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- PDB-4b9b: The structure of the omega aminotransferase from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 4b9b
TitleThe structure of the omega aminotransferase from Pseudomonas aeruginosa
ComponentsBETA-ALANINE-PYRUVATE TRANSAMINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


beta-alanine-pyruvate transaminase / beta-alanine:pyruvate transaminase activity / beta-alanine biosynthetic process / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / 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 ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / 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
PYRIDOXAL-5'-PHOSPHATE / : / Beta-alanine--pyruvate aminotransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsSayer, C. / Isupov, M.N. / Westlake, A. / Littlechild, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Studies with Pseudomonas and Chromobacterium [Omega]-Aminotransferases Provide Insights Into Their Differing Substrate Specificity.
Authors: Sayer, C. / Isupov, M.N. / Westlake, A. / Littlechild, J.A.
History
DepositionSep 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 8, 2013Group: Derived calculations
Revision 1.3May 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_atom_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_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_atom_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.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_conn.ptnr2_label_seq_id / _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-ALANINE-PYRUVATE TRANSAMINASE
B: BETA-ALANINE-PYRUVATE TRANSAMINASE
C: BETA-ALANINE-PYRUVATE TRANSAMINASE
D: BETA-ALANINE-PYRUVATE TRANSAMINASE
E: BETA-ALANINE-PYRUVATE TRANSAMINASE
F: BETA-ALANINE-PYRUVATE TRANSAMINASE
G: BETA-ALANINE-PYRUVATE TRANSAMINASE
H: BETA-ALANINE-PYRUVATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,80538
Polymers387,4638
Non-polymers3,34230
Water82,4014574
1
C: BETA-ALANINE-PYRUVATE TRANSAMINASE
D: BETA-ALANINE-PYRUVATE TRANSAMINASE
E: BETA-ALANINE-PYRUVATE TRANSAMINASE
F: BETA-ALANINE-PYRUVATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,31018
Polymers193,7324
Non-polymers1,57914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32440 Å2
ΔGint-220.9 kcal/mol
Surface area49300 Å2
MethodPISA
2
A: BETA-ALANINE-PYRUVATE TRANSAMINASE
B: BETA-ALANINE-PYRUVATE TRANSAMINASE
G: BETA-ALANINE-PYRUVATE TRANSAMINASE
H: BETA-ALANINE-PYRUVATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,49520
Polymers193,7324
Non-polymers1,76316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33110 Å2
ΔGint-223.1 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.380, 133.160, 161.960
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.494, 0.675, 0.548), (0.675, -0.099, 0.731), (0.548, 0.731, -0.407)152.02095, -52.05841, -76.1788
2given(0.041, -0.999), (0.002, -1), (-0.999, -0.002, -0.041)153.08199, 103.77618, 241.10294
3given(-0.567, -0.704, 0.427), (-0.676, 0.102, -0.73), (0.471, -0.702, -0.534)235.47984, 156.16718, 92.25562
4given(-0.474, 0.715, 0.514), (0.66, -0.098, 0.745), (0.583, 0.692, -0.425)146.86276, -50.43912, 1.83597
5given(0.998, -0.015, 0.054), (0.016, 1, -0.012), (-0.054, 0.013, 0.998)0.01427, -0.01419, 0.5368
6given(-0.599, -0.666, 0.444), (-0.66, 0.096, -0.745), (0.454, -0.74, -0.497)238.44862, 154.68759, 15.31637
7given(0.088, -0.014, -0.996), (-0.018, -1, 0.013), (-0.996, 0.016, -0.089)148.54758, 106.20161, 160.61624

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
BETA-ALANINE-PYRUVATE TRANSAMINASE / AMINOTRANSFERASE


Mass: 48432.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: A3LGU8, UniProt: Q9I700*PLUS, beta-alanine-pyruvate transaminase

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Non-polymers , 5 types, 4604 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4574 / 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: 1.86 Å3/Da / Density % sol: 33.47 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.64→42 Å / Num. obs: 393083 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.3
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.64→66.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.308 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21887 20738 5 %RANDOM
Rwork0.1745 ---
obs0.17672 393083 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-1.18 Å2
2---1 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.64→66.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26556 0 200 4574 31330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01929526
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.96340411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27554080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63324.0751411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.823155031
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.51515214
X-RAY DIFFRACTIONr_chiral_restr0.1190.24358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02123198
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.638→1.681 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 1531 -
Rwork0.275 28669 -
obs--99.74 %

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