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- PDB-9dri: Crystal structure of SphA in complex with VGQ intermedaite -

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Basic information

Entry
Database: PDB / ID: 9dri
TitleCrystal structure of SphA in complex with VGQ intermedaite
Components8-amino-7-oxononanoate synthase
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent enzyme
Function / homology
Function and homology information


biotin biosynthetic process / 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
: / Aminotransferase class I/classII large domain-containing protein
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsXi, W. / Hai, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151205 United States
CitationJournal: To Be Published
Title: Crystal structure of SphA in complex with VGQ intermedaite
Authors: Xi, W. / Hai, Y.
History
DepositionSep 25, 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

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Assembly

Deposited unit
B: 8-amino-7-oxononanoate synthase
C: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0525
Polymers107,2702
Non-polymers7833
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-33 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.200, 71.873, 90.531
Angle α, β, γ (deg.)90.000, 113.813, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 53634.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: KXV57_002439 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8H4HX52, 8-amino-7-oxononanoate synthase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-A1BC7 / (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}but-3-enoic acid


Mass: 330.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.73 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.85→35.94 Å / Num. obs: 78980 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Net I/σ(I): 39.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.712 / Num. unique obs: 3939 / CC1/2: 0.879 / Rpim(I) all: 0.29 / % possible all: 99.5

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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: 1.85→35.94 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.26
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2296 3936 4.99 %
Rwork0.194 74951 -
obs0.1958 78887 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.58 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7097 0 52 321 7470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00787298
X-RAY DIFFRACTIONf_angle_d0.869907
X-RAY DIFFRACTIONf_chiral_restr0.05381126
X-RAY DIFFRACTIONf_plane_restr0.00671273
X-RAY DIFFRACTIONf_dihedral_angle_d14.992635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.37461220.3212334X-RAY DIFFRACTION85.81
1.87-1.890.34941290.30682719X-RAY DIFFRACTION98.85
1.89-1.920.31741380.3192647X-RAY DIFFRACTION98.62
1.92-1.940.35361560.30982721X-RAY DIFFRACTION99.31
1.94-1.970.29331480.25422689X-RAY DIFFRACTION99.33
1.97-20.26731510.23042742X-RAY DIFFRACTION99.35
2-2.030.231460.22492684X-RAY DIFFRACTION99.3
2.03-2.070.27671160.23072743X-RAY DIFFRACTION99.03
2.07-2.10.30661540.24172692X-RAY DIFFRACTION99.41
2.1-2.140.25161400.22382687X-RAY DIFFRACTION99.23
2.14-2.180.26731480.22152716X-RAY DIFFRACTION99
2.18-2.230.27351340.21792746X-RAY DIFFRACTION98.94
2.23-2.270.27091390.24952607X-RAY DIFFRACTION96.69
2.27-2.330.2311540.20962675X-RAY DIFFRACTION98.23
2.33-2.390.20521200.20472704X-RAY DIFFRACTION97.95
2.39-2.450.24591530.1972634X-RAY DIFFRACTION96.77
2.45-2.520.2311250.20482474X-RAY DIFFRACTION90.81
2.52-2.60.20931310.20082634X-RAY DIFFRACTION95.67
2.6-2.70.24311640.21242727X-RAY DIFFRACTION99.9
2.7-2.80.26471630.20442694X-RAY DIFFRACTION99.65
2.8-2.930.27031620.21362713X-RAY DIFFRACTION99.38
2.93-3.090.22031240.20892759X-RAY DIFFRACTION99.38
3.09-3.280.25681450.20232728X-RAY DIFFRACTION99.1
3.28-3.530.26311180.19442711X-RAY DIFFRACTION98.43
3.53-3.890.20331510.17362675X-RAY DIFFRACTION97.05
3.89-4.450.18091320.15082655X-RAY DIFFRACTION94.67
4.45-5.60.17671240.1472616X-RAY DIFFRACTION94.19
5.6-35.940.17111490.14992825X-RAY DIFFRACTION99.1
Refinement TLS params.Method: refined / Origin x: 14.2738155038 Å / Origin y: -10.1381462422 Å / Origin z: 23.1275406288 Å
111213212223313233
T0.143115312594 Å2-0.0132487605893 Å2-0.0188610857823 Å2-0.137280897134 Å20.0194640170804 Å2--0.129518819898 Å2
L0.110409722891 °20.124078182774 °2-0.163746771885 °2-0.348221386385 °2-0.0675482416222 °2--0.0969817392944 °2
S-0.0688624255941 Å °-0.0362200216035 Å °0.0750491075546 Å °-0.119594506697 Å °0.0830198613867 Å °0.0151271140442 Å °0.0372061850676 Å °-0.0516963242343 Å °-1.92555065406E-11 Å °
Refinement TLS groupSelection details: all

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