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- PDB-4uuu: 1.7 A resolution structure of human cystathionine beta-synthase r... -

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Basic information

Entry
Database: PDB / ID: 4uuu
Title1.7 A resolution structure of human cystathionine beta-synthase regulatory domain (del 516-525) in complex with SAM
ComponentsCYSTATHIONINE BETA-SYNTHASECystathionine beta synthase
KeywordsLYASE
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. / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-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. / 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 / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Cystathionine beta-synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.71 Å
AuthorsKopec, J. / McCorvie, T.J. / Fitzpatrick, F. / Strain-Damerell, C. / Froese, D.S. / Tallant, C. / Burgess-Brown, N. / 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
DepositionJul 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Structure summary
Revision 1.2Sep 17, 2014Group: Structure summary
Revision 1.3Nov 5, 2014Group: Database references
Revision 1.4Jan 14, 2015Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,43616
Polymers34,8942
Non-polymers1,54214
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-7.8 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.850, 78.650, 90.800
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


Mass: 17447.162 Da / Num. of mol.: 2 / Fragment: REGULATORY DOMAIN, RESIDUES 406-547
Source method: isolated from a genetically manipulated source
Details: (DELETION RESIDUES 515-526) / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P35520, cystathionine beta-synthase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDEL 515-526

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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: 2.44 Å3/Da / Density % sol: 49.66 % / Description: NONE
Crystal growDetails: 36% PEG550MME, 0.1M TRIS PH 7.5, 0.2M CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.71→39.09 Å / Num. obs: 31258 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 21.57 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 1.71→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.71→36.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.427 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DELETION RESIDUES 515-526
RfactorNum. reflection% reflectionSelection details
Rfree0.19858 1532 4.9 %RANDOM
Rwork0.15909 ---
obs0.16101 29673 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2--2.62 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.71→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 102 157 2476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192397
X-RAY DIFFRACTIONr_bond_other_d00.022384
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9893243
X-RAY DIFFRACTIONr_angle_other_deg0.78335458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6815291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99424.59298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64115404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1031510
X-RAY DIFFRACTIONr_chiral_restr0.1420.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.022606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
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_it2.6011.741146
X-RAY DIFFRACTIONr_mcbond_other2.5981.741146
X-RAY DIFFRACTIONr_mcangle_it3.2472.5951422
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9912.3051251
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: 1.712→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 111 -
Rwork0.241 2092 -
obs--96.79 %
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)
11.3794-0.0136-0.58920.4881-0.2011.05130.0106-0.0966-0.02850.0071-0.0548-0.0355-0.08510.08740.04420.0538-0.0255-0.02040.12170.00760.0116-6.192412.6365-21.1568
29.04165.3595-4.35787.6423-2.41552.56210.3190.09090.96520.14730.16470.3566-0.5476-0.2002-0.48370.35250.12020.04740.1505-0.00960.1168-12.819613.6466-11.9557
33.42840.9560.43892.73660.2422.8919-0.033-0.08310.26420.1068-0.00280.1568-0.1667-0.09640.03590.06370.01290.02010.12640.01940.0549-11.32898.5895-13.9404
41.6491-2.2484-4.78266.33317.250114.033-0.10450.03370.00020.6992-0.08160.86080.4111-0.11030.18610.11430.05120.1460.317-0.0230.2276-8.247933.2677-40.7387
50.87890.4398-0.12991.1666-0.42790.906-0.0558-0.0238-0.0905-0.0306-0.0277-0.01970.1386-0.10620.08340.0347-0.00640.010.1344-0.01280.0369-16.93792.9352-36.8451
61.38671.2690.32831.94630.27450.8584-0.05630.0575-0.0182-0.0601-0.03990.059-0.0789-0.08190.09620.02630.01370.00010.1247-0.00820.0267-10.1948.0024-42.8585
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 483
2X-RAY DIFFRACTION2A484 - 498
3X-RAY DIFFRACTION3A499 - 545
4X-RAY DIFFRACTION4B-14 - -1
5X-RAY DIFFRACTION5B406 - 502
6X-RAY DIFFRACTION6B503 - 547

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