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- PDB-6zur: Psychrophilic aromatic amino acids aminotransferase from Psychrob... -

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Basic information

Entry
Database: PDB / ID: 6zur
TitlePsychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 cocrystalized with substrate analog - L-p-hydroxyphenyllactic acid
ComponentsAminotransferaseTransaminase
KeywordsTRANSFERASE / psychrophilic / aminotranasferase / cold-adapted / enzyme / complex / hydroxyphenyllactic acid / inhibitor
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
NITRATE ION / PYRIDOXAL-5'-PHOSPHATE / (2S)-2-hydroxy-3-(4-hydroxyphenyl)propanoic acid / Aminotransferase
Similarity search - Component
Biological speciesPsychrobacter sp. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsBujacz, A. / Rum, J. / Rutkiewicz, M. / Pietrzyk-Brzezinska, A.J. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/ST5/00555 Poland
Citation
Journal: Materials (Basel) / Year: 2021
Title: Structural Evidence of Active Site Adaptability towards Different Sized Substrates of Aromatic Amino Acid Aminotransferase from Psychrobacter Sp. B6.
Authors: Bujacz, A. / Rum, J. / Rutkiewicz, M. / Pietrzyk-Brzezinska, A.J. / Bujacz, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6.
Authors: Bujacz, A. / Rutkiewicz-Krotewicz, M. / Nowakowska-Sapota, K. / Turkiewicz, M.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,86417
Polymers88,3982
Non-polymers1,46515
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-46 kcal/mol
Surface area28760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.730, 63.858, 82.847
Angle α, β, γ (deg.)90.000, 102.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aminotransferase / Transaminase


Mass: 44199.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter sp. B6 (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: C7E5X4, Transferases; Transferring nitrogenous groups; Transaminases

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Non-polymers , 5 types, 320 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TYF / (2S)-2-hydroxy-3-(4-hydroxyphenyl)propanoic acid


Mass: 182.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M MgNO3, 20% PEG 2000, HEPES pH 7.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2017 / Details: Mirrors
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.31→43.65 Å / Num. obs: 31189 / % possible obs: 96.4 % / Redundancy: 3.229 % / Biso Wilson estimate: 44.525 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.11 / Χ2: 0.951 / Net I/σ(I): 9.71 / Num. measured all: 100722
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.453.2460.5081.8715260516547010.8650.60791
2.45-2.623.2270.4022.5415679490548580.8940.48299
2.62-2.833.1780.2963.6214216454744730.9430.35798.4
2.83-3.13.4840.1816.0814435417341430.9760.21499.3
3.1-3.463.3330.1139.7712477381237440.9890.13598.2
3.46-3.992.9420.07115.339211336931310.9930.08792.9
3.99-4.883.1760.04323.118647286827230.9970.05294.9
4.88-6.863.1990.04423.556987222821840.9960.05398
6.86-43.653.0930.03233.733810129012320.9970.03895.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RKC

4rkc


Resolution: 2.31→43.65 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.171 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1051 3.4 %RANDOM
Rwork0.1979 ---
obs0.1995 30138 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 112.81 Å2 / Biso mean: 44.612 Å2 / Biso min: 21.72 Å2
Baniso -1Baniso -2Baniso -3
1--31.23 Å2-0 Å2-21 Å2
2--40.38 Å20 Å2
3----9.15 Å2
Refinement stepCycle: final / Resolution: 2.31→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 0 95 305 6600
Biso mean--50.47 44.71 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196435
X-RAY DIFFRACTIONr_bond_other_d0.0060.025981
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9218692
X-RAY DIFFRACTIONr_angle_other_deg1.045313783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.645794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10224.384292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.673151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8741536
X-RAY DIFFRACTIONr_chiral_restr0.1020.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217293
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021441
LS refinement shellResolution: 2.31→2.369 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.32 64 -
Rwork0.23 1881 -
obs--81.24 %

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