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

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Basic information

Entry
Database: PDB / ID: 6zvg
TitlePsychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 cocrystalized with substrate analog - L-indole-3-lactic acid
ComponentsAminotransferase
KeywordsTRANSFERASE / psychrophilic / aminotranasferase / cold-adapted / enzyme / complex / indole-3-lactic 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
3-(INDOL-3-YL) LACTATE / NITRATE ION / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesPsychrobacter sp. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 Å
AuthorsRum, J. / Rutkiewicz, M. / Pruska, A. / Bujacz, A. / 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 24, 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 / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,39315
Polymers176,7974
Non-polymers1,59611
Water2,936163
1
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2719
Polymers88,3982
Non-polymers8727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1226
Polymers88,3982
Non-polymers7244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.267, 82.286, 98.208
Angle α, β, γ (deg.)90.000, 106.420, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEILEILEAA5 - 355 - 35
211ILEILEILEILECC5 - 355 - 35
121TYRTYRALAALAAA37 - 21337 - 213
221TYRTYRALAALACC37 - 21337 - 213
131GLNGLNASPASPAA215 - 398215 - 398
231GLNGLNASPASPCC215 - 398215 - 398
112ASPASPILEILEBB11 - 3511 - 35
212ASPASPILEILEDD11 - 3511 - 35
122TYRTYRILEILEBB37 - 20737 - 207
222TYRTYRILEILEDD37 - 20737 - 207
132GLNGLNVALVALBB215 - 279215 - 279
232GLNGLNVALVALDD215 - 279215 - 279
142SERSERASPASPBB284 - 398284 - 398
242SERSERASPASPDD284 - 398284 - 398

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.889001, 0.005724, -0.45787), (-0.004572, -0.999983, -0.003623), (-0.457883, -0.001127, 0.889012)162.36702, 100.24147, 39.52943

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aminotransferase


Mass: 44199.203 Da / Num. of mol.: 4
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, 174 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-3IL / 3-(INDOL-3-YL) LACTATE / (2S)-2-HYDROXY-3-(1H-INDOL-3-YL)PROPANOIC ACID


Mass: 205.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 35.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M MgNO3, 20% PEG 3350, HEPES pH 7.5,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 29, 2019 / 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: 2.59→47.1 Å / Num. obs: 41474 / % possible obs: 98.3 % / Redundancy: 6.764 % / Biso Wilson estimate: 66.409 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.142 / Χ2: 0.925 / Net I/σ(I): 10.37 / Num. measured all: 280530
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
2.59-2.756.6741.4291.1642499673063680.5821.54694.6
2.75-2.946.9090.852.1143885636863520.7890.91899.7
2.94-3.186.5940.5863.138833596258890.8630.63698.8
3.18-3.487.0090.36.2437980545054190.9650.32499.4
3.48-3.896.5880.16410.5432303497049030.9880.17898.7
3.89-4.487.0040.08518.4930396437143400.9970.09299.3
4.48-5.486.7040.0722.4824645372836760.9960.07698.6
5.48-7.696.6620.05627.0819088290528650.9970.06198.6
7.69-47.16.5590.04239.0810901170316620.9980.04597.6

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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: 2.59→47.1 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 35.864 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 2074 5 %RANDOM
Rwork0.1908 ---
obs0.1936 39400 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.33 Å2 / Biso mean: 79.24 Å2 / Biso min: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å2-0 Å2-1.1 Å2
2--0.2 Å2-0 Å2
3---2.48 Å2
Refinement stepCycle: final / Resolution: 2.59→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12228 0 101 163 12492
Biso mean--72.07 56.1 -
Num. residues----1572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912610
X-RAY DIFFRACTIONr_angle_refined_deg1.341.92417074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94451568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22724.441572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.481152084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9021570
X-RAY DIFFRACTIONr_chiral_restr0.090.21862
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219612
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A30382.91
2B29002.71
LS refinement shellResolution: 2.595→2.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 137 -
Rwork0.349 2604 -
all-2741 -
obs--88.85 %
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)
13.32-0.9480.85522.0536-0.75071.90130.1715-0.3155-1.1969-0.02650.03160.59380.6344-0.6284-0.20310.3457-0.1410.02440.3240.05340.489647.787232.608177.2634
23.1059-0.72310.02793.0950.80812.32180.20180.672-0.5978-0.5577-0.1833-0.14110.17460.1396-0.01850.24670.05320.06910.1579-0.13070.168960.971229.340957.5794
31.0578-0.4120.17774.9023-0.6552.04340.0491-0.1228-0.89320.1668-0.07260.22960.6926-0.41940.02350.3235-0.10440.01860.1630.07910.770556.65416.992478.6163
41.91881.231-0.34325.7802-2.08661.7498-0.03880.25560.2796-0.44380.0311-0.1555-0.07240.28090.00770.138-0.01150.02980.1767-0.00490.116952.901358.755970.697
53.3692-0.40690.63893.5513-0.64522.24180.0560.4104-0.0956-0.63950.02920.7240.0925-0.437-0.08530.1669-0.0013-0.10980.1761-0.00720.157432.153249.356960.4558
62.43870.1422-0.28363.5509-0.87122.92940.15570.43460.6839-0.22060.10670.1842-0.8129-0.2515-0.26230.29360.07770.08270.16280.07650.254143.555571.136564.2414
71.9759-0.32520.14123.22420.69181.7243-0.0946-0.29960.61820.2619-0.0135-0.7501-0.54330.55320.1080.375-0.1049-0.14040.36670.01540.356884.805166.9786.1955
82.1909-0.42580.43113.1792-1.19092.7503-0.02470.57160.4348-0.476-0.2009-0.3159-0.20990.35220.22560.1918-0.04240.04890.18510.10960.125282.189470.301762.7303
91.512-0.5627-0.022.84810.6662.7482-0.21-0.21370.8146-0.0427-0.0786-0.0489-0.95320.3530.28860.406-0.0519-0.19570.1636-0.07730.489576.469182.5983.4541
101.3258-0.1342-0.13315.89592.6451.922-0.0210.3115-0.2901-0.3350.0293-0.06120.1447-0.0448-0.00830.18870.0173-0.00370.21330.0170.162683.291840.691177.9479
113.3838-0.7334-0.20512.48190.26541.41730.01280.20610.1117-0.1138-0.0938-0.80260.03140.60210.0810.10220.04080.03420.29970.08820.2905106.363650.377378.5291
121.47770.49990.42783.28540.25523.395-0.12140.2215-0.5443-0.09430.2742-0.39341.12140.5892-0.15280.42710.14630.03610.2532-0.04260.260394.760128.447476.5863
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
7X-RAY DIFFRACTION7C1 - 66
8X-RAY DIFFRACTION8C67 - 287
9X-RAY DIFFRACTION9C288 - 398
10X-RAY DIFFRACTION10D1 - 66
11X-RAY DIFFRACTION11D67 - 287
12X-RAY DIFFRACTION12D288 - 398

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