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- PDB-4l28: Crystal structure of delta516-525 human cystathionine beta-syntha... -

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Basic information

Entry
Database: PDB / ID: 4l28
TitleCrystal structure of delta516-525 human cystathionine beta-synthase D444N mutant containing C-terminal 6xHis tag
ComponentsCystathionine beta-synthaseCystathionine 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 / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / L-serine catabolic process / carbon monoxide binding ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / L-serine catabolic process / carbon monoxide binding / hydrogen sulfide biosynthetic process / cartilage development involved in endochondral bone morphogenesis / L-serine metabolic 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 / endochondral ossification / transsulfuration / 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 / 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / 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 / 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. / 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: 2.626 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 4, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,87212
Polymers246,4174
Non-polymers3,4558
Water0
1
A: Cystathionine beta-synthase
C: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9366
Polymers123,2092
Non-polymers1,7274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-76 kcal/mol
Surface area38920 Å2
MethodPISA
2
B: Cystathionine beta-synthase
D: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9366
Polymers123,2092
Non-polymers1,7274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-75 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.482, 131.074, 207.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 61604.363 Da / Num. of mol.: 4 / Mutation: D444N
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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.085 M HEPES, pH 7.5, 8.5% isopropanol, 17% w/v PEG4000, 15% v/v Glycerol anhydrous, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.626→48.393 Å / Num. all: 87797 / Num. obs: 87797 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.36 / Net I/σ(I): 4.3
Reflection shellResolution: 2.626→2.7 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.1 / % possible all: 89.29

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.626→48.393 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 37.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.281 4423 5.04 %
Rwork0.2562 --
obs0.2575 87796 98.07 %
all-87797 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.626→48.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15223 0 232 0 15455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01415774
X-RAY DIFFRACTIONf_angle_d1.06221434
X-RAY DIFFRACTIONf_dihedral_angle_d12.9145842
X-RAY DIFFRACTIONf_chiral_restr0.092415
X-RAY DIFFRACTIONf_plane_restr0.0072734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6257-2.65560.4531330.45612189X-RAY DIFFRACTION79
2.6556-2.68680.48371320.4442617X-RAY DIFFRACTION94
2.6868-2.71960.44381230.45672688X-RAY DIFFRACTION95
2.7196-2.7540.42641420.43182697X-RAY DIFFRACTION96
2.754-2.79020.46261520.42092736X-RAY DIFFRACTION97
2.7902-2.82850.44711540.41162701X-RAY DIFFRACTION98
2.8285-2.86890.35911530.40512770X-RAY DIFFRACTION99
2.8689-2.91170.41291420.40232787X-RAY DIFFRACTION99
2.9117-2.95720.39821280.39272801X-RAY DIFFRACTION99
2.9572-3.00570.40961460.37492765X-RAY DIFFRACTION99
3.0057-3.05750.35351450.34592787X-RAY DIFFRACTION99
3.0575-3.11310.38221430.35042791X-RAY DIFFRACTION99
3.1131-3.17290.35981640.34092743X-RAY DIFFRACTION99
3.1729-3.23770.311550.32372821X-RAY DIFFRACTION99
3.2377-3.30810.32411370.30712810X-RAY DIFFRACTION99
3.3081-3.3850.39281330.29452785X-RAY DIFFRACTION99
3.385-3.46960.30051370.27492815X-RAY DIFFRACTION99
3.4696-3.56340.32331340.26562849X-RAY DIFFRACTION100
3.5634-3.66820.2991440.24932807X-RAY DIFFRACTION100
3.6682-3.78660.26921380.23572839X-RAY DIFFRACTION100
3.7866-3.92190.241470.21952820X-RAY DIFFRACTION100
3.9219-4.07880.25651570.2192833X-RAY DIFFRACTION100
4.0788-4.26430.24581510.21172828X-RAY DIFFRACTION100
4.2643-4.4890.21851610.19672823X-RAY DIFFRACTION100
4.489-4.770.1991710.19542838X-RAY DIFFRACTION100
4.77-5.13790.25281560.19622841X-RAY DIFFRACTION100
5.1379-5.65430.21791550.20842863X-RAY DIFFRACTION100
5.6543-6.47080.24221680.22192877X-RAY DIFFRACTION100
6.4708-8.14630.22591530.19752929X-RAY DIFFRACTION100
8.1463-48.40120.21431690.17082923X-RAY DIFFRACTION96

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