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- PDB-9gnf: A novel aminotransferase from Streptomyces sp. Gabaculine complex -

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Basic information

Entry
Database: PDB / ID: 9gnf
TitleA novel aminotransferase from Streptomyces sp. Gabaculine complex
ComponentsStreptomyces aminotransferase
KeywordsTRANSFERASE / Aminotransferase / SBV333
Function / homologyDI(HYDROXYETHYL)ETHER / 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID
Function and homology information
Biological speciesStreptomyces sp. BV333 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsDe Rose, S.A. / Isupov, M.N. / Patti, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: To be Published
Title: a novel aminotransferase from Streptomyces sp.
Authors: De Rose, S.A. / Isupov, M.N. / Patti, S.
History
DepositionSep 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptomyces aminotransferase
B: Streptomyces aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,56923
Polymers102,6352
Non-polymers1,93321
Water19,4741081
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint5 kcal/mol
Surface area36320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.463, 177.253, 112.359
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-871-

HOH

21A-989-

HOH

31A-1043-

HOH

41B-613-

HOH

51B-876-

HOH

61B-1106-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 9 - 461 / Label seq-ID: 9 - 461

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Streptomyces aminotransferase


Mass: 51317.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. BV333 (bacteria) / Plasmid: pETITE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: aspartate transaminase

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Non-polymers , 6 types, 1102 molecules

#2: Chemical ChemComp-PXG / 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID


Mass: 368.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N2O7P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1081 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 292.15 K / Method: microbatch / pH: 6.5
Details: 0.2 M Potassium thiocynate 0.1 M Bis_tris propane 6.5 20% w/v PEG 3350 1 mM PLP

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Data collection

DiffractionMean temperature: 113.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.31→69.59 Å / Num. obs: 237241 / % possible obs: 99.3 % / Redundancy: 5 % / CC1/2: 1 / Net I/σ(I): 16.4
Reflection shellResolution: 1.31→1.344 Å / Redundancy: 13.3 % / Num. unique obs: 15399 / CC1/2: 1 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
xia2data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→69.585 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.341 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.047 / ESU R Free: 0.049 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.185 11569 4.88 %
Rwork0.1646 225478 -
all0.166 --
obs-237047 99.303 %
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: 24.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.007 Å20 Å2-0 Å2
2---1.219 Å2-0 Å2
3---1.227 Å2
Refinement stepCycle: LAST / Resolution: 1.31→69.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7090 0 123 1081 8294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0127894
X-RAY DIFFRACTIONr_angle_refined_deg2.0141.84110809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30551048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.599553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88101266
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.22810384
X-RAY DIFFRACTIONr_chiral_restr0.1290.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026240
X-RAY DIFFRACTIONr_nbd_refined0.2230.24013
X-RAY DIFFRACTIONr_nbtor_refined0.3230.25291
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2906
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.2551
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.2150
X-RAY DIFFRACTIONr_mcbond_it2.0692.0273790
X-RAY DIFFRACTIONr_mcangle_it3.0493.6364773
X-RAY DIFFRACTIONr_scbond_it3.1592.3444104
X-RAY DIFFRACTIONr_scangle_it4.4884.1575963
X-RAY DIFFRACTIONr_lrange_it6.89529.67313192
X-RAY DIFFRACTIONr_ncsr_local_group_10.0830.0515783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.083070.05009
12BX-RAY DIFFRACTIONLocal ncs0.083070.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.31-1.3440.3998000.375153990.376175510.8730.88192.29670.382
1.344-1.3810.3357700.343160280.342170880.8470.85198.30290.344
1.381-1.4210.3238350.315157420.316165840.9070.90799.95780.314
1.421-1.4650.2748700.276153100.276161800.930.9291000.269
1.465-1.5130.2386950.239149400.239156350.9550.9541000.225
1.513-1.5660.2356960.218144950.218151920.9610.96699.99340.196
1.566-1.6250.2197300.201138860.202146170.9680.97399.99320.176
1.625-1.6910.2017080.181133810.182140890.9740.9791000.153
1.691-1.7660.2136870.172128680.174135550.9710.9811000.144
1.766-1.8520.1936400.162122920.164129330.9760.98399.99230.136
1.852-1.9520.1916220.164116630.165122850.9760.9831000.139
1.952-2.0710.1985460.161111240.163116700.9770.9851000.143
2.071-2.2140.1825290.158104940.159110230.9820.9871000.142
2.214-2.3910.1824670.15497590.156102260.980.9871000.137
2.391-2.6190.1684660.14389800.14494460.9820.9881000.128
2.619-2.9270.1673590.13982000.1485590.9830.9881000.127
2.927-3.3790.1524300.13471630.13575930.9850.9891000.127
3.379-4.1360.1443080.11661240.11864320.9880.9921000.115
4.136-5.8390.1242710.11548000.11550710.9920.9931000.121
5.839-69.5850.2231370.20627730.20729100.9780.9711000.215

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