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- PDB-1m32: Crystal Structure of 2-aminoethylphosphonate Transaminase -

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Basic information

Entry
Database: PDB / ID: 1m32
TitleCrystal Structure of 2-aminoethylphosphonate Transaminase
Components2-aminoethylphosphonate-pyruvate aminotransferase
KeywordsTRANSFERASE / PLP-dependent aminotransferase fold
Function / homology
Function and homology information


2-aminoethylphosphonate-pyruvate transaminase / 2-aminoethylphosphonate-pyruvate transaminase activity / organic phosphonate catabolic process
Similarity search - Function
2-aminoethylphosphonate--pyruvate transaminase / Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class V domain / Aminotransferase class-V / 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 ...2-aminoethylphosphonate--pyruvate transaminase / Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class V domain / Aminotransferase class-V / 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 / PHOSPHATE ION / PHOSPHONOACETALDEHYDE / 2-aminoethylphosphonate--pyruvate transaminase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsChen, C.C.H. / Zhang, H. / Kim, A.D. / Howard, A. / Sheldrick, G.M. / Mariano-Dunnaway, D. / Herzberg, O.
CitationJournal: Biochemistry / Year: 2002
Title: Degradation Pathway of the Phosphonate Ciliatine: Crystal Structure of 2-Aminoethylphosphonate Transaminase
Authors: Chen, C.C.H. / Zhang, H. / Kim, A.D. / Howard, A. / Sheldrick, G.M. / Mariano-Dunnaway, D. / Herzberg, O.
History
DepositionJun 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-aminoethylphosphonate-pyruvate aminotransferase
B: 2-aminoethylphosphonate-pyruvate aminotransferase
C: 2-aminoethylphosphonate-pyruvate aminotransferase
D: 2-aminoethylphosphonate-pyruvate aminotransferase
E: 2-aminoethylphosphonate-pyruvate aminotransferase
F: 2-aminoethylphosphonate-pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,16318
Polymers244,0536
Non-polymers2,11112
Water54,6583034
1
A: 2-aminoethylphosphonate-pyruvate aminotransferase
B: 2-aminoethylphosphonate-pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0646
Polymers81,3512
Non-polymers7134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-40 kcal/mol
Surface area25250 Å2
MethodPISA
2
C: 2-aminoethylphosphonate-pyruvate aminotransferase
D: 2-aminoethylphosphonate-pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0646
Polymers81,3512
Non-polymers7134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-46 kcal/mol
Surface area24950 Å2
MethodPISA
3
E: 2-aminoethylphosphonate-pyruvate aminotransferase
F: 2-aminoethylphosphonate-pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0356
Polymers81,3512
Non-polymers6844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-51 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.6, 155.3, 168.6
Angle α, β, γ (deg.)90.0, 90.6, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
2-aminoethylphosphonate-pyruvate aminotransferase / AEP-transaminase


Mass: 40675.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): B384(DE3)
References: UniProt: P96060, 2-aminoethylphosphonate-pyruvate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-POA / PHOSPHONOACETALDEHYDE


Mass: 124.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O4P
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3034 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium acetate, sodium citrate, mmPEG5K, PLP, phosphate, DTT, phosphonoacetaldehyde, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium acetate1reservoir
20.1 Msodium citrate1reservoirpH6.0
310-13 %PEG5000 MME1reservoir
418 mg/mlprotein1drop
58 mMphosphate1droppH7.5
60.8 mMdithiothreitol1drop
720 mMphosphonoacetaldehyde1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID10.9790, 0.9791, 0.95
SYNCHROTRONNSLS X12C20.9787, 0.9791, 0.95
SYNCHROTRONAPS 17-ID31
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMar 4, 1999
BRANDEIS - B42CCDAug 23, 1999
MARRESEARCH3CCDMar 5, 1999
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1cryogenically cooled Si(111) crystal system.MADMx-ray1
2Toroidal mirrorMADMx-ray1
3cryogenically cooled Si(111) crystal system.SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97911
30.951
40.97871
511
ReflectionResolution: 2.15→19.92 Å / Num. all: 264452 / Num. obs: 264452 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.037 / Net I/σ(I): 15.5
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.152 / % possible all: 83
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 496002
Reflection shell
*PLUS
% possible obs: 83 % / Mean I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
MADNESSdata collection
TRUNCATEdata reduction
caddata reduction
XPREPdata reduction
AMoREphasing
SHELXDphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
CNSrefinement
MADNESSdata reduction
CCP4(TRUNCATE)data scaling
CADdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 12668 -random
Rwork0.166 ---
all0.171 128378 --
obs0.17 127266 98.6 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16692 0 118 3034 19844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
Refinement
*PLUS
% reflection Rfree: 9.8 % / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.005
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.188

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