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- PDB-1o4s: Crystal structure of Aspartate aminotransferase (TM1255) from The... -

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Basic information

Entry
Database: PDB / ID: 1o4s
TitleCrystal structure of Aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / TM1255 / ASPARTATE AMINOTRANSFERASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
: / 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 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...: / 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 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 / Aspartate aminotransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution
Authors: Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. ...Authors: Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJun 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,23013
Polymers87,8712
Non-polymers1,35911
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-142 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.048, 79.509, 170.184
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 / Transaminase A / AspAT


Mass: 43935.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1255 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0Y2, aspartate transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#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.: 587 / 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: 2.31 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K
Details: 2.4 (NH4)2SO4 9 CHES , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
418 mg/mlprotein1drop
52.4 Mammonium sulfate1reservoir
60.1 MCHES1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2003
RadiationMonochromator: BENT GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→43.03 Å / Num. obs: 59510 / % possible obs: 85.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 36.89 Å2 / Rsym value: 0.063 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.422 / % possible all: 50.6
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 43 Å / Num. measured all: 249027 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 50.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 1BKG

1bkg


Resolution: 1.9→43 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.764 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SHORT STRETCHES OF UNEXPLAINED CONTINUOUS DENSITY MODELED AS WATER CHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1249 2.1 %RANDOM
Rwork0.159 ---
obs0.16 58261 85.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2---0.19 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 75 587 6657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226225
X-RAY DIFFRACTIONr_bond_other_d0.0020.025747
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9768423
X-RAY DIFFRACTIONr_angle_other_deg1.2313379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44523.897272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.962151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9151540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021259
X-RAY DIFFRACTIONr_nbd_refined0.210.21236
X-RAY DIFFRACTIONr_nbd_other0.2390.26765
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.23652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3660.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3120.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7491.53784
X-RAY DIFFRACTIONr_mcangle_it1.45926163
X-RAY DIFFRACTIONr_scbond_it2.47332441
X-RAY DIFFRACTIONr_scangle_it4.2374.52260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 59
Rwork0.307 2312
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)
11.20190.4362-0.14830.9414-0.53831.46920.040.01320.08540.0803-0.0380.0143-0.05950.051-0.002-0.19510.0181-0.0061-0.16650.01-0.13993.21513.68619.681
21.31940.4888-0.13071.2625-0.42651.72760.02130.1344-0.186-0.20680.04220.05930.4326-0.2296-0.06350.0238-0.0231-0.0562-0.1075-0.004-0.0846-10.513-17.48121.828
320.1147-17.08449.793852.9456-7.8475.3137-0.3269-0.02531.15952.4110.50480.049-0.26850.1868-0.17790.1896-0.0082-0.04530.23860.07890.2416-22.74819.4444.01
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 37114 - 383
2X-RAY DIFFRACTION2BB1 - 37113 - 383
3X-RAY DIFFRACTION3BB-4 - 08 - 12
Software
*PLUS
Name: REFMAC / Version: 5.1.995 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 2.1 % / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.62
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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