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- PDB-4xq2: Ensemble refinement of cystathione gamma lyase (CalE6) D7G from M... -

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Basic information

Entry
Database: PDB / ID: 4xq2
TitleEnsemble refinement of cystathione gamma lyase (CalE6) D7G from Micromonospora echinospora
ComponentsCalE6
KeywordsLYASE / NATURAL PRODUCT BIOSYNTHESIS / NATPRO / Structural Genomics / PSI-Biology / Enzyme Discovery for Natural Product Biosynthesis
Function / homology
Function and homology information


carbon-sulfur lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsWang, F. / Yennamalli, R.M. / Singh, S. / Tan, K. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: To Be Published
Title: The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora
Authors: Yennamalli, R.M. / Tan, K. / Wang, F. / Bigelow, L. / Jedrzejczak, R. / Babnigg, G. / Bingman, C.A. / Joachimiak, A. / Kharel, M.K. / Singh, S. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionJan 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalE6
B: CalE6
C: CalE6
D: CalE6
E: CalE6
F: CalE6
G: CalE6
H: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,20059
Polymers330,4968
Non-polymers4,70451
Water26,1761453
1
A: CalE6
B: CalE6
C: CalE6
D: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,61230
Polymers165,2484
Non-polymers2,36426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24400 Å2
ΔGint-114 kcal/mol
Surface area46790 Å2
MethodPISA
2
E: CalE6
F: CalE6
G: CalE6
H: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,58829
Polymers165,2484
Non-polymers2,34025
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24190 Å2
ΔGint-113 kcal/mol
Surface area46570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.855, 146.981, 349.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Number of models10

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
CalE6


Mass: 41312.000 Da / Num. of mol.: 8 / Mutation: D7G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calE6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KNG3

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Non-polymers , 5 types, 1504 molecules

#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1453 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 12%(w/v)20,000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→33.97 Å / Num. obs: 219087 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.23
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.9 / Num. unique all: 10831 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.ENSEMBLE_REFINEMENT: DEV_1839)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 2.1→33.97 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.14
RfactorNum. reflection% reflectionSelection details
Rfree0.183 11002 5.02 %Random selection
Rwork0.143 ---
obs0.145 219086 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22606 0 285 1453 24344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.342
X-RAY DIFFRACTIONf_dihedral_angle_d16.28
X-RAY DIFFRACTIONf_chiral_restr0.085
X-RAY DIFFRACTIONf_plane_restr0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0993-2.12320.24374050.17666773X-RAY DIFFRACTION99
2.1232-2.14820.22723500.17646818X-RAY DIFFRACTION100
2.1482-2.17440.22413850.16976872X-RAY DIFFRACTION100
2.1744-2.20190.22153360.1596966X-RAY DIFFRACTION100
2.2019-2.23080.21363620.15686854X-RAY DIFFRACTION100
2.2308-2.26140.21573350.15676967X-RAY DIFFRACTION100
2.2614-2.29370.20273870.15766851X-RAY DIFFRACTION100
2.2937-2.32790.21193790.15376856X-RAY DIFFRACTION100
2.3279-2.36430.20953830.14996944X-RAY DIFFRACTION100
2.3643-2.4030.22123650.15066855X-RAY DIFFRACTION100
2.403-2.44450.20653950.14446880X-RAY DIFFRACTION100
2.4445-2.48890.20864000.14346863X-RAY DIFFRACTION100
2.4889-2.53680.20463630.14516925X-RAY DIFFRACTION100
2.5368-2.58850.19173370.13556857X-RAY DIFFRACTION100
2.5885-2.64480.19273480.13366981X-RAY DIFFRACTION100
2.6448-2.70630.20673840.13956857X-RAY DIFFRACTION100
2.7063-2.77390.19433560.13926963X-RAY DIFFRACTION100
2.7739-2.84890.19873620.14336888X-RAY DIFFRACTION100
2.8489-2.93270.19363530.14756972X-RAY DIFFRACTION100
2.9327-3.02730.19633520.14816941X-RAY DIFFRACTION100
3.0273-3.13540.18383530.14886969X-RAY DIFFRACTION100
3.1354-3.26090.17623740.14076920X-RAY DIFFRACTION100
3.2609-3.40910.17183160.1396980X-RAY DIFFRACTION100
3.4091-3.58870.17933890.13796963X-RAY DIFFRACTION100
3.5887-3.81330.16163540.13946947X-RAY DIFFRACTION100
3.8133-4.10720.15263750.13297002X-RAY DIFFRACTION100
4.1072-4.51970.14923980.12566997X-RAY DIFFRACTION100
4.5197-5.17170.14363660.12767023X-RAY DIFFRACTION100
5.1717-6.50830.18913520.15367107X-RAY DIFFRACTION100
6.5083-33.97430.15683880.14027293X-RAY DIFFRACTION100

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