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- PDB-3ppl: Crystal structure of an aspartate transaminase (NCgl0237, Cgl0240... -

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Basic information

Entry
Database: PDB / ID: 3ppl
TitleCrystal structure of an aspartate transaminase (NCgl0237, Cgl0240) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 1.25 A resolution
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / DIMER / PLP-DEPENDENT TRANSFERASE-LIKE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity
Similarity search - Function
Aspartate aminotransferase Ic / Aspartate amino-transferase / 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 ...Aspartate aminotransferase Ic / Aspartate amino-transferase / 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 / Unknown ligand / : / Aspartate aminotransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an aspartate transaminase (NCgl0237, Cgl0240) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 1.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7678
Polymers94,0892
Non-polymers6786
Water22,1221228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-21 kcal/mol
Surface area29330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.755, 54.424, 176.340
Angle α, β, γ (deg.)90.000, 101.600, 90.000
Int Tables number5
Space group name H-MC121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 47044.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 KITASATO / Gene: aspB, cg0294 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: Q6M8B5, UniProt: Q8NTR2*PLUS, aspartate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1228 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M sodium chloride, 20.0% polyethylene glycol 8000, 0.1M phosphate-citrate pH 4.2, Additive: 0.001 M alpha-ketoglutaric acid, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97944,0.97908
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2010
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979441
30.979081
ReflectionResolution: 1.25→29.324 Å / Num. obs: 241991 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 10.292 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.25-1.290.2762.75657493760684.8
1.29-1.350.2273.71045675371193.9
1.35-1.410.1814.6879964515394.3
1.41-1.480.1365.9857084399794.5
1.48-1.570.0998881474527594.1
1.57-1.70.0710.9960224937493.3
1.7-1.870.04815.1869164485792.2
1.87-2.140.03221.1854424426990.5
2.14-2.690.02526.6852664424290.8
2.690.0232.1874154563392.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.25→29.324 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 0.86 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.031
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. A PYRIDOXAL-5'-PHOSPHATE (PLP) MOLECULE IS MODELED IN THE ACTIVE SITE OF EACH MONOMER. 4. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED NEAR PLP. 5. THE OCCUPANCIES OF ATOMS IN ALTERNATE CONFORMATIONS WERE REFINED BY PHENIX SOFTWARE. 3. GLYCEROL (GOL) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1242 12140 5 %RANDOM
Rwork0.1049 ---
obs0.1059 241986 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.3 Å2 / Biso mean: 14.5267 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.16 Å2
2--0.2 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6483 0 66 1228 7777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227404
X-RAY DIFFRACTIONr_bond_other_d0.0010.024975
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.96110198
X-RAY DIFFRACTIONr_angle_other_deg0.966312206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99151018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58124.37341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.128151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8421548
X-RAY DIFFRACTIONr_chiral_restr0.1010.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218713
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021545
X-RAY DIFFRACTIONr_mcbond_it1.4781.54632
X-RAY DIFFRACTIONr_mcbond_other0.7151.51861
X-RAY DIFFRACTIONr_mcangle_it2.17827557
X-RAY DIFFRACTIONr_scbond_it3.23132772
X-RAY DIFFRACTIONr_scangle_it4.7894.52600
X-RAY DIFFRACTIONr_rigid_bond_restr1.382312379
X-RAY DIFFRACTIONr_sphericity_free8.92431303
X-RAY DIFFRACTIONr_sphericity_bonded4.085312135
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 838 -
Rwork0.159 15868 -
all-16706 -
obs--90.94 %

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