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- PDB-3l8a: Crystal structure of MetC from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 3l8a
TitleCrystal structure of MetC from Streptococcus mutans
ComponentsPutative aminotransferase, probable beta-cystathionaseTransaminase
KeywordsLYASE / MetC / smu.1674 / beta-cystathionase / Streptococcus mutans / Aminotransferase / Transferase
Function / homology
Function and homology information


cystathionine beta-lyase / : / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / 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
PYRIDOXAL-5'-PHOSPHATE / Putative aminotransferase probable beta-cystathionase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.539 Å
AuthorsWang, X.J. / Fu, T.M. / Su, X.D.
CitationJournal: To be Published
Title: Crystal structure of MetC from Streptococcus mutans
Authors: Wang, X.J. / Fu, T.M. / Mi, W. / Su, X.D.
History
DepositionDec 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _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: Putative aminotransferase, probable beta-cystathionase
B: Putative aminotransferase, probable beta-cystathionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5014
Polymers96,0072
Non-polymers4942
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-24 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.377, 64.346, 99.315
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative aminotransferase, probable beta-cystathionase / Transaminase / MetC


Mass: 48003.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_1674 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DST5, cystathionine beta-lyase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 1.94 Å3/Da / Density % sol: 36.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% PEG MME 550, 0.1M Na Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9798 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Nov 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.539→50 Å / Num. obs: 106510 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.42 Å2
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 2.5 % / Num. unique all: 9423 / % possible all: 87.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.539→24.567 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.882 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 5328 5 %
Rwork0.1761 101149 -
obs0.1772 106477 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.848 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 53.36 Å2 / Biso mean: 14.832 Å2 / Biso min: 6.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.382 Å2-0 Å22.024 Å2
2---0.981 Å20 Å2
3----1.401 Å2
Refinement stepCycle: LAST / Resolution: 1.539→24.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 30 554 6757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056409
X-RAY DIFFRACTIONf_angle_d1.0168726
X-RAY DIFFRACTIONf_chiral_restr0.067970
X-RAY DIFFRACTIONf_plane_restr0.0041128
X-RAY DIFFRACTIONf_dihedral_angle_d16.8862322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.538-1.5560.2981080.2682273238166
1.556-1.5740.2471470.2233178332592
1.574-1.5940.251700.1913298346896
1.594-1.6140.221770.1883330350797
1.614-1.6350.2371720.1813361353398
1.635-1.6570.2251670.183420358799
1.657-1.6810.221750.1733386356199
1.681-1.7060.2181990.1753376357599
1.706-1.7330.2012130.1673386359999
1.733-1.7610.191700.1673377354799
1.761-1.7910.2061800.1683447362799
1.791-1.8240.2051890.1733374356399
1.824-1.8590.231530.1863433358699
1.859-1.8970.2041770.1863403358099
1.897-1.9380.1961840.1793413359799
1.938-1.9830.2391850.1723420360599
1.983-2.0330.2071760.1753422359899
2.033-2.0880.1911740.1623425359999
2.088-2.1490.1831920.1683405359799
2.149-2.2190.2252070.1743415362299
2.219-2.2980.221640.1763449361399
2.298-2.390.2041710.17334263597100
2.39-2.4980.2011890.17134463635100
2.498-2.630.1911960.17234203616100
2.63-2.7950.1861920.17634503642100
2.795-3.010.1911690.17834733642100
3.01-3.3120.2051820.18234643646100
3.312-3.790.172070.16134433650100
3.79-4.7690.1561650.14234933658100
4.769-24.570.1671780.1623543372199

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