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- PDB-1dty: CRYSTAL STRUCTURE OF ADENOSYLMETHIONINE-8-AMINO-7-OXONANOATE AMIN... -

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Basic information

Entry
Database: PDB / ID: 1dty
TitleCRYSTAL STRUCTURE OF ADENOSYLMETHIONINE-8-AMINO-7-OXONANOATE AMINOTRANSFERASE WITH PYRIDOXAL PHOSPHATE COFACTOR.
ComponentsADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
KeywordsTRANSFERASE / biotin biosynthesis / dapa / diaminopelargonic acid / diaminonanonoic acid
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
PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å
AuthorsAlexeev, D. / Sawyer, L. / Baxter, R.L. / Alexeeva, M.V. / Campopiano, D.
CitationJournal: to be published
Title: Crystal structure of adenosylmethionine-8-amino-7-oxonanoate aminotransferase with pyridoxal phosphate cofactor
Authors: Alexeev, D. / Sawyer, L. / Baxter, R.L. / Alexeeva, M.V. / Campopiano, D.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
B: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4498
Polymers94,8632
Non-polymers5866
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-133 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.280, 56.270, 121.930
Angle α, β, γ (deg.)90.00, 96.96, 90.00
Int Tables number4
Space group name H-MP1211
Detailshe biological assembly is a dimer constructed from chains A and B related by the non-crystallographic two-fold. The cofactor PLP is bonded to the K274.

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Components

#1: Protein ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE


Mass: 47431.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P12995, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MethoxyPEG 5000 in Bis-tris propane/HC buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONSRS PX7.211.488
ROTATING ANODEENRAF-NONIUS FR57121.542
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJan 1, 1997
MARRESEARCH2IMAGE PLATEJan 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4881
21.5421
ReflectionResolution: 2.14→119.52 Å / Num. all: 43635 / Num. obs: 43620 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.4
Reflection shellResolution: 2.14→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Num. unique all: 514 / % possible all: 96.2

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Processing

Software
NameClassification
MOLREPphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.14→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: CGLS in SHELX97 with NCS restraints between monomers A and B
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1344 -RANDOM
Rwork0.196 ---
all0.196 41811 --
obs0.196 41782 100 %-
Refinement stepCycle: LAST / Resolution: 2.14→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 34 334 7006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.017

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