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- PDB-4l0d: Crystal structure of delta516-525 human cystathionine beta-syntha... -

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Basic information

Entry
Database: PDB / ID: 4l0d
TitleCrystal structure of delta516-525 human cystathionine beta-synthase containing C-terminal 6xHis-tag
ComponentsCystathionine 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 / cystathionine beta-synthase / modified amino acid binding / cystathionine beta-synthase activity / L-serine catabolic process / regulation of nitric oxide mediated signal transduction / Metabolism of ingested SeMet, Sec, MeSec into H2Se / cysteine biosynthetic process via cystathionine / carbon monoxide binding ...Cysteine formation from homocysteine / homocysteine catabolic process / cystathionine beta-synthase / modified amino acid binding / cystathionine beta-synthase activity / L-serine catabolic process / regulation of nitric oxide mediated signal transduction / Metabolism of ingested SeMet, Sec, MeSec into H2Se / cysteine biosynthetic process via cystathionine / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine metabolic process / homocysteine metabolic process / cartilage development involved in endochondral bone morphogenesis / L-cysteine catabolic process / cerebellum morphogenesis / cysteine biosynthetic process / response to folic acid / endochondral ossification / transsulfuration / cysteine biosynthetic process from serine / nitric oxide binding / DNA protection / S-adenosyl-L-methionine binding / nitrite reductase (NO-forming) activity / regulation of JNK cascade / superoxide metabolic process / blood vessel remodeling / maternal process involved in female pregnancy / blood vessel diameter maintenance / oxygen binding / pyridoxal phosphate binding / cellular response to hypoxia / heme binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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 / Pyridoxal-phosphate dependent enzyme / 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 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsEreno, J. / Majtan, T. / Oyenarte, I. / Kraus, J.P. / Martinez-Cruz, L.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis of regulation and oligomerization of human cystathionine beta-synthase, the central enzyme of transsulfuration.
Authors: Ereno-Orbea, J. / Majtan, T. / Oyenarte, I. / Kraus, J.P. / Martinez-Cruz, L.A.
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Oct 16, 2013Group: Database references
Revision 1.3Sep 20, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,9386
Polymers121,2112
Non-polymers1,7274
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-79 kcal/mol
Surface area39030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.365, 136.203, 169.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 60605.305 Da / Num. of mol.: 2 / Mutation: P2G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 M sodium acetate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.97→53.062 Å / Num. all: 30036 / Num. obs: 29364 / % possible obs: 97.79 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.37
Reflection shellResolution: 2.97→3.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.16 / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1JBQ AND 3KPC

1jbq

3kpc


Resolution: 2.97→53.062 Å / SU ML: 0.46 / σ(F): 1.09 / Phase error: 33.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2839 1495 5.1 %
Rwork0.2402 --
obs0.2424 29328 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.97→53.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7593 0 116 0 7709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077894
X-RAY DIFFRACTIONf_angle_d1.08710744
X-RAY DIFFRACTIONf_dihedral_angle_d13.4662915
X-RAY DIFFRACTIONf_chiral_restr0.0711213
X-RAY DIFFRACTIONf_plane_restr0.0051367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.02120.38231520.38762477X-RAY DIFFRACTION91
3.0212-3.07610.47031350.37712612X-RAY DIFFRACTION96
3.0761-3.13530.35371500.3752617X-RAY DIFFRACTION96
3.1353-3.19930.3891620.35252613X-RAY DIFFRACTION97
3.1993-3.26880.43291310.35812578X-RAY DIFFRACTION94
3.2688-3.34490.33081240.31262639X-RAY DIFFRACTION98
3.3449-3.42850.3911470.31872652X-RAY DIFFRACTION97
3.4285-3.52120.31851140.30352644X-RAY DIFFRACTION97
3.5212-3.62480.33541450.282716X-RAY DIFFRACTION99
3.6248-3.74170.33871400.30852617X-RAY DIFFRACTION96
3.7417-3.87540.2891650.25382628X-RAY DIFFRACTION97
3.8754-4.03060.32591250.2442610X-RAY DIFFRACTION95
4.0306-4.21390.21871440.22742579X-RAY DIFFRACTION96
4.2139-4.4360.29311230.22532573X-RAY DIFFRACTION94
4.436-4.71380.26941240.20852563X-RAY DIFFRACTION94
4.7138-5.07740.27181300.19192659X-RAY DIFFRACTION97
5.0774-5.58790.24341560.19982639X-RAY DIFFRACTION97
5.5879-6.39530.25021600.20062601X-RAY DIFFRACTION96
6.3953-8.05290.22851530.18252531X-RAY DIFFRACTION93
8.0529-53.07080.18511140.15792458X-RAY DIFFRACTION89

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