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- PDB-4pcu: Crystal structure of delta516-525 E201S human cystathionine beta-... -

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Basic information

Entry
Database: PDB / ID: 4pcu
TitleCrystal structure of delta516-525 E201S human cystathionine beta-synthase with AdoMet
ComponentsCystathionine beta-synthaseCystathionine beta synthase
KeywordsLYASE / CBS domain / homocyteine / cysteine biosynthesis / heme / pyridoxal 5'-phosphate / S-adenosylmethionine / transsulfuration pathway
Function / homology
Function and homology information


Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / cystathionine beta-synthase activity / carbon monoxide binding / hydrogen sulfide biosynthetic process ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / cystathionine beta-synthase activity / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine metabolic process / cartilage development involved in endochondral bone morphogenesis / L-serine catabolic process / regulation of nitric oxide mediated signal transduction / L-cysteine catabolic process / cysteine biosynthetic 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 / 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme ...Cystathionine beta-synthase, C-terminal domain / 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 / 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. / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PYRIDOXAL-5'-PHOSPHATE / S-ADENOSYLMETHIONINE / Cystathionine beta-synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.578 Å
AuthorsEreno-Orbea, J. / Majtan, T. / Oyenarte, I. / Kraus, J.P. / Martinez-Cruz, L.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural insight into the molecular mechanism of allosteric activation of human cystathionine beta-synthase by S-adenosylmethionine.
Authors: Ereno-Orbea, J. / Majtan, T. / Oyenarte, I. / Kraus, J.P. / Martinez-Cruz, L.A.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification / _software.name
Revision 1.3Dec 27, 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 / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6518
Polymers121,1272
Non-polymers2,5246
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-86 kcal/mol
Surface area38450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.354, 141.354, 108.528
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 60563.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli (E. coli) / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (vol/vol) polyethylene glycol monomethyl ether 3350 and 0.34mM SAM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.578→40.805 Å / Num. obs: 14903 / % possible obs: 98.6 % / Redundancy: 3.39 % / Biso Wilson estimate: 105.51 Å2 / Net I/σ(I): 5.01

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementResolution: 3.578→40.805 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 755 5.08 %
Rwork0.2572 14096 -
obs0.2582 14851 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 270.61 Å2 / Biso mean: 117.7928 Å2 / Biso min: 72.38 Å2
Refinement stepCycle: final / Resolution: 3.578→40.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7395 0 170 0 7565
Biso mean--120.7 --
Num. residues----975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097730
X-RAY DIFFRACTIONf_angle_d1.30210540
X-RAY DIFFRACTIONf_chiral_restr0.4281198
X-RAY DIFFRACTIONf_plane_restr0.0111344
X-RAY DIFFRACTIONf_dihedral_angle_d11.9942799
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5782-3.85430.36131400.35952704284495
3.8543-4.24180.33731780.29172792297099
4.2418-4.85470.26621450.24512817296299
4.8547-6.11310.28651440.250428683012100
6.1131-40.8080.22551480.22562915306398
Refinement TLS params.Method: refined / Origin x: -47.7086 Å / Origin y: 21.7549 Å / Origin z: 1.6786 Å
111213212223313233
T0.5871 Å20.0165 Å2-0.0782 Å2-0.6328 Å2-0.1558 Å2--0.6729 Å2
L-0.0867 °20.1802 °20.2909 °2-0.4702 °2-0.1454 °2--0.2592 °2
S0.118 Å °0.2192 Å °-0.0652 Å °0.0965 Å °0.1024 Å °-0.1944 Å °0.0179 Å °0.0359 Å °-0.0013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA43 - 3000
2X-RAY DIFFRACTION1allB43 - 3000

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