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

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Basic information

Entry
Database: PDB / ID: 6zup
TitlePsychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 cocrystalized with substrate analog - L-(-)-3-phenyllactic acid
ComponentsAminotransferase
KeywordsTRANSFERASE / psychrophilic / aminotranasferase / cold-adapted / enzyme / complex / phenyllactic 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
ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID / NITRATE ION / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesPsychrobacter sp. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Aminotransferase
A: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,49711
Polymers88,3982
Non-polymers1,0999
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-54 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.390, 60.390, 81.940
Angle α, β, γ (deg.)90.000, 103.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Aminotransferase


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, 88 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-HFA / ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID


Type: L-peptide linking / Mass: 166.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.91 Å3/Da / Density % sol: 35.72 %
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: 2.49→79.84 Å / Num. obs: 23715 / % possible obs: 98.8 % / Redundancy: 3.35 % / Biso Wilson estimate: 65.53 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.123 / Χ2: 0.965 / Net I/σ(I): 8.29 / Num. measured all: 79436
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
2.49-2.643.2211.3560.8611992387137230.4181.62696.2
2.64-2.833.3070.8081.4611855359735850.6830.96799.7
2.83-3.053.5670.4992.5411926335733430.8530.58799.6
3.05-3.343.5110.2854.2810932312531140.9440.33699.6
3.34-3.733.3290.1467.69282280327880.9830.17599.5
3.73-4.313.1740.07413.77863249624770.9930.08999.2
4.31-5.263.4940.0520.527316211420940.9960.05999.1
5.26-7.43.1910.04322.045230166916390.9970.05298.2
7.4-79.843.1930.0333.8630409719520.9980.03698

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.9-1692refinement
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RKC

4rkc


Resolution: 2.5→79.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 38.538 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 967 4.1 %RANDOM
Rwork0.1989 ---
obs0.2007 22687 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.3 Å2 / Biso mean: 70.45 Å2 / Biso min: 39.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å2-0 Å20.11 Å2
2--1.19 Å20 Å2
3---1.24 Å2
Refinement stepCycle: final / Resolution: 2.5→79.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 72 79 6353
Biso mean--80.43 64.38 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196414
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.928677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17624.384292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.543151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3061536
X-RAY DIFFRACTIONr_chiral_restr0.0960.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214902
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 78 -
Rwork0.388 1653 -
all-1731 -
obs--99.71 %
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)
11.92470.32020.18740.73310.42380.2682-0.0496-0.110.2345-0.19340.01910.0771-0.08650.06930.03050.1719-0.02330.07010.2978-0.05350.222536.501611.950614.0697
21.56820.1390.22360.08250.08160.91370.0238-0.7583-0.2645-0.10030.0025-0.029-0.04980.0554-0.02630.1576-0.04250.01310.65360.09370.2343.8317-2.240331.5528
31.24420.4698-0.12161.20420.31480.52810.0136-0.23560.1066-0.04680.1014-0.1572-0.07290.2191-0.1150.0598-0.03420.03450.3507-0.14930.272752.955417.361320.0852
41.05970.7307-0.14580.5482-0.0690.0517-0.0316-0.1092-0.2675-0.1048-0.0873-0.1454-0.03690.01470.11880.1979-0.0680.02970.3429-0.00280.317826.3056-12.414211.1907
51.15210.0389-0.49950.78910.08580.43570.0193-0.20650.0389-0.0884-0.03020.0043-0.0469-0.08380.01080.07320.01120.00820.4163-0.01740.22910.60832.657320.7832
60.73930.5237-0.51792.0105-0.00650.5171-0.06880.13110.0224-0.0642-0.01410.15630.1327-0.14160.08290.1522-0.0698-0.00290.3377-0.01090.19839.2839-17.6517.0134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 66
2X-RAY DIFFRACTION2A67 - 287
3X-RAY DIFFRACTION3A288 - 398
4X-RAY DIFFRACTION4B1 - 66
5X-RAY DIFFRACTION5B67 - 287
6X-RAY DIFFRACTION6B288 - 398

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