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- PDB-5vjz: Joint X-ray/neutron structure of aspartate aminotransferase with ... -

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Basic information

Entry
Database: PDB / ID: 5vjz
TitleJoint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5
Components(Aspartate aminotransferase, cytoplasmicAspartate transaminase) x 2
KeywordsTRANSFERASE / neutron structure / aspartate aminotransferase
Function / homology
Function and homology information


Aspartate and asparagine metabolism / phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / aspartate biosynthetic process / glycerol biosynthetic process / aspartate metabolic process / Gluconeogenesis ...Aspartate and asparagine metabolism / phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / aspartate biosynthetic process / glycerol biosynthetic process / aspartate metabolic process / Gluconeogenesis / glutamate metabolic process / aspartate catabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DEUTERATED WATER / Chem-PLA / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / Resolution: 2 Å
AuthorsDajnowicz, S. / Kovalevsky, A.Y. / Mueser, T.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)N-125688-01 United States
CitationJournal: Nat Commun / Year: 2017
Title: Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme.
Authors: Dajnowicz, S. / Johnston, R.C. / Parks, J.M. / Blakeley, M.P. / Keen, D.A. / Weiss, K.L. / Gerlits, O. / Kovalevsky, A. / Mueser, T.C.
History
DepositionApr 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection / Category: atom_site / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Mar 16, 2022Group: Author supporting evidence / Data collection / Database references
Category: database_2 / diffrn_source / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate aminotransferase, cytoplasmic
B: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3933
Polymers93,0152
Non-polymers3781
Water4,288238
1
A: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7722
Polymers46,3941
Non-polymers3781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aspartate aminotransferase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)46,6221
Polymers46,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.532, 124.986, 130.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartate aminotransferase, cytoplasmic / Aspartate transaminase / cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate ...cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate oxaloacetate transaminase 1 / Transaminase A


Mass: 46393.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: GOT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00503, aspartate transaminase, cysteine transaminase
#2: Protein Aspartate aminotransferase, cytoplasmic / Aspartate transaminase / cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate ...cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate oxaloacetate transaminase 1 / Transaminase A


Mass: 46621.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: GOT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00503, aspartate transaminase, cysteine transaminase
#3: Chemical ChemComp-PLA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID / N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE


Mass: 378.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N2O9P
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION2

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 7.5 / Details: 40mM sodium acetate 8% PEG 6,000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54178
NUCLEAR REACTORILL H14223.6 to 4.7
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEDec 7, 2016
MARRESEARCH2IMAGE PLATEDec 13, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
23.61
34.71
ReflectionResolution: 2→40 Å / Num. obs: 62791 / % possible obs: 95.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 28.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.47 / Num. unique obs: 32950 / % possible all: 72.9

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Processing

SoftwareName: nCNS / Version: 1.0.0 / Classification: refinement
Refinement

Biso max: 95.42 Å2 / Biso mean: 29.28 Å2 / Biso min: 4 Å2 / % reflection Rfree: 5 % / Cross valid method: FREE R-VALUE / Bsol: 36.8043 Å2 / ksol: 0.295207 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection obs (%)
2-39.56X-RAY DIFFRACTION0.2210.0040.1972794622125549389.2
2.21-39.56NEUTRON DIFFRACTION0.2570.0060.2341623461713255870.5
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.240.22
Luzzati d res low-5
Luzzati sigma a0.170.14
Luzzati d res high-2
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.340.29
Luzzati d res low-5
Luzzati sigma a0.490.43
Luzzati d res high-2.21
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6563 0 25 238 6826
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.009
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg27.9
NEUTRON DIFFRACTIONx_torsion_impr_deg1.8
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.090.2512824.70.21757620.0157672604478.8
2.09-2.20.2373074.80.21460690.0147706637682.7
2.2-2.340.2253254.90.20762560.0127688658185.6
2.21-2.310.4061424.50.3730110.0345709315355.2
2.31-2.430.3521524.40.3133180.0295678347061.1
2.34-2.520.2413304.80.20965410.0137743687188.7
2.43-2.590.3331664.70.28933890.0265698355562.4
2.52-2.770.2343565.10.21965630.0127721691989.6
2.59-2.790.3081764.80.28734680.0235748364463.4
2.77-3.170.2354085.60.21668620.0127768727093.6
2.79-3.070.2692105.30.22837890.0195733399969.8
3.07-3.510.242385.40.21141860.0165767442476.7
3.17-40.2073674.90.18571230.0117857749095.3
3.51-4.420.2012454.90.18947420.0135821498785.7
4-39.560.2034195.30.17675230.018123794297.8
4.42-39.560.1892945.50.17350320.0116060532687.9

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