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- PDB-1jbq: STRUCTURE OF HUMAN CYSTATHIONINE BETA-SYNTHASE: A UNIQUE PYRIDOXA... -

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Basic information

Entry
Database: PDB / ID: 1jbq
TitleSTRUCTURE OF HUMAN CYSTATHIONINE BETA-SYNTHASE: A UNIQUE PYRIDOXAL 5'-PHOSPHATE DEPENDENT HEMEPROTEIN
ComponentsCYSTATHIONINE BETA-SYNTHASE
KeywordsLYASE / Fold type II of PLP enzymes
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 / 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. ...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 / 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. / 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: 2.6 Å
AuthorsMeier, M. / Janosik, M. / Kery, V. / Kraus, J.P. / Burkhard, P.
Citation
Journal: EMBO J. / Year: 2001
Title: Structure of human cystathionine beta-synthase: a unique pyridoxal 5'-phosphate-dependent heme protein.
Authors: Meier, M. / Janosik, M. / Kery, V. / Kraus, J.P. / Burkhard, P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray diffraction analysis of the active core of human recombinant cystathionine beta-synthase: an enzyme involved in vascular disease.
Authors: Janosik, M. / Meier, M. / Kery, V. / Oliveriusova, J. / Burkhard, P. / Kraus, J.P.
History
DepositionJun 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_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_label_seq_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

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)290,30218
Polymers285,1206
Non-polymers5,18212
Water2,774154
1
A: CYSTATHIONINE BETA-SYNTHASE
B: CYSTATHIONINE BETA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7676
Polymers95,0402
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-56 kcal/mol
Surface area26160 Å2
MethodPISA
2
C: CYSTATHIONINE BETA-SYNTHASE
D: CYSTATHIONINE BETA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7676
Polymers95,0402
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-56 kcal/mol
Surface area25980 Å2
MethodPISA
3
E: CYSTATHIONINE BETA-SYNTHASE
F: CYSTATHIONINE BETA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7676
Polymers95,0402
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-56 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.520, 144.520, 108.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Cell settingtrigonal
Space group name H-MP31

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Components

#1: Protein
CYSTATHIONINE BETA-SYNTHASE / E.C.4.2.1.22 / CYSTATHIONINE-BETA-SYNTHASE / SERINE SULFHYDRASE / BETA-THIONASE


Mass: 47520.074 Da / Num. of mol.: 6 / Fragment: THE ACTIVE CORE / Mutation: DELETION 414-551, EXTRA 23 RESIDUES AT N-TERMINUS
Source method: isolated from a genetically manipulated source
Details: MINOR ISOFORM / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-5X-1HCBSD414-551 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE MRF / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 1000, HEPES, pH 7.5 , VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
pH: 7.4
Details: Janosik, M., (2001) Acta Crystallogr., Sect.D, 57, 289.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
126 mg/mlprotein1drop
220 mMHEPES1drop
330 %PEG10001reservoir
480 mMHEPES1reservoir
50.4 mM1reservoirFeCl3

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1A10.97
SYNCHROTRONEMBL/DESY, HAMBURG BW7A21.74
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATESep 26, 1999
MARRESEARCH2CCDJan 26, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1channel-cut monochromator Si (111)SINGLE WAVELENGTHMx-ray1
2Double crystal focussing monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.741
ReflectionResolution: 2.6→50 Å / Num. all: 87368 / Num. obs: 63971 / % possible obs: 82.4 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 29.2 Å2 / Rsym value: 0.076 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 4 / Rsym value: 0.31 / % possible all: 65.1
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 63.9 % / Rmerge(I) obs: 0.309

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D6S

1d6s


Resolution: 2.6→43.34 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3036819.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues THR 193 and GLU 201 are disordered in all chains.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 3219 5 %RANDOM
Rwork0.257 ---
obs0.257 63971 82.3 %-
all-87368 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.57 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.78 Å28.67 Å20 Å2
2--4.78 Å20 Å2
3----9.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.6→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16020 0 348 154 16522
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it3.671.5
X-RAY DIFFRACTIONc_mcangle_it5.442
X-RAY DIFFRACTIONc_scbond_it5.72
X-RAY DIFFRACTIONc_scangle_it7.292.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 121 3.9 %
Rwork0.3 2991 -
obs-2991 21.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP_HEM.PARAMPLP_HEM.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / % reflection Rfree: 3.9 % / Rfactor Rwork: 0.3

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