111
Water2,738152
1
A: Cystathionine beta-synthase
hetero molecules

A: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,83424
Polymers82,5732
Non-polymers2,26122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area8020 Å2
ΔGint-34 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)81.107, 81.107, 208.519
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-752-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cystathionine beta-synthase / Cystathionine beta synthase / Beta-thionase / Serine sulfhydrase / Sulfur transfer protein 4


Mass: 41286.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Strain: ATCC 204508 / S288c / Gene: CYS4, STR4, YGR155W, G6667 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) / References: UniProt: P32582, cystathionine beta-synthase

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Non-polymers , 8 types, 163 molecules

#2: Chemical ChemComp-EVM / L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene]


Mass: 333.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG400, 100 mM calcium acetate, 100 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 22476 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.066 / Χ2: 0.9 / Net I/σ(I): 12.4 / Num. measured all: 252461
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.17-2.219.50.27710790.9870.0930.2920.905100
2.21-2.2510.20.22211010.9870.0710.2340.967100
2.25-2.2911.10.20710810.990.0620.2170.939100
2.29-2.3411.80.19411040.9930.0560.2030.948100
2.34-2.3911.70.17110950.9930.050.1781.003100
2.39-2.4411.80.15310900.9950.0440.160.978100
2.44-2.5111.80.14510930.9950.0420.1511.01100
2.51-2.5711.70.13211040.9940.0380.1370.989100
2.57-2.6511.80.11511050.9970.0330.121.021100
2.65-2.7311.70.10611080.9950.0310.1110.996100
2.73-2.8311.80.09511070.9970.0280.0990.992100
2.83-2.9511.60.08511130.9970.0250.0880.97699.9
2.95-3.0811.70.07411100.9980.0220.0770.948100
3.08-3.2411.60.06311240.9980.0180.0660.869100
3.24-3.4411.50.05611270.9980.0170.0580.83100
3.44-3.7111.40.04911450.9980.0150.0510.774100
3.71-4.0811.20.04811370.9980.0150.050.817100
4.08-4.6710.80.04811560.9980.0150.050.89799.9
4.67-5.8910.50.04411950.9980.0140.0460.721100
5.89-509.70.02713020.9990.0090.0290.40199.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHENIXphasing
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JBQ
Resolution: 2.17→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.122 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.167 / Details: PHENIX, PDB-REDO, REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1195 5.3 %RANDOM
Rwork0.159 ---
obs0.1613 21199 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.04 Å2 / Biso mean: 31.347 Å2 / Biso min: 13.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.17→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 71 152 2898
Biso mean--48.29 35.13 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192848
X-RAY DIFFRACTIONr_bond_other_d0.0020.022683
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9913850
X-RAY DIFFRACTIONr_angle_other_deg0.93536255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51525.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39515497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0451513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213143
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02522
LS refinement shellResolution: 2.167→2.223 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 79 -
Rwork0.195 1499 -
all-1578 -
obs--98.93 %

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