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- PDB-2ykv: Structural Determinants of the Beta-Selectivity of a Bacterial Am... -

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Basic information

Entry
Database: PDB / ID: 2ykv
TitleStructural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase
ComponentsBETA-TRANSAMINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase class-III / Aminotransferase class-III / 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 ...Aminotransferase class-III / Aminotransferase class-III / 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
4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE / Beta-transaminase
Similarity search - Component
Biological speciesMESORHIZOBIUM SP. LUK (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWybenga, G.G. / Crismaru, C.G. / Janssen, D.B. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase.
Authors: Wybenga, G.G. / Crismaru, C.G. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionMay 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: BETA-TRANSAMINASE
B: BETA-TRANSAMINASE
C: BETA-TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,98626
Polymers148,7783
Non-polymers2,20823
Water11,241624
1
A: BETA-TRANSAMINASE
B: BETA-TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,57516
Polymers99,1862
Non-polymers1,38914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-20.4 kcal/mol
Surface area27330 Å2
MethodPISA
2
C: BETA-TRANSAMINASE
hetero molecules

C: BETA-TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,82320
Polymers99,1862
Non-polymers1,63818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12770 Å2
ΔGint-14.2 kcal/mol
Surface area27530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.582, 94.321, 102.307
Angle α, β, γ (deg.)90.00, 113.99, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.3336, 0.124, 0.9345), (0.1218, -0.9773, 0.1731), (0.9348, 0.1716, 0.3109)0.1788, 149, -19.75
2given(-0.7005, 0.5786, 0.4177), (0.573, 0.1072, 0.8125), (0.4254, 0.8085, -0.4066)-39.12, 67.22, -64.58

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Components

#1: Protein BETA-TRANSAMINASE / BETA-PHENYLALANINE AMINOTRANSFERASE


Mass: 49592.793 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MESORHIZOBIUM SP. LUK (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A3EYF7
#2: Chemical ChemComp-IK2 / 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsIK2: LINK BETWEEN THE C4A ATOM OF THE PLP COFACTOR AND THE AMINE-GROUP OF 2-AMINOOXYACETIC ACID

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.77 % / Description: USING RIGID BODY REFINEMENT
Crystal growDetails: SAME AS WILD-TYPE APO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.9→48.09 Å / Num. obs: 125289 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MES_BFAT_APO

Resolution: 1.9→48.09 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.709 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20603 6257 5 %RANDOM
Rwork0.17585 ---
obs0.17737 119028 99.88 %-
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 mean: 21.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20.55 Å2
2--0.14 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9689 0 143 624 10456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02110121
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.95513669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89951321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17422.521468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.015151527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.29615100
X-RAY DIFFRACTIONr_chiral_restr0.0910.21489
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217886
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5931.56446
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.111210177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06733675
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4164.53489
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 472 -
Rwork0.238 8776 -
obs--99.99 %

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