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- PDB-9gh9: A novel aminotransferase from Streptomyces sp. -

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Basic information

Entry
Database: PDB / ID: 9gh9
TitleA novel aminotransferase from Streptomyces sp.
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
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase family protein
Similarity search - Component
Biological speciesStreptomyces sp. BV333 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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
DepositionAug 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,61919
Polymers103,0922
Non-polymers1,52717
Water21,0601169
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14190 Å2
ΔGint-87 kcal/mol
Surface area27460 Å2
Unit cell
Length a, b, c (Å)78.32, 176.1, 60.85
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-652-

HOH

21A-734-

HOH

31A-1193-

HOH

41A-1209-

HOH

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

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 asym-ID: A / Label asym-ID: A / Auth seq-ID: 9 - 461 / Label seq-ID: 9 - 461

Dom-ID
1
2

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

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Components

#1: Protein Aspartate aminotransferase family protein


Mass: 51545.812 Da / Num. of mol.: 2
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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 292.15 K / Method: microbatch / pH: 6.5
Details: 0.2 M Potassium thiocyanate 0.1 M Bis-Tris propane 6.5 20 % w/v PEG 3350 1 mM PLP
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.49→60.85 Å / Num. obs: 112260 / % possible obs: 81.38 % / Observed criterion σ(F): 0 / Redundancy: 10.33 % / Biso Wilson estimate: 11.89 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.012 / Rrim(I) all: 0.043 / Net I/σ(I): 31.8
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 724 / CC1/2: 0.9 / Rpim(I) all: 0.188 / Rrim(I) all: 0.269 / % possible all: 10.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia23.9data reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→60.85 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.053 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1585 5565 4.957 %
Rwork0.1285 106694 -
all0.13 --
obs-112259 81.383 %
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: 16.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.091 Å2-0 Å2-0 Å2
2---0.904 Å20 Å2
3---0.813 Å2
Refinement stepCycle: LAST / Resolution: 1.49→60.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7094 0 95 1169 8358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0127649
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167042
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.8310440
X-RAY DIFFRACTIONr_angle_other_deg0.6551.74716247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.92554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.563101172
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.83810362
X-RAY DIFFRACTIONr_chiral_restr0.10.21117
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021812
X-RAY DIFFRACTIONr_nbd_refined0.2270.21640
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.26770
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23780
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2892
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2970.257
X-RAY DIFFRACTIONr_nbd_other0.2650.2226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1260.21
X-RAY DIFFRACTIONr_mcbond_it1.4571.4133724
X-RAY DIFFRACTIONr_mcbond_other1.4571.4133724
X-RAY DIFFRACTIONr_mcangle_it2.1572.5314678
X-RAY DIFFRACTIONr_mcangle_other2.1572.5334679
X-RAY DIFFRACTIONr_scbond_it2.4511.6813925
X-RAY DIFFRACTIONr_scbond_other2.4231.6783914
X-RAY DIFFRACTIONr_scangle_it3.6442.9675731
X-RAY DIFFRACTIONr_scangle_other3.6112.965714
X-RAY DIFFRACTIONr_lrange_it5.75120.6269318
X-RAY DIFFRACTIONr_lrange_other5.75120.6269319
X-RAY DIFFRACTIONr_ncsr_local_group_10.0760.0515514
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.076330.05009
12AX-RAY DIFFRACTIONLocal ncs0.076330.05009
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
1.49-1.5290.262700.23213800.234101190.9610.96914.32950.22
1.529-1.5710.2161820.18931730.19198180.970.9834.17190.171
1.571-1.6160.2232520.16547570.16895390.9730.98552.51070.147
1.616-1.6660.213010.15358830.15693060.9730.98666.45180.137
1.666-1.7210.1673700.13768890.13989870.9830.98980.77220.124
1.721-1.7810.1794150.12775440.1387670.9790.9990.78360.116
1.781-1.8480.1723960.12877160.1384350.9820.9996.17070.119
1.848-1.9230.1594020.11977040.12181400.9840.99199.58230.112
1.923-2.0090.1553400.12374590.12477990.9850.9911000.118
2.009-2.1070.1573640.12671160.12774800.9850.9911000.123
2.107-2.2210.1513520.12467360.12570880.9860.9911000.123
2.221-2.3550.1473590.11163990.11367580.9870.9931000.113
2.355-2.5170.1363100.10960560.11163660.9890.9931000.113
2.517-2.7190.1442900.11656310.11859210.9870.9921000.123
2.719-2.9780.1672590.12252180.12454770.9820.9911000.131
2.978-3.3280.1542640.1347220.13149860.9850.991000.143
3.328-3.8410.1452400.12541990.12644390.9880.9911000.145
3.841-4.70.141780.11836030.11937810.9890.9921000.144
4.7-6.6270.171420.15728300.15729720.9860.991000.188
6.627-60.850.209790.1916790.19117590.9720.97599.94310.235

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