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- PDB-3lqs: Complex Structure of D-Amino Acid Aminotransferase and 4-amino-4,... -

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Basic information

Entry
Database: PDB / ID: 3lqs
TitleComplex Structure of D-Amino Acid Aminotransferase and 4-amino-4,5-dihydro-thiophenecarboxylic acid (ADTA)
ComponentsD-alanine aminotransferase
KeywordsTRANSFERASE / PLP aminotransferase / mechanism-based inhibitor / stereo-specificity / R-ADTA / Aminotransferase / Pyridoxal phosphate
Function / homology
Function and homology information


D-amino acid biosynthetic process / D-alanine:2-oxoglutarate aminotransferase activity / D-amino-acid transaminase / D-amino acid catabolic process / pyridoxal phosphate binding
Similarity search - Function
D-amino acid aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal ...D-amino acid aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Chem-PSZ / D-alanine aminotransferase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLepore, B.W. / Liu, D. / Peng, Y. / Fu, M. / Yasuda, C. / Manning, J.M. / Silverman, R.B. / Ringe, D.
CitationJournal: Biochemistry / Year: 2010
Title: Chiral discrimination among aminotransferases: inactivation by 4-amino-4,5-dihydrothiophenecarboxylic acid.
Authors: Lepore, B.W. / Liu, D. / Peng, Y. / Fu, M. / Yasuda, C. / Manning, J.M. / Silverman, R.B. / Ringe, D.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: D-alanine aminotransferase
B: D-alanine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9305
Polymers64,1212
Non-polymers8093
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-32 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.011, 90.728, 88.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-alanine aminotransferase / D-aspartate aminotransferase / D-amino acid aminotransferase / D-amino acid transaminase / DAAT


Mass: 32060.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM-1 / Gene: dat / Plasmid: pEMBL 18 / Production host: Escherichia coli (E. coli) / References: UniProt: P19938, D-amino-acid transaminase
#2: Chemical ChemComp-PSZ / 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC ACID


Mass: 374.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N2O7PS
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals were grown by the hanging drop method . The enzyme was dialyzed in 0.2 M potassium phosphate buffer pH 7.2, concentrated to 40mg/mL, and incubated with an R-ADTA:protein molecular ...Details: Crystals were grown by the hanging drop method . The enzyme was dialyzed in 0.2 M potassium phosphate buffer pH 7.2, concentrated to 40mg/mL, and incubated with an R-ADTA:protein molecular ratio of 200:1 prior to crystallization. The enzyme solution was mixed with crystallization buffer at pH 8.5 and incubated initially at 30-40 C, then allowed to return to room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→63.5 Å / Num. obs: 48439 / % possible obs: 97.4 % / Redundancy: 4 % / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4660 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→63.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.83 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19585 2465 5.1 %RANDOM
Rwork0.16052 ---
obs0.16234 45930 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--1.02 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 52 297 4863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224828
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9696578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43625.021235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00315891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4941524
X-RAY DIFFRACTIONr_chiral_restr0.1060.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023668
X-RAY DIFFRACTIONr_nbd_refined0.1980.21954
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.25
X-RAY DIFFRACTIONr_mcbond_it1.0091.52974
X-RAY DIFFRACTIONr_mcangle_it1.64924724
X-RAY DIFFRACTIONr_scbond_it2.7132111
X-RAY DIFFRACTIONr_scangle_it4.2774.51830
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 152 -
Rwork0.218 3210 -
obs--93.36 %

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