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- PDB-5jay: Crystal Structure of an 8-amino-7-oxononanoate Synthase from Burk... -

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Basic information

Entry
Database: PDB / ID: 5jay
TitleCrystal Structure of an 8-amino-7-oxononanoate Synthase from Burkholderia xenovorans
Components8-amino-7-oxononanoate synthase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of an 8-amino-7-oxononanoate Synthase from Burkholderia xenovorans
Authors: Dranow, D.M. / Conrady, D.G. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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


Theoretical massNumber of molelcules
Total (without water)84,8382
Polymers84,8382
Non-polymers00
Water9,818545
1
A: 8-amino-7-oxononanoate synthase


Theoretical massNumber of molelcules
Total (without water)42,4191
Polymers42,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 8-amino-7-oxononanoate synthase


Theoretical massNumber of molelcules
Total (without water)42,4191
Polymers42,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 8-amino-7-oxononanoate synthase
B: 8-amino-7-oxononanoate synthase

A: 8-amino-7-oxononanoate synthase
B: 8-amino-7-oxononanoate synthase


Theoretical massNumber of molelcules
Total (without water)169,6764
Polymers169,6764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area13070 Å2
ΔGint-99 kcal/mol
Surface area52190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.870, 63.200, 65.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-647-

HOH

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Components

#1: Protein 8-amino-7-oxononanoate synthase / / AONS / 7-keto-8-amino-pelargonic acid synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase


Mass: 42418.996 Da / Num. of mol.: 2 / Fragment: BuxeA.00096.b.B1 / Mutation: G241D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: bioF, Bxeno_A0198, Bxe_A4264 / Plasmid: BuxeA.00096.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q146K3, 8-amino-7-oxononanoate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: BuxeA.00096.b.B1.PS37838 at 22.85 mg/ml was mixed 1:1 with MCSG1(e9) 0.2 M calcium chloride, 20% (w/v) PEG-3350, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 72463 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 22.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 22.99
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.80.5493.111100
1.8-1.840.4184.091100
1.84-1.90.3225.341100
1.9-1.960.2437.171100
1.96-2.020.1819.421100
2.02-2.090.14411.81100
2.09-2.170.11414.871100
2.17-2.260.09317.961100
2.26-2.360.07820.771100
2.36-2.470.06724.081100
2.47-2.610.05628.21100
2.61-2.770.04932.041100
2.77-2.960.04236.41100
2.96-3.20.03642.971100
3.2-3.50.0349.11100
3.5-3.910.02653.65199.9
3.91-4.520.02456.98199.9
4.52-5.530.02357.61199.9
5.53-7.830.02356.71199.9
7.830.02255.46196.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G6W

2g6w


Resolution: 1.75→30.406 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.42
RfactorNum. reflection% reflection
Rfree0.2039 1912 2.64 %
Rwork0.1714 --
obs0.1722 72442 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.91 Å2 / Biso mean: 29.7996 Å2 / Biso min: 10.47 Å2
Refinement stepCycle: final / Resolution: 1.75→30.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5378 0 0 555 5933
Biso mean---33.69 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065537
X-RAY DIFFRACTIONf_angle_d0.7367567
X-RAY DIFFRACTIONf_chiral_restr0.052898
X-RAY DIFFRACTIONf_plane_restr0.005998
X-RAY DIFFRACTIONf_dihedral_angle_d12.2523296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7499-1.79370.27921200.22349425062100
1.7937-1.84220.2771390.214849845123100
1.8422-1.89640.22361520.205449525104100
1.8964-1.95760.26441370.184349855122100
1.9576-2.02750.22181440.173549905134100
2.0275-2.10870.23051180.177350315149100
2.1087-2.20460.23131390.174549705109100
2.2046-2.32080.19441460.165650085154100
2.3208-2.46620.20341360.172750055141100
2.4662-2.65650.21461420.172650465188100
2.6565-2.92360.22681210.182150745195100
2.9236-3.34620.20271320.17350865218100
3.3462-4.21410.17231390.154751415280100
4.2141-30.41050.17881470.16095316546399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3555-0.2406-1.69620.63740.86332.5514-0.1479-0.1458-0.22730.1385-0.0502-0.09080.42820.0520.19440.24960.0098-0.02610.21440.02490.2347141.1086-10.86310.2877
21.12620.01550.2331.28990.09463.06960.08420.09460.1228-0.1058-0.0361-0.1497-0.03380.6681-0.01020.18250.00090.02510.2943-0.03530.1718152.843512.864518.0518
32.2839-0.48030.52053.62690.22962.4750.1541-0.0174-0.3506-0.0042-0.0223-0.18960.4856-0.0785-0.0840.2371-0.056-0.02550.1862-0.02030.1742141.3037-8.818228.8848
41.6322-0.31982.63230.7247-0.54964.2432-0.0939-0.88891.1086-0.015-0.6033-0.3365-0.2457-0.17260.63850.4115-0.11630.11670.5858-0.06250.5871152.364829.36391.4189
51.33010.2956-1.33971.1074-0.29952.0561-0.0401-0.1526-0.19270.1573-0.08210.0290.10030.00150.12910.1501-0.0004-0.01820.17580.01450.1994134.19024.4152-0.979
62.43780.1335-0.09811.2018-0.21490.9362-0.066-0.1839-0.09990.0550.0045-0.09160.05190.06590.06040.14490.01350.00020.1247-0.02310.1389156.6197-1.9974-10.1914
72.1161-1.2601-0.25722.6011-0.52961.234-0.1591-0.2153-0.2780.19230.08080.16940.07280.00020.08640.15510.01130.00090.12340.02140.1858147.0568-6.0432-5.1362
82.6705-0.7992-1.61792.82861.10351.153-0.0687-0.3999-0.08440.18780.05430.0522-0.0216-0.0721-0.0510.1538-0.01870.02480.16780.03080.1725135.08032.6271-1.7066
93.41680.9658-1.54273.8432-1.16052.94620.09350.21770.0316-0.22490.0485-0.0817-0.1412-0.1383-0.16710.16110.0427-0.01470.1333-0.00740.1219140.610315.6631-22.7583
100.493-0.0122-0.44111.34790.25630.67610.0949-0.0570.46960.07530.1272-0.657-0.26470.3363-0.03450.2656-0.0431-0.0250.2339-0.10730.4988155.850924.9819-14.7491
113.72330.51851.08561.52230.53333.00730.02580.19040.4167-0.12190.1331-0.4144-0.4565-0.0274-0.13730.23580.03650.04690.1236-0.01720.2707145.121425.4416-18.6609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 55 )A-2 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 291 )A56 - 291
3X-RAY DIFFRACTION3chain 'A' and (resid 292 through 389 )A292 - 389
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 42 )B3 - 42
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 97 )B43 - 97
6X-RAY DIFFRACTION6chain 'B' and (resid 98 through 227 )B98 - 227
7X-RAY DIFFRACTION7chain 'B' and (resid 228 through 264 )B228 - 264
8X-RAY DIFFRACTION8chain 'B' and (resid 265 through 291 )B265 - 291
9X-RAY DIFFRACTION9chain 'B' and (resid 292 through 313 )B292 - 313
10X-RAY DIFFRACTION10chain 'B' and (resid 314 through 363 )B314 - 363
11X-RAY DIFFRACTION11chain 'B' and (resid 364 through 388 )B364 - 388

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