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- PDB-9qc2: BV333 aminotransferase from Streptomyces sp. mutant W89A -

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Basic information

Entry
Database: PDB / ID: 9qc2
TitleBV333 aminotransferase from Streptomyces sp. mutant W89A
ComponentsAspartate aminotransferase family protein
KeywordsTRANSFERASE
Function / homology
Function and homology information


biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-1PG / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Aspartate aminotransferase family protein
Similarity search - Component
Biological speciesStreptomyces sp. BV333 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsDe Rose, S.A. / Isupov, M.N. / Patti, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2025
Title: Functional and structural insights into a thermostable (S)-selective amine transaminase and its improved substrate scope by protein engineering.
Authors: Patti, S. / De Rose, S.A. / Isupov, M.N. / Magrini Alunno, I. / Riva, S. / Ferrandi, E.E. / Littlechild, J.A. / Monti, D.
History
DepositionMar 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate aminotransferase family protein
B: Aspartate aminotransferase family protein
C: Aspartate aminotransferase family protein
D: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,097173
Polymers203,5404
Non-polymers11,557169
Water22,8791270
1
A: Aspartate aminotransferase family protein
B: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,12292
Polymers101,7702
Non-polymers6,35290
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24870 Å2
ΔGint-90 kcal/mol
Surface area29400 Å2
MethodPISA
2
C: Aspartate aminotransferase family protein
D: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,97581
Polymers101,7702
Non-polymers5,20579
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24930 Å2
ΔGint-59 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.825, 90.242, 99.446
Angle α, β, γ (deg.)66.943, 73.259, 69.644
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

End auth comp-ID: HIS / End label comp-ID: HIS

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERAA8 - 4607 - 460
211SERSERBB8 - 4607 - 460
322VALVALAA7 - 4606 - 460
422VALVALCC7 - 4606 - 460
533VALVALAA7 - 4596 - 459
633VALVALDD7 - 4596 - 459
744SERSERBB8 - 4607 - 460
844SERSERCC8 - 4607 - 460
955SERSERBB8 - 4597 - 459
1055SERSERDD8 - 4597 - 459
1166VALVALCC7 - 4596 - 459
1266VALVALDD7 - 4596 - 459

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aspartate aminotransferase family protein


Mass: 50885.047 Da / Num. of mol.: 4 / Mutation: W89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. BV333 (bacteria) / Gene: OIM89_06295 / Plasmid: pETITE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AA46ZEV9

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Non-polymers , 9 types, 1439 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 93 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#8: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1270 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 292.15 K / Method: microbatch / Details: Morpheus Fusion Screen A7 / Temp details: Memmert incubator

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Data collection

DiffractionMean temperature: 113.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.852 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.852 Å / Relative weight: 1
ReflectionResolution: 1.24→80.02 Å / Num. obs: 515140 / % possible obs: 94.84 % / Redundancy: 3.6 % / CC1/2: 1 / Rrim(I) all: 0.11 / Net I/σ(I): 13.7
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 506909 / CC1/2: 1 / Rrim(I) all: 2.822 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALS3.7data reduction
DIALS3.7data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→80.02 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.084 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.045 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1954 2004 0.395 %
Rwork0.171 504905 -
all0.171 --
obs-506909 94.85 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.017 Å2
Baniso -1Baniso -2Baniso -3
1-2.051 Å21.462 Å20.489 Å2
2--0.232 Å20.521 Å2
3----0.534 Å2
Refinement stepCycle: LAST / Resolution: 1.24→80.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14259 0 726 1270 16255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01216001
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.82821639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24752064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.879594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7102457
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.69910737
X-RAY DIFFRACTIONr_chiral_restr0.1240.22326
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212192
X-RAY DIFFRACTIONr_nbd_refined0.2330.28813
X-RAY DIFFRACTIONr_nbtor_refined0.3220.210616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21427
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.225
X-RAY DIFFRACTIONr_mcbond_it2.2821.987563
X-RAY DIFFRACTIONr_mcangle_it3.4313.5439513
X-RAY DIFFRACTIONr_scbond_it3.6022.4768438
X-RAY DIFFRACTIONr_scangle_it5.0574.2512004
X-RAY DIFFRACTIONr_lrange_it7.84825.73825989
X-RAY DIFFRACTIONr_ncsr_local_group_10.0690.0515893
X-RAY DIFFRACTIONr_ncsr_local_group_20.0730.0515933
X-RAY DIFFRACTIONr_ncsr_local_group_30.0710.0515951
X-RAY DIFFRACTIONr_ncsr_local_group_40.0750.0515879
X-RAY DIFFRACTIONr_ncsr_local_group_50.070.0515898
X-RAY DIFFRACTIONr_ncsr_local_group_60.0710.0515941
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.069470.05009
12BX-RAY DIFFRACTIONLocal ncs0.069470.05009
23AX-RAY DIFFRACTIONLocal ncs0.073330.05009
24CX-RAY DIFFRACTIONLocal ncs0.073330.05009
35AX-RAY DIFFRACTIONLocal ncs0.070590.05009
36DX-RAY DIFFRACTIONLocal ncs0.070590.05009
47BX-RAY DIFFRACTIONLocal ncs0.074780.05009
48CX-RAY DIFFRACTIONLocal ncs0.074780.05009
59BX-RAY DIFFRACTIONLocal ncs0.070030.05009
510DX-RAY DIFFRACTIONLocal ncs0.070030.05009
611CX-RAY DIFFRACTIONLocal ncs0.071170.05009
612DX-RAY DIFFRACTIONLocal ncs0.071170.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.2720.3981340.38833523X-RAY DIFFRACTION85.0354
1.272-1.3070.3981260.36833728X-RAY DIFFRACTION87.8184
1.307-1.3450.3681310.35133876X-RAY DIFFRACTION90.9302
1.345-1.3860.3381420.3334246X-RAY DIFFRACTION94.3429
1.386-1.4320.291290.30933409X-RAY DIFFRACTION95.2162
1.432-1.4820.2731380.28632495X-RAY DIFFRACTION95.4907
1.482-1.5380.251220.2631380X-RAY DIFFRACTION95.8177
1.538-1.6010.2541100.23830347X-RAY DIFFRACTION96.1122
1.601-1.6720.2341280.21629153X-RAY DIFFRACTION96.4682
1.672-1.7530.2111190.19327926X-RAY DIFFRACTION96.7236
1.753-1.8480.181300.17326707X-RAY DIFFRACTION97.0702
1.848-1.960.1831000.1625303X-RAY DIFFRACTION97.3295
1.96-2.0960.178970.15223874X-RAY DIFFRACTION97.6575
2.096-2.2630.169900.14322300X-RAY DIFFRACTION97.9269
2.263-2.4790.196890.14420552X-RAY DIFFRACTION98.2484
2.479-2.7710.163660.1418664X-RAY DIFFRACTION98.5323
2.771-3.1990.142600.13816505X-RAY DIFFRACTION98.8483
3.199-3.9170.158430.12213963X-RAY DIFFRACTION99.1365
3.917-5.5330.144270.10910833X-RAY DIFFRACTION99.405
5.533-80.020.168230.1785974X-RAY DIFFRACTION99.6345

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