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- PDB-8stw: K384N HUMAN CYSTATHIONINE BETA-SYNTHASE (delta 411-551) -

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Basic information

Entry
Database: PDB / ID: 8stw
TitleK384N HUMAN CYSTATHIONINE BETA-SYNTHASE (delta 411-551)
ComponentsCystathionine beta-synthase, K384N variantCystathionine beta synthase
KeywordsLYASE / PLP / Heme / hydrogen sulfide
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 / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / 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 ...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. / 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.
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: 2.4 Å
AuthorsMascarenhas, R. / Roman, J. / Banerjee, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130183 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Disease-causing cystathionine beta-synthase linker mutations impair allosteric regulation.
Authors: Roman, J.V. / Mascarenhas, R. / Ceric, K. / Ballou, D.P. / Banerjee, R.
History
DepositionMay 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine beta-synthase, K384N variant
B: Cystathionine beta-synthase, K384N variant
C: Cystathionine beta-synthase, K384N variant
D: Cystathionine beta-synthase, K384N variant
E: Cystathionine beta-synthase, K384N variant
F: Cystathionine beta-synthase, K384N variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,62818
Polymers239,4466
Non-polymers5,18212
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.462, 90.189, 104.224
Angle α, β, γ (deg.)106.15, 105.49, 107.47
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Cystathionine beta-synthase, K384N variant / Cystathionine beta synthase / Beta-thionase / Serine sulfhydrase


Mass: 39907.648 Da / Num. of mol.: 6 / Mutation: K384N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22 % PEG 3,350, 6 % Tacsimate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.976 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→43.11 Å / Num. obs: 100667 / % possible obs: 93.3 % / Redundancy: 3.8 % / CC1/2: 0.997 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 5138 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.792 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24295 4883 4.9 %RANDOM
Rwork0.21044 ---
obs0.21206 94925 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.643 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å21.32 Å2-6.11 Å2
2--2.51 Å2-5.77 Å2
3---3.12 Å2
Refinement stepCycle: 1 / Resolution: 2.4→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16059 0 348 74 16481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01316741
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715707
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.67622754
X-RAY DIFFRACTIONr_angle_other_deg1.3151.59236414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40652107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31622.013780
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.823152843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.15215117
X-RAY DIFFRACTIONr_chiral_restr0.0810.22219
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218731
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023354
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_it4.2554.2928461
X-RAY DIFFRACTIONr_mcbond_other4.254.2918460
X-RAY DIFFRACTIONr_mcangle_it6.5866.43110557
X-RAY DIFFRACTIONr_mcangle_other6.5866.43210558
X-RAY DIFFRACTIONr_scbond_it4.4824.7328280
X-RAY DIFFRACTIONr_scbond_other4.4824.7328278
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9976.91612197
X-RAY DIFFRACTIONr_long_range_B_refined9.88150.37718042
X-RAY DIFFRACTIONr_long_range_B_other9.8850.37918042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A102630.1
12B102630.1
21A104270.09
22C104270.09
31A101970.1
32D101970.1
41A101520.1
42E101520.1
51A102340.09
52F102340.09
61B103210.1
62C103210.1
71B101570.11
72D101570.11
81B100820.11
82E100820.11
91B100640.11
92F100640.11
101C102620.1
102D102620.1
111C101430.11
112E101430.11
121C103150.09
122F103150.09
131D101200.11
132E101200.11
141D102450.1
142F102450.1
151E101750.11
152F101750.11
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 418 -
Rwork0.351 6960 -
obs--92.03 %

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