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- PDB-4l3v: Crystal structure of delta516-525 human cystathionine beta-synthase -

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Basic information

Entry
Database: PDB / ID: 4l3v
TitleCrystal structure of delta516-525 human cystathionine beta-synthase
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: 3.628 Å
AuthorsEreno, J. / Majtan, T. / Oyenarte, I. / Kraus, J.P. / Martinez, 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
DepositionJun 7, 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_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 / _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_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
B: Cystathionine beta-synthase
A: Cystathionine beta-synthase
C: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,1939
Polymers181,6033
Non-polymers2,5916
Water00
1
B: Cystathionine beta-synthase
hetero molecules

B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7966
Polymers121,0682
Non-polymers1,7274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_353-x-2,y,-z-3/21
Buried area10590 Å2
ΔGint-74 kcal/mol
Surface area38880 Å2
MethodPISA
2
A: Cystathionine beta-synthase
C: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7966
Polymers121,0682
Non-polymers1,7274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-75 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.750, 342.655, 107.253
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 60534.180 Da / Num. of mol.: 3
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) GOLD / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 616.487 Da / Num. of mol.: 3 / 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: 5.76 Å3/Da / Density % sol: 78.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30% v/v PEG550, 0.1 M sodium citrate tribasic dehydrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.628→48.516 Å / Num. all: 46253 / Num. obs: 46253 / % possible obs: 96.55 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.44 % / Rmerge(I) obs: 0.31 / Net I/σ(I): 7.25
Reflection shellResolution: 3.628→3.75 Å / Redundancy: 2.37 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 2.28 / % possible all: 72.47

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LOD

4lod
PDB Unreleased entry


Resolution: 3.628→48.516 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 2340 5.06 %
Rwork0.2161 --
obs0.2169 46253 96.45 %
all-46253 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.628→48.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11546 0 174 0 11720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711968
X-RAY DIFFRACTIONf_angle_d1.16516268
X-RAY DIFFRACTIONf_dihedral_angle_d13.0024449
X-RAY DIFFRACTIONf_chiral_restr0.0731825
X-RAY DIFFRACTIONf_plane_restr0.0092080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6276-3.70160.397640.41071439X-RAY DIFFRACTION54
3.7016-3.7820.30281500.31532587X-RAY DIFFRACTION99
3.782-3.870.30541290.28822628X-RAY DIFFRACTION98
3.87-3.96670.28941430.26772596X-RAY DIFFRACTION99
3.9667-4.07390.29591220.25852633X-RAY DIFFRACTION99
4.0739-4.19370.27171230.25112618X-RAY DIFFRACTION98
4.1937-4.3290.29391430.23922613X-RAY DIFFRACTION99
4.329-4.48360.22841440.22962639X-RAY DIFFRACTION99
4.4836-4.6630.23191380.21632660X-RAY DIFFRACTION100
4.663-4.87510.23261400.21572625X-RAY DIFFRACTION99
4.8751-5.13180.22611450.20152662X-RAY DIFFRACTION100
5.1318-5.45290.23771300.20162669X-RAY DIFFRACTION100
5.4529-5.87330.22511730.21252645X-RAY DIFFRACTION100
5.8733-6.46310.23511430.20022692X-RAY DIFFRACTION100
6.4631-7.39550.23111470.1882687X-RAY DIFFRACTION100
7.3955-9.30680.1661490.152752X-RAY DIFFRACTION100
9.3068-48.52030.16671570.17482768X-RAY DIFFRACTION97

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