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- PDB-4coo: Crystal structure of human cystathionine beta-synthase (delta516-... -

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Basic information

Entry
Database: PDB / ID: 4coo
TitleCrystal structure of human cystathionine beta-synthase (delta516-525) at 2.0 angstrom resolution
ComponentsCYSTATHIONINE BETA-SYNTHASE
KeywordsLYASE / METHIONINE CYCLE / METABOLIC PATHWAY / ALLOSTERIC REGULATION / SERINE METABOLISM
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 / homocysteine metabolic process / hydrogen sulfide biosynthetic process / L-serine 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 / regulation of JNK cascade / nitrite reductase (NO-forming) activity / 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 / ubiquitin protein ligase binding / heme binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / identical protein 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 / 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
ACETATE ION / 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 Å
AuthorsMcCorvie, T.J. / Kopec, J. / Vollamar, M. / Strain-Damerell, C. / Bushell, S. / Bradley, A. / Tallant, C. / Kiyani, W. / Froese, D.S. / Carpenter, E.S. ...McCorvie, T.J. / Kopec, J. / Vollamar, M. / Strain-Damerell, C. / Bushell, S. / Bradley, A. / Tallant, C. / Kiyani, W. / Froese, D.S. / Carpenter, E.S. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Inter-Domain Communication of Human Cystathionine Beta Synthase: Structural Basis of S-Adenosyl-L-Methionine Activation.
Authors: Mccorvie, T.J. / Kopec, J. / Hyung, S. / Fitzpatrick, F. / Feng, X. / Termine, D. / Strain-Damerell, C. / Vollmar, M. / Fleming, J. / Janz, J.M. / Bulawa, C. / Yue, W.W.
History
DepositionJan 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _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_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

Downloads & links

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Assembly

Deposited unit
A: CYSTATHIONINE BETA-SYNTHASE
B: CYSTATHIONINE BETA-SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,12321
Polymers124,2662
Non-polymers2,85719
Water5,296294
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-75.8 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.264, 116.193, 167.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYSTATHIONINE BETA-SYNTHASE / BETA-THIONASE / SERINE SULFHYDRASE


Mass: 62132.949 Da / Num. of mol.: 2
Fragment: CATALYTIC AND REGULATORY DOMAINS, RESIDUES 1-515,526-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P35520, cystathionine beta-synthase

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Non-polymers , 7 types, 313 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT USED HERE CONTAINS A DELETION OF AMINO ACIDS 516-525

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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: 2.89 Å3/Da / Density % sol: 57.42 % / Description: NONE
Crystal growDetails: 18% PEG8000, 0.1 M CACODYLATE, PH 6.6 0.2 M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→48.89 Å / Num. obs: 93295 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XIAdata reduction
XIAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JBQ

1jbq


Resolution: 2→95.56 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.023 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20068 4662 5 %RANDOM
Rwork0.17381 ---
obs0.17517 88563 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.704 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--1.56 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→95.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7495 0 173 294 7962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197926
X-RAY DIFFRACTIONr_bond_other_d0.0010.027689
X-RAY DIFFRACTIONr_angle_refined_deg1.431.98910773
X-RAY DIFFRACTIONr_angle_other_deg0.804317671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87323.912317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.092151351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.871554
X-RAY DIFFRACTIONr_chiral_restr0.0820.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218899
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021733
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3882.3993959
X-RAY DIFFRACTIONr_mcbond_other1.3862.3963953
X-RAY DIFFRACTIONr_mcangle_it2.2613.5824944
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8732.6983967
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 329 -
Rwork0.275 6445 -
obs--99.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3336-1.1901-2.50154.94430.15932.0107-0.1214-0.1290.21280.5120.34380.2731-0.02190.011-0.22240.2130.04530.11490.1728-0.05390.124-6.574722.3016-16.6075
21.7085-0.3098-0.34451.74940.10871.32710.07940.00480.16750.1381-0.00430.0889-0.2567-0.0349-0.07510.07130.00240.03630.0036-0.00450.03962.050717.2694-30.0989
32.59840.5496-0.67231.10360.18673.571-0.01240.0646-0.42260.1635-0.00090.20040.4096-0.16360.01330.0661-0.01670.03110.0104-0.00460.1664-5.33352.3445-31.9338
42.06520.8248-2.06642.0464-1.30514.0385-0.11810.0341-0.1875-0.12630.0026-0.1240.14260.25570.11550.17880.01910.01590.1269-0.03890.065219.9128-7.4538-75.3584
54.422.2133-1.18965.3212-0.34913.4389-0.0934-0.0216-0.3357-0.09920.0807-0.20760.35380.18650.01270.18940.01890.03870.064-0.01650.041213.5843-10.216-66.1733
65.5803-0.37431.48696.806-2.44834.60410.35360.450.0738-0.4475-0.40220.9901-0.4459-0.6650.04860.46130.141-0.15820.4569-0.03410.2837-4.361324.4204-76.4282
713.87093.6384-6.75650.991-1.7523.30630.49180.79911.20260.01290.08620.367-0.3322-0.4519-0.5780.63850.3531-0.15230.4202-0.05480.2922-12.788719.5126-50.5188
80.90410.141-0.33892.39760.55472.50230.1560.20760.1565-0.406-0.11820.0092-0.4847-0.1396-0.03780.18670.07960.04260.07950.03660.03677.437619.0352-60.9485
92.14230.2204-2.01141.1948-1.66266.0151-0.15-0.198-0.16590.1878-0.017-0.31630.3350.3840.1670.15370.0692-0.09080.1841-0.02340.164225.1355-2.314-15.7523
105.76391.6864-0.35214.8221-1.68086.06830.0277-0.2863-0.14880.14-0.1462-0.74810.10240.5170.11850.0090.0169-0.02820.1918-0.00180.131129.57744.8737-25.707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 74
2X-RAY DIFFRACTION2A75 - 272
3X-RAY DIFFRACTION3A273 - 400
4X-RAY DIFFRACTION4A408 - 479
5X-RAY DIFFRACTION5A480 - 548
6X-RAY DIFFRACTION6B45 - 71
7X-RAY DIFFRACTION7B72 - 88
8X-RAY DIFFRACTION8B89 - 408
9X-RAY DIFFRACTION9B409 - 481
10X-RAY DIFFRACTION10B482 - 548

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