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- PDB-3pj0: Crystal structure of a putative L-allo-threonine aldolase (lmo030... -

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Basic information

Entry
Database: PDB / ID: 3pj0
TitleCrystal structure of a putative L-allo-threonine aldolase (lmo0305) from Listeria monocytogenes EGD-E at 1.80 A resolution
ComponentsLmo0305 protein
KeywordsLYASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


threonine catabolic process / L-allo-threonine aldolase activity / glycine biosynthetic process / cytosol
Similarity search - Function
Low specificity L-threonine aldolase / 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 ...Low specificity L-threonine aldolase / 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
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative L-allo-threonine aldolase (lmo0305) from Listeria monocytogenes EGD-E at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Lmo0305 protein
B: Lmo0305 protein
C: Lmo0305 protein
D: Lmo0305 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,55614
Polymers161,6484
Non-polymers90910
Water27,4191522
1
A: Lmo0305 protein
B: Lmo0305 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3558
Polymers80,8242
Non-polymers5316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-21 kcal/mol
Surface area27730 Å2
MethodPISA
2
C: Lmo0305 protein
D: Lmo0305 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2016
Polymers80,8242
Non-polymers3784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-34 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.593, 96.642, 99.478
Angle α, β, γ (deg.)90.000, 110.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A0 - 358
2116B0 - 358
3116C0 - 358
4116D0 - 358
DetailsCRYSTAL PACKING INDICATES THAT A DIMER IS AN OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Lmo0305 protein


Mass: 40411.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: lmo0305 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8YA56

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Non-polymers , 5 types, 1532 molecules

#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1522 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 277 K / pH: 8.36
Details: 53.80% 2-methyl-2,4-pentanediol, 0.1M TRIS pH 8.36, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.96109,0.97915,0.97936
DetectorType: MAR MAR325 / Detector: CCD / Date: May 13, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961091
20.979151
30.979361
ReflectionResolution: 1.8→29.699 Å / Num. obs: 138522 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.78 Å2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1.9 / % possible all: 95.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
qfit0.9model building
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.21 / SU B: 4.781 / SU ML: 0.079 / ESU R: 0.124 / ESU R Free: 0.116
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.ELECTRON DENSITY INDICATES THAT LYS 207 ON THE FOUR SUBUNITS IN THE ASYMMETRIC UNIT ARE COVALENTLY ATTACHED TO PYRIDOXAL-5'- PHOSPHATE; THERFORE THESE RESIDUES WERE MODELED AS 2-LYSINE (3- HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)(LLP). 6. 2-METHYL-2,4-PENTANEDIOL (MPD,MRD), CHLORIDE (CL), AND SODIUM IONS FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 7. THE PROGARM QFIT THAT AUTOMATICALLY IDENTIFIES AND MODELS DISCRETE HETEROGENEITY IN ELECTRON DENSITY MAPS WITH A A CONVEX OPTIMIZATION ALGORITHM WAS IMPLEMENTED DURING REFINEMENT TO MODEL ALTERNATE CONFORMATIONS.
RfactorNum. reflection% reflection
Rfree0.198 6965 5 %
Rwork0.162 --
obs0.163 138490 98.9 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 18.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.38 Å2
2--0.67 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11243 0 59 1522 12824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212211
X-RAY DIFFRACTIONr_bond_other_d0.0010.028284
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.98216645
X-RAY DIFFRACTIONr_angle_other_deg0.931320394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.45851554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22725.113573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.187152171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3381556
X-RAY DIFFRACTIONr_chiral_restr0.0890.21842
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022396
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_it0.591.57432
X-RAY DIFFRACTIONr_mcbond_other0.1841.53023
X-RAY DIFFRACTIONr_mcangle_it1.016212080
X-RAY DIFFRACTIONr_scbond_it1.83534779
X-RAY DIFFRACTIONr_scangle_it2.9624.54535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3978 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.385
2Bloose positional0.445
3Cloose positional0.415
4Dloose positional0.375
1Aloose thermal2.3210
2Bloose thermal1.4910
3Cloose thermal2.5810
4Dloose thermal2.0310
LS refinement shellResolution: 1.8→1.85 Å
RfactorNum. reflection% reflection
Rfree0.263 481 -
Rwork0.231 9799 -
obs--99.54 %
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)
10.4648-0.05130.05820.2552-0.02540.4183-0.006-0.02380.0328-0.00260.0064-0.0667-0.04520.0514-0.00040.03940.00040.0010.0166-0.00480.045334.652940.215748.864
20.3490.02060.07830.263-0.02840.48470.00520.0161-0.0303-0.04390.00430.03840.0296-0.1074-0.00950.02920.0047-0.00270.03380.0050.0236-0.188144.380637.3668
30.5931-0.07770.08110.22970.0641.1464-0.00030.00880.07090.00230.0291-0.059-0.10070.1914-0.02880.0563-0.00610.00460.0356-0.00990.0398100.729338.067996.5647
40.51360.00480.19020.1982-0.03420.54150.00850.0046-0.0525-0.01130.02510.0313-0.0015-0.1535-0.03360.02660.01220.00650.0580.01150.015567.618743.34682.4787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 358
2X-RAY DIFFRACTION2B0 - 358
3X-RAY DIFFRACTION3C3 - 355
4X-RAY DIFFRACTION4D0 - 358

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