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- PDB-4ao4: Structural Determinants of the beta-Selectivity of a Bacterial Am... -

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Basic information

Entry
Database: PDB / ID: 4ao4
TitleStructural Determinants of the beta-Selectivity of a Bacterial Aminotransferase
ComponentsBeta-transaminase
KeywordsTRANSFERASE / AMINOTRANSFERASE
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
Chem-PLK / Beta-transaminase
Similarity search - Component
Biological speciesMesorhizobium sp. LUK (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionMar 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Dec 5, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)150,40414
Polymers148,7783
Non-polymers1,62611
Water11,277626
1
A: Beta-transaminase
B: Beta-transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,31110
Polymers99,1862
Non-polymers1,1258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-31.6 kcal/mol
Surface area27520 Å2
MethodPISA
2
C: Beta-transaminase
hetero molecules

C: Beta-transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1878
Polymers99,1862
Non-polymers1,0016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9470 Å2
ΔGint-38.9 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.387, 94.864, 102.973
Angle α, β, γ (deg.)90.00, 113.77, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.3316, 0.1312, 0.9343), (0.1326, -0.974, 0.1838), (0.9341, 0.1849, 0.3055)-0.3677, 149.1, -20.8
2given(-0.7004, 0.5804, 0.4154), (0.5753, 0.1147, 0.8098), (0.4223, 0.8062, -0.4143)-39.35, 66.78, -64.53

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Components

#1: Protein Beta-transaminase


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 BL21(DE3) (bacteria) / References: UniProt: A3EYF7
#2: Chemical ChemComp-PLK / (3R)-3-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-5-METHYLHEXANOIC ACID / R-3-amino-5-methylhexanoicacid-pyridoxal-5p-phosphate


Mass: 376.342 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H25N2O7P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.95→48.38 Å / Num. obs: 116568 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.43 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.199 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21631 5790 5 %RANDOM
Rwork0.18333 ---
obs0.18498 110560 98.43 %-
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: 19.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20.4 Å2
2---0.17 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9685 0 107 626 10418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02110105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06651324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90822.521468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.383151529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.69915100
X-RAY DIFFRACTIONr_chiral_restr0.1040.21496
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217906
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_it0.7761.56456
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.381210198
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5533649
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1094.53481
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 427 -
Rwork0.218 8239 -
obs--99.56 %

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