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- PDB-9ds0: Crystal structure of sphA with MeVGQ -

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Basic information

Entry
Database: PDB / ID: 9ds0
TitleCrystal structure of sphA with MeVGQ
Components8-amino-7-oxononanoate synthase
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent
Function / homology
Function and homology information


Transferases / biotin biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / 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
: / ACETIC ACID / : / DI(HYDROXYETHYL)ETHER / Aminotransferase, putative
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsXi, W. / Hai, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM151205 United States
CitationJournal: To Be Published
Title: strucutre of PLP-dependent enzyme sphA with MeVGQ
Authors: Xi, W. / Hai, Y. / Chai, W. / He, X.
History
DepositionSep 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 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: 8-amino-7-oxononanoate synthase
B: 8-amino-7-oxononanoate synthase
C: 8-amino-7-oxononanoate synthase
D: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,68920
Polymers214,5394
Non-polymers2,14916
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-31 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.348, 88.752, 91.596
Angle α, β, γ (deg.)64.224, 86.930, 90.009
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
8-amino-7-oxononanoate synthase


Mass: 53634.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_3G14690 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WYY5, 8-amino-7-oxononanoate synthase

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Non-polymers , 9 types, 312 molecules

#2: Chemical
ChemComp-A1BDC / (2E,3E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}pent-3-enoic acid


Mass: 344.257 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H17N2O7P
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: K
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 4% (v/v) 2-propanol, 0.1 M Bis-Tris propane (pH 9.0), 20% (w/v) polyethyleneglycol monomethyl ether 5000
PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 99896 / % possible obs: 88.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 30.98 Å2 / CC1/2: 0.979 / Net I/σ(I): 13.66
Reflection shellResolution: 2.14→2.17 Å / Num. unique obs: 99896 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→45.55 Å / SU ML: 0.2604 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.9898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 5024 5.03 %
Rwork0.2045 94803 -
obs0.207 99827 87.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.11 Å2
Refinement stepCycle: LAST / Resolution: 2.14→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14234 0 136 296 14666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007414668
X-RAY DIFFRACTIONf_angle_d0.913219894
X-RAY DIFFRACTIONf_chiral_restr0.05242257
X-RAY DIFFRACTIONf_plane_restr0.00732565
X-RAY DIFFRACTIONf_dihedral_angle_d15.01925302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.160.27251160.22332008X-RAY DIFFRACTION56.5
2.16-2.190.25611320.21852738X-RAY DIFFRACTION75.51
2.19-2.210.27241580.2223092X-RAY DIFFRACTION86.02
2.21-2.240.2891740.2123264X-RAY DIFFRACTION90.78
2.24-2.270.2711870.20933237X-RAY DIFFRACTION90.75
2.27-2.30.30711970.19963248X-RAY DIFFRACTION90.47
2.3-2.330.23672470.20253242X-RAY DIFFRACTION90.48
2.33-2.370.28551630.20523192X-RAY DIFFRACTION90.63
2.37-2.410.2751840.20313257X-RAY DIFFRACTION89.82
2.41-2.440.27781640.20513218X-RAY DIFFRACTION89.59
2.44-2.490.28491700.20523276X-RAY DIFFRACTION90.16
2.49-2.530.29771700.21653211X-RAY DIFFRACTION89.71
2.53-2.580.32561520.22513226X-RAY DIFFRACTION89.6
2.58-2.630.32111850.22543188X-RAY DIFFRACTION89.45
2.63-2.690.26741490.22023215X-RAY DIFFRACTION87.88
2.69-2.750.29471570.21362982X-RAY DIFFRACTION84.16
2.75-2.820.29841450.22342789X-RAY DIFFRACTION77.21
2.82-2.90.28531630.22813230X-RAY DIFFRACTION89.57
2.9-2.980.27161920.22063370X-RAY DIFFRACTION93.47
2.98-3.080.27471800.22483361X-RAY DIFFRACTION92.87
3.08-3.190.25461450.21633333X-RAY DIFFRACTION92.8
3.19-3.320.27231560.21273318X-RAY DIFFRACTION91.61
3.32-3.470.28231690.20843282X-RAY DIFFRACTION91.03
3.47-3.650.21991560.20613298X-RAY DIFFRACTION91.01
3.65-3.880.261680.19713138X-RAY DIFFRACTION87.41
3.88-4.180.2271530.19432812X-RAY DIFFRACTION78.31
4.18-4.60.21651510.18053423X-RAY DIFFRACTION94.03
4.6-5.260.22721490.19263362X-RAY DIFFRACTION93.3
5.27-6.630.23922170.21473250X-RAY DIFFRACTION91.28
6.63-45.550.19961750.1733243X-RAY DIFFRACTION90.14
Refinement TLS params.Method: refined / Origin x: 9.00954582413 Å / Origin y: -12.1875693567 Å / Origin z: 9.57771873056 Å
111213212223313233
T0.10804153819 Å20.00207997477602 Å20.00764070291783 Å2-0.0925733881503 Å20.00628077769212 Å2--0.078271942457 Å2
L0.315999634819 °20.0181134187124 °20.0499419265222 °2-0.0748072214377 °20.00566151323091 °2--0.0480811035052 °2
S0.0161365724188 Å °-0.00209921317536 Å °0.0108909408198 Å °-0.00460073382486 Å °-0.0157667151311 Å °0.012909627132 Å °-0.00307053435007 Å °0.0125966727252 Å °0 Å °
Refinement TLS groupSelection details: all

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