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- PDB-1m54: CYSTATHIONINE-BETA SYNTHASE: REDUCED VICINAL THIOLS -

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Basic information

Entry
Database: PDB / ID: 1m54
TitleCYSTATHIONINE-BETA SYNTHASE: REDUCED VICINAL THIOLS
ComponentsCYSTATHIONINE BETA-SYNTHASECystathionine beta synthase
KeywordsLYASE / PLP PROTEIN FOLD TYPE II (TRYPTOPHAN SYNTHASE) / PLP AND HEME BOUND TO PROTEIN / REDUCED VICINAL CYSTEINES
Function / homology
Function and homology information


Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / L-serine catabolic process / carbon monoxide binding ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / L-serine catabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / cartilage development involved in endochondral bone morphogenesis / L-serine metabolic process / regulation of nitric oxide mediated signal transduction / cysteine biosynthetic process / L-cysteine catabolic process / cerebellum morphogenesis / nitric oxide binding / cysteine biosynthetic process from serine / DNA protection / transsulfuration / endochondral ossification / S-adenosyl-L-methionine binding / response to folic acid / nitrite reductase (NO-forming) activity / superoxide metabolic process / maternal process involved in female pregnancy / blood vessel remodeling / blood vessel diameter maintenance / oxygen binding / pyridoxal phosphate binding / cellular response to hypoxia / ubiquitin protein ligase binding / heme binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / identical protein binding / metal ion binding / nucleus / cytosol / 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
PROTOPORPHYRIN IX CONTAINING FE / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTaoka, S. / Lepore, B.W. / Kabil, O. / Ojha, S. / Ringe, D. / Banerjee, R.
Citation
Journal: BIOCHEMISTRY / Year: 2002
Title: HUMAN CYSTATHIONINE BETA-SYNTHASE IS A HEME SENSOR PROTEIN. EVIDENCE THAT THE REDOX SENSOR IS HEME AND NOT THE VICINAL CYSTEINES IN THE CXXC MOTIF SEEN IN THE CRYSTAL STRUCTURE OF THE TRUNCATED ENZYME
Authors: Taoka, S. / Lepore, B.W. / Kabil, O. / Ojha, S. / Ringe, D. / Banerjee, R.
#1: Journal: Embo J. / Year: 2001
Title: STRUCTURE OF HUMAN CYSTATHIONINE-SYNTHASE: A UNIQUE PYRIDOXAL 5'-PHOSPHATE-DEPENDENT HEME PROTEIN
Authors: Meier, M. / Janosik, M. / Kery, V. / Kraus, J.P. / Burkhard, P.
History
DepositionJul 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: CYSTATHIONINE BETA-SYNTHASE
B: CYSTATHIONINE BETA-SYNTHASE
C: CYSTATHIONINE BETA-SYNTHASE
D: CYSTATHIONINE BETA-SYNTHASE
E: CYSTATHIONINE BETA-SYNTHASE
F: CYSTATHIONINE BETA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,71818
Polymers239,5366
Non-polymers5,18212
Water1,874104
1
A: CYSTATHIONINE BETA-SYNTHASE
B: CYSTATHIONINE BETA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5736
Polymers79,8452
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-62 kcal/mol
Surface area27700 Å2
MethodPISA
2
C: CYSTATHIONINE BETA-SYNTHASE
D: CYSTATHIONINE BETA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5736
Polymers79,8452
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-57 kcal/mol
Surface area27240 Å2
MethodPISA
3
E: CYSTATHIONINE BETA-SYNTHASE
F: CYSTATHIONINE BETA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5736
Polymers79,8452
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-63 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.740, 85.626, 97.082
Angle α, β, γ (deg.)102.01, 101.53, 112.60
Int Tables number1
Space group name H-MP1
Detailsthe biologically relevant entity is a dimer. three dimers occupy the assymetric unit. chain A is related to chain B by the followin 3x3 matrix: ( 0.78094 -0.51950 -0.34677 ) ( -0.51627 -0.84936 0.10976 ) ( -0.35155 0.09331 -0.93151 ) translation: (-0.12746 -0.20056 -0.68113)

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Components

#1: Protein
CYSTATHIONINE BETA-SYNTHASE / Cystathionine beta synthase / Serine sulfhydrase / Beta-thionase


Mass: 39922.727 Da / Num. of mol.: 6 / Fragment: RESIDUES 44-406 / Mutation: I44M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Organ: blood / Plasmid: pCBS-deltaN43/deltaC143 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 323 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 10K, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
145 mg/mlprotein1drop
20.1 MTris-HCl1droppH8.0
318-22 %PEG100001reservoir
41 mMdithiothreitol1reservoir
50.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.7401, 1.7372
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2001 / Details: Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.74011
21.73721
ReflectionResolution: 2.9→50 Å / Num. all: 87507 / Num. obs: 87507 / % possible obs: 83.2 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 58.127 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 9.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 10 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3 / Num. unique all: 53028 / Rsym value: 0.459 / % possible all: 10
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 53028 / % possible obs: 93.8 % / Num. measured all: 628994 / Rmerge(I) obs: 0.14
Reflection shell
*PLUS
Highest resolution: 2.9 Å / % possible obs: 93.2 % / Rmerge(I) obs: 0.459

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JBQ

1jbq


Resolution: 2.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.365 7535 -random
Rwork0.271 ---
all-87507 --
obs-79364 83.3 %-
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.88 Å2-2.86 Å2-2.02 Å2
2--15.93 Å22.91 Å2
3---3.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.44 Å
Luzzati d res low-50 Å
Luzzati sigma a0.59 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15951 0 348 104 16403
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_improper_angle_d1.18
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.405 1110 -
Rwork0.336 --
obs-10105 63.9 %
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. reflection all: 628994 / Num. reflection obs: 53028 / Num. reflection Rfree: 8143 / % reflection Rfree: 7.7 % / Rfactor Rfree: 0.348 / Rfactor Rwork: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18
LS refinement shell
*PLUS
Rfactor Rfree: 0.405 / Rfactor Rwork: 0.336

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