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- PDB-6ed7: Crystal structure of 7,8-diaminopelargonic acid synthase bound to... -

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Basic information

Entry
Database: PDB / ID: 6ed7
TitleCrystal structure of 7,8-diaminopelargonic acid synthase bound to inhibitor MAC13772
Components7,8-diamino-pelargonic acid aminotransferase
KeywordsTRANSFERASE/ANTIBIOTIC / Inhibitor adduct complex / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
2-[(2-nitrophenyl)sulfanyl]acetohydrazide / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.43 Å
AuthorsBrown, C.M. / Zlitni, S. / Chan, J. / Brown, E.D. / Junop, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Crystal structure of 7,8-diaminopelargonic acid synthase bound to inhibitor MAC13772
Authors: Brown, C.M. / Zlitni, S. / Chan, J. / Brown, E.D. / Junop, M.S.
History
DepositionAug 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-diamino-pelargonic acid aminotransferase
B: 7,8-diamino-pelargonic acid aminotransferase
C: 7,8-diamino-pelargonic acid aminotransferase
D: 7,8-diamino-pelargonic acid aminotransferase
E: 7,8-diamino-pelargonic acid aminotransferase
F: 7,8-diamino-pelargonic acid aminotransferase
G: 7,8-diamino-pelargonic acid aminotransferase
H: 7,8-diamino-pelargonic acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,20032
Polymers378,5878
Non-polymers5,61324
Water15,025834
1
A: 7,8-diamino-pelargonic acid aminotransferase
B: 7,8-diamino-pelargonic acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0508
Polymers94,6472
Non-polymers1,4036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-78 kcal/mol
Surface area26020 Å2
MethodPISA
2
C: 7,8-diamino-pelargonic acid aminotransferase
D: 7,8-diamino-pelargonic acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0508
Polymers94,6472
Non-polymers1,4036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-77 kcal/mol
Surface area25820 Å2
MethodPISA
3
E: 7,8-diamino-pelargonic acid aminotransferase
F: 7,8-diamino-pelargonic acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0508
Polymers94,6472
Non-polymers1,4036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-77 kcal/mol
Surface area25890 Å2
MethodPISA
4
G: 7,8-diamino-pelargonic acid aminotransferase
H: 7,8-diamino-pelargonic acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0508
Polymers94,6472
Non-polymers1,4036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-82 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.430, 111.570, 136.120
Angle α, β, γ (deg.)90.00, 92.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
7,8-diamino-pelargonic acid aminotransferase / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / DAPA aminotransferase / 8- ...Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / DAPA aminotransferase / 8-diaminononanoate synthase / DANS / Diaminopelargonic acid synthase


Mass: 47323.324 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bioA, EL75_3021, EL79_3111, EL80_3072 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0A0GYM0, UniProt: P12995*PLUS, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-J4J / 2-[(2-nitrophenyl)sulfanyl]acetohydrazide


Mass: 227.240 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C8H9N3O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.05 M Ammonium Citrate, Dibasic 5% w/v Peg3350 0.45mM Spermidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.425→200 Å / Num. obs: 104748 / % possible obs: 99.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.3
Reflection shellResolution: 2.43→2.51 Å / Rmerge(I) obs: 0.354 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.43→42.79 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 5304 5.06 %
Rwork0.177 --
obs0.18 104748 75.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26075 0 359 834 27268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00927077
X-RAY DIFFRACTIONf_angle_d1.25436828
X-RAY DIFFRACTIONf_dihedral_angle_d13.2019635
X-RAY DIFFRACTIONf_chiral_restr0.0514043
X-RAY DIFFRACTIONf_plane_restr0.0074801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4251-2.45270.2734430.2162944X-RAY DIFFRACTION22
2.4527-2.48150.3149750.21591209X-RAY DIFFRACTION28
2.4815-2.51180.3609520.22961378X-RAY DIFFRACTION31
2.5118-2.54360.3369840.2221558X-RAY DIFFRACTION36
2.5436-2.5770.3192830.22221707X-RAY DIFFRACTION39
2.577-2.61230.3581010.22411876X-RAY DIFFRACTION43
2.6123-2.64960.32161170.21662092X-RAY DIFFRACTION48
2.6496-2.68920.30951330.21562362X-RAY DIFFRACTION54
2.6892-2.73120.27461390.22152517X-RAY DIFFRACTION58
2.7312-2.7760.29511530.22862712X-RAY DIFFRACTION62
2.776-2.82380.30711580.2332815X-RAY DIFFRACTION65
2.8238-2.87520.31571420.24752988X-RAY DIFFRACTION68
2.8752-2.93050.29261860.24513315X-RAY DIFFRACTION76
2.9305-2.99030.27032020.23773519X-RAY DIFFRACTION81
2.9903-3.05530.29082200.2423722X-RAY DIFFRACTION85
3.0553-3.12630.30382040.24413867X-RAY DIFFRACTION88
3.1263-3.20450.30682220.234002X-RAY DIFFRACTION92
3.2045-3.29110.27062240.21184082X-RAY DIFFRACTION94
3.2911-3.38790.27992300.21264298X-RAY DIFFRACTION97
3.3879-3.49720.24932300.1974353X-RAY DIFFRACTION100
3.4972-3.62210.25142490.19684331X-RAY DIFFRACTION100
3.6221-3.76710.23631970.17874431X-RAY DIFFRACTION100
3.7671-3.93840.22432500.16254350X-RAY DIFFRACTION100
3.9384-4.14590.2072120.14154448X-RAY DIFFRACTION100
4.1459-4.40540.19232320.12674403X-RAY DIFFRACTION100
4.4054-4.74510.1862270.12294395X-RAY DIFFRACTION100
4.7451-5.22190.1792190.13014409X-RAY DIFFRACTION100
5.2219-5.97580.19762390.15154419X-RAY DIFFRACTION100
5.9758-7.52220.19412350.1574462X-RAY DIFFRACTION100
7.5222-42.79220.19322460.14364480X-RAY DIFFRACTION99

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