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- PDB-3lws: Crystal structure of Putative aromatic amino acid beta-eliminatin... -

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Entry
Database: PDB / ID: 3lws
TitleCrystal structure of Putative aromatic amino acid beta-eliminating lyase/threonine aldolase. (YP_001813866.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution
ComponentsAromatic amino acid beta-eliminating lyase/threonine aldolase
KeywordsLYASE / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Pyridoxal phosphate / glycine biosynthesis
Function / homology
Function and homology information


glycine biosynthetic process / L-allo-threonine aldolase activity / L-threonine catabolic process / cytosol
Similarity search - Function
Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / 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 ...Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / 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
Aromatic amino acid beta-eliminating lyase/threonine aldolase
Similarity search - Component
Biological speciesExiguobacterium sibiricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative aromatic amino acid beta-eliminating lyase/threonine aldolase. (YP_001813866.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_distant_solvent_atoms / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aromatic amino acid beta-eliminating lyase/threonine aldolase
B: Aromatic amino acid beta-eliminating lyase/threonine aldolase
C: Aromatic amino acid beta-eliminating lyase/threonine aldolase
D: Aromatic amino acid beta-eliminating lyase/threonine aldolase
E: Aromatic amino acid beta-eliminating lyase/threonine aldolase
F: Aromatic amino acid beta-eliminating lyase/threonine aldolase


Theoretical massNumber of molelcules
Total (without water)241,7586
Polymers241,7586
Non-polymers00
Water23,9241328
1
A: Aromatic amino acid beta-eliminating lyase/threonine aldolase
B: Aromatic amino acid beta-eliminating lyase/threonine aldolase


Theoretical massNumber of molelcules
Total (without water)80,5862
Polymers80,5862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-22 kcal/mol
Surface area26640 Å2
MethodPISA
2
C: Aromatic amino acid beta-eliminating lyase/threonine aldolase
D: Aromatic amino acid beta-eliminating lyase/threonine aldolase


Theoretical massNumber of molelcules
Total (without water)80,5862
Polymers80,5862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-20 kcal/mol
Surface area26800 Å2
MethodPISA
3
E: Aromatic amino acid beta-eliminating lyase/threonine aldolase
F: Aromatic amino acid beta-eliminating lyase/threonine aldolase


Theoretical massNumber of molelcules
Total (without water)80,5862
Polymers80,5862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-22 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.150, 142.150, 102.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A3 - 355
2112B3 - 355
3112C3 - 355
4112D3 - 355
5112E3 - 355
6112F3 - 355
DetailsSIZE EXCLUSION CHROMATOGRAPHY AND LIGHT SCATTERING SPECTROSCOPY SUPPORTS ASSIGNMENT OF A DIMER AS BIOLOGICALLY SIGNIFICANT OLIGOMERIC STATE.

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Components

#1: Protein
Aromatic amino acid beta-eliminating lyase/threonine aldolase


Mass: 40293.020 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum (bacteria) / Strain: DSM 17290 / JCM 13490 / 255-15 / Gene: Exig_1379 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: B1YFH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1328 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 0.2000M Mg(oAc)2, 20.0000% PEG-8000, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97874
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.537
11K, H, -L20.463
ReflectionResolution: 2→46.53 Å / Num. obs: 156755 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 24.16 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.92
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→46.53 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 3.669 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE STRUCTURE WAS PHASED AND TRACED IN APPARENT SPACE GROUP P3121 AND REFINED IN P31 DUE TO TWINNING. TWINNING FACTOR WAS REFINED TO 0.46 FOR TWINNING OPERATOR (K, H, -L). FREE REFLECTIONS WERE EXPANDED BY THE TWIN LAW. 4. PYRIDOXAL-5'-PHOSPHATE (PLP) IS COVALENTLY ATTACHED TO LYSINE 205 VIA A SCHIFF-BASE LINKAGE AND IS MODELED AS LLP.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 7779 5 %RANDOM + TWIN LAW
Rwork0.144 ---
obs0.146 156744 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.51 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å20 Å2
2--3.73 Å20 Å2
3----7.46 Å2
Refinement stepCycle: LAST / Resolution: 2→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16931 0 0 1339 18270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02217341
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211662
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.96723560
X-RAY DIFFRACTIONr_angle_other_deg1.029328345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70752199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69923.962848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75152842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.01915118
X-RAY DIFFRACTIONr_chiral_restr0.0920.22540
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02119710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023660
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_it1.164310649
X-RAY DIFFRACTIONr_mcbond_other0.6334402
X-RAY DIFFRACTIONr_mcangle_it1.955517053
X-RAY DIFFRACTIONr_scbond_it3.72486692
X-RAY DIFFRACTIONr_scangle_it5.477116469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2028tight positional0.190.3
2B2028tight positional0.230.3
3C2028tight positional0.20.3
4D2028tight positional0.260.3
5E2028tight positional0.220.3
6F2028tight positional0.20.3
1A2413medium positional0.290.6
2B2413medium positional0.310.6
3C2413medium positional0.310.6
4D2413medium positional0.310.6
5E2413medium positional0.310.6
6F2413medium positional0.320.6
1A2028tight thermal0.40.75
2B2028tight thermal0.380.75
3C2028tight thermal0.360.75
4D2028tight thermal0.440.75
5E2028tight thermal0.380.75
6F2028tight thermal0.440.75
1A2413medium thermal0.321.5
2B2413medium thermal0.311.5
3C2413medium thermal0.321.5
4D2413medium thermal0.351.5
5E2413medium thermal0.31.5
6F2413medium thermal0.341.5
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 533 -
Rwork0.162 10895 -
obs--98.53 %

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