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- PDB-6t3v: Psychrophilic aromatic amino acids aminotransferase from Psychrob... -

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Basic information

Entry
Database: PDB / ID: 6t3v
TitlePsychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 cocrystalized with substrate analog - malic acid
ComponentsAminotransferase
KeywordsTRANSFERASE / psychrophilic / aminotranasferase / cold-adapted / enzyme / complex / malic 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 transaminase activity / pyridoxal phosphate binding / metal ion binding / identical protein 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
(2S)-2-hydroxybutanedioic acid / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesPsychrobacter sp. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsRutkiewicz, M. / Bujacz, A. / Rum, J. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/ST5/00555 Poland
Citation
Journal: Materials / 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
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5803
Polymers44,1991
Non-polymers3812
Water9,188510
1
A: Aminotransferase
hetero molecules

A: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1616
Polymers88,3982
Non-polymers7624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area7990 Å2
ΔGint-38 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.209, 90.209, 241.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Aminotransferase


Mass: 44199.203 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M DL-malic acid pH 7.0

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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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 72901 / % possible obs: 97 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.056 / Χ2: 1.048 / Net I/σ(I): 16.1 / Num. measured all: 993205
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.62-1.68100.3957551.018178.1
1.68-1.7511.70.32769731.111194.5
1.75-1.8214.60.2473341.114199.5
1.82-1.9214.60.16573691.121199.6
1.92-2.0414.60.1173921.072199.7
2.04-2.214.50.07974531.038199.8
2.2-2.4214.50.06274681.022199.9
2.42-2.7714.30.05575350.9681100
2.77-3.4913.70.05276561.055199.9
3.49-5012.80.04179660.958198.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RKC

4rkc


Resolution: 1.62→35 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.287 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1637 3674 5 %RANDOM
Rwork0.1236 ---
obs0.1256 69085 97.02 %-
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: 120.3 Å2 / Biso mean: 37.709 Å2 / Biso min: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å2-0 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.62→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 24 510 3635
Biso mean--34.9 48.85 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193334
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9634554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46324.581155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88315566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2091518
X-RAY DIFFRACTIONr_chiral_restr0.120.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212580
X-RAY DIFFRACTIONr_rigid_bond_restr3.81733333
X-RAY DIFFRACTIONr_sphericity_free23.041596
X-RAY DIFFRACTIONr_sphericity_bonded12.52753653
LS refinement shellResolution: 1.62→1.66 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.172 231 -
Rwork0.124 3911 -
obs--76.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29710.0561-0.29610.0228-0.09530.423-0.0227-0.0203-0.01020.0148-0.0357-0.0168-0.04810.10290.05840.0765-0.016-0.05830.07010.01610.046537.187742.754727.9031
20.1084-0.16160.04340.3342-0.03960.3751-0.074-0.0094-0.03750.1040.06380.0478-0.0191-0.04270.01020.06680.01910.02890.05340.00150.0316.167535.273136.3386
30.24690.07880.08990.54350.20950.4653-0.1097-0.043-0.00070.08230.0105-0.0363-0.04980.05450.09920.11620.0364-0.0430.03110.00530.04836.657844.914945.4997
400000000000000-00.0244000.024400.0244000
500000000000000-00.0244000.024400.0244000
600000000000000-00.0244000.024400.0244000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 66
2X-RAY DIFFRACTION2A67 - 287
3X-RAY DIFFRACTION3A288 - 397

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