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- PDB-6c2z: Crystal Structures of Cystathionine beta-Synthase from Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 6c2z
TitleCrystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-Aminoacrylate 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 / traversing start control point of mitotic cell cycle / cysteine biosynthetic process from serine / transsulfuration / cytoplasmic stress granule / mRNA binding ...Cysteine formation from homocysteine / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / hydrogen sulfide biosynthetic process / traversing start control point of mitotic cell cycle / cysteine biosynthetic process from serine / transsulfuration / cytoplasmic stress granule / mRNA binding / mitochondrion / cytoplasm
Similarity search - Function
Cystathionine beta-synthase, C-terminal 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme ...Cystathionine beta-synthase, C-terminal 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / CBS domain / CBS domain / CBS domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-P1T / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cystathionine beta-synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_special_symmetry
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
Revision 1.4Oct 4, 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 / refine_hist / struct_conn
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_asym_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_asym_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 / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,50015
Polymers41,2871
Non-polymers1,21414
Water6,305350
1
A: Cystathionine beta-synthase
hetero molecules

A: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,00130
Polymers82,5732
Non-polymers2,42728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area8720 Å2
ΔGint-23 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.465, 81.465, 209.486
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-505-

PEG

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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 / Fragment: UNP residues 1-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CYS4, STR4, YGR155W, G6667 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32582, cystathionine beta-synthase

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Non-polymers , 8 types, 364 molecules

#2: Chemical ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7P
#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.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG400, 100 mM calcium acetate, 100 mM Tris, pH 6.5

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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: 1.37→50 Å / Num. obs: 86357 / % possible obs: 99.6 % / Redundancy: 20.1 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.025 / Rrim(I) all: 0.107 / Χ2: 0.958 / Net I/σ(I): 7.1 / Num. measured all: 1732784
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.37-1.3912.642110.860.3520.59499.5
1.39-1.4215.842340.9030.3290.61199.7
1.42-1.4519.242450.940.2750.64599.7
1.45-1.4820.342750.9570.2340.67399.7
1.48-1.5120.942600.9680.1940.7299.80.8720.893
1.51-1.5421.142260.9710.1560.77999.90.7010.718
1.54-1.5821.142720.9790.1310.84899.90.590.605
1.58-1.6221.142800.9790.1110.89799.90.4990.511
1.62-1.6721.242620.9860.0920.96999.90.4140.424
1.67-1.7321.243030.9880.0791.0391000.3520.361
1.73-1.7921.242840.990.0661.1161000.2960.303
1.79-1.8621.243150.9860.0561.1791000.2480.255
1.86-1.9421.243150.9930.0461.2351000.2080.213
1.94-2.0521.243240.9950.041.2931000.180.185
2.05-2.1721.243510.9950.0351.2841000.1550.159
2.17-2.3421.143560.9970.031.2581000.1360.14
2.34-2.582143770.9970.0281.2331000.1250.128
2.58-2.9520.744400.9970.0241.0691000.1060.109
2.95-3.7219.944920.9980.0170.77799.80.0750.077
3.72-501845350.9970.0150.55894.50.060.061

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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

1jbq


Resolution: 1.37→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.72 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: PHENIX, PDB-REDO, REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.1631 4072 5.1 %RANDOM
Rwork0.134 ---
obs0.1355 75277 91.55 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.89 Å2 / Biso mean: 18.638 Å2 / Biso min: 7.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 76 350 3101
Biso mean--33.38 33.66 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192970
X-RAY DIFFRACTIONr_bond_other_d0.0030.022831
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9914029
X-RAY DIFFRACTIONr_angle_other_deg0.98836612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0425.484124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67615526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4731513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213338
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02549
X-RAY DIFFRACTIONr_rigid_bond_restr1.90935795
X-RAY DIFFRACTIONr_sphericity_free26.3275205
X-RAY DIFFRACTIONr_sphericity_bonded11.24255890
LS refinement shellResolution: 1.372→1.407 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 117 -
Rwork0.194 2575 -
all-2692 -
obs--42.75 %

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