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- PDB-2gb3: Crystal structure of Aspartate aminotransferase (tm1698) from The... -

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Basic information

Entry
Database: PDB / ID: 2gb3
TitleCrystal structure of Aspartate aminotransferase (tm1698) from Thermotoga maritima at 2.50 A resolution
Componentsaspartate aminotransferase
KeywordsTRANSFERASE / tm1698 / Aspartate aminotransferase / Structural Genomics / PSI / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding
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
: / Aminotransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Aspartate aminotransferase (tm1698) from Thermotoga maritima at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aspartate aminotransferase
B: aspartate aminotransferase
C: aspartate aminotransferase
D: aspartate aminotransferase
E: aspartate aminotransferase
F: aspartate aminotransferase


Theoretical massNumber of molelcules
Total (without water)283,0766
Polymers283,0766
Non-polymers00
Water3,423190
1
A: aspartate aminotransferase
B: aspartate aminotransferase


Theoretical massNumber of molelcules
Total (without water)94,3592
Polymers94,3592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-28 kcal/mol
Surface area27830 Å2
MethodPISA
2
C: aspartate aminotransferase
D: aspartate aminotransferase


Theoretical massNumber of molelcules
Total (without water)94,3592
Polymers94,3592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-27 kcal/mol
Surface area27470 Å2
MethodPISA
3
E: aspartate aminotransferase
F: aspartate aminotransferase


Theoretical massNumber of molelcules
Total (without water)94,3592
Polymers94,3592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-30 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.094, 214.051, 76.839
Angle α, β, γ (deg.)90.000, 112.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: 2

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERAA4 - 39216 - 404
2SERSERBB4 - 39216 - 404
3SERSERCC4 - 39216 - 404
4PHEPHEDD4 - 39016 - 402
5CYSCYSEE4 - 39116 - 403
6CYSCYSFF4 - 39116 - 403

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Components

#1: Protein
aspartate aminotransferase


Mass: 47179.410 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1698 / Production host: Escherichia coli (E. coli) / References: GenBank: 4982275, UniProt: Q9X224*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5
Details: 35.0% 2-propanol, 0.1M Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979386
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2005 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979386 Å / Relative weight: 1
ReflectionResolution: 2.496→107.211 Å / Num. obs: 75747 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
2.5-2.561.90.23.5958451580.289.4
2.56-2.631.90.16941001352900.16996
2.63-2.711.90.1444.5989052070.14495.4
2.71-2.791.90.1126960250400.11295.5
2.79-2.881.90.0997.1931548850.09995.1
2.88-2.981.90.0867.5890646720.08694.8
2.98-3.14.10.4471.41955847340.44799.4
3.1-3.224.50.3861.62088646130.386100
3.22-3.374.50.2972.11988544090.297100
3.37-3.534.50.2281.61915142330.228100
3.53-3.724.50.1742.91799139990.17499.8
3.72-3.954.50.1383.91719838030.13899.8
3.95-4.224.50.1144.51595535710.11499.9
4.22-4.564.50.0995.21480033090.09999.7
4.56-4.994.40.0935.11362830690.09399.6
4.99-5.584.40.0984.71195327420.09899.7
5.58-6.444.20.0885.11022624410.08899.5
6.44-7.894.30.076.6891720690.0799.6
7.89-11.164.60.0527.2744816150.052100
11.16-107.214.40.0575.338948880.05798.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1xi9A

Resolution: 2.5→107.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 27.542 / SU ML: 0.282 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ELECTRON DENSITY MAPS INDICATE THAT THE SIDECHAINS OF LYS 232 ON THE SIX SUBUNITS IN THE ASYMMETRIC UNIT FORM A SCHIFF BASE COVALENT ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ELECTRON DENSITY MAPS INDICATE THAT THE SIDECHAINS OF LYS 232 ON THE SIX SUBUNITS IN THE ASYMMETRIC UNIT FORM A SCHIFF BASE COVALENT BOND WITH THE BOUND PYRIDOXAL PHOSPHATE COFACTOR. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE CONFORMATION OF GLU 206 IN ALL SIX SUBUNITS IS IS SUPPORTED BY ELECTRON DENSITY EVEN THOUGH THIS RESIDUE IS A RAMACHANDRAN OUTLIER.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3781 5 %RANDOM
Rwork0.229 ---
obs0.231 75283 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.427 Å2
Baniso -1Baniso -2Baniso -3
1--3.1 Å20 Å21.06 Å2
2--1.78 Å20 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.5→107.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18179 0 0 190 18369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218624
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217357
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.97625290
X-RAY DIFFRACTIONr_angle_other_deg0.927339962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.53752350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.26523.164787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.558153040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2115132
X-RAY DIFFRACTIONr_chiral_restr0.0910.22881
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023939
X-RAY DIFFRACTIONr_nbd_refined0.1890.33940
X-RAY DIFFRACTIONr_nbd_other0.1530.318045
X-RAY DIFFRACTIONr_nbtor_refined0.1770.59489
X-RAY DIFFRACTIONr_nbtor_other0.0850.510656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.5894
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.030.55
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.354
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.3154
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.516
X-RAY DIFFRACTIONr_symmetry_hbond_other0.070.51
X-RAY DIFFRACTIONr_mcbond_it0.508212184
X-RAY DIFFRACTIONr_mcbond_other0.16724753
X-RAY DIFFRACTIONr_mcangle_it0.629418834
X-RAY DIFFRACTIONr_scbond_it1.73167479
X-RAY DIFFRACTIONr_scangle_it2.47286453
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2260TIGHT POSITIONAL0.020.05
2B2260TIGHT POSITIONAL0.020.05
3C2260TIGHT POSITIONAL0.030.05
4D2260TIGHT POSITIONAL0.020.05
5E2260TIGHT POSITIONAL0.020.05
6F2260TIGHT POSITIONAL0.020.05
1A3275MEDIUM POSITIONAL0.470.5
2B3275MEDIUM POSITIONAL0.480.5
3C3275MEDIUM POSITIONAL0.420.5
4D3275MEDIUM POSITIONAL0.50.5
5E3275MEDIUM POSITIONAL0.50.5
6F3275MEDIUM POSITIONAL0.470.5
1A2260TIGHT THERMAL0.040.5
2B2260TIGHT THERMAL0.040.5
3C2260TIGHT THERMAL0.040.5
4D2260TIGHT THERMAL0.030.5
5E2260TIGHT THERMAL0.040.5
6F2260TIGHT THERMAL0.040.5
1A3275MEDIUM THERMAL0.262
2B3275MEDIUM THERMAL0.252
3C3275MEDIUM THERMAL0.252
4D3275MEDIUM THERMAL0.222
5E3275MEDIUM THERMAL0.262
6F3275MEDIUM THERMAL0.32
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 249 -
Rwork0.321 5014 -
obs-5263 92.48 %
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)
12.32360.0931-0.78782.77650.63011.6221-0.00980.0153-0.2046-0.2468-0.0041-0.2627-0.00010.22230.01390.00180.02720.0042-0.0269-0.0263-0.0517-5.6330.11715.537
23.32990.2097-0.35791.61260.15281.35830.1855-0.00650.02080.0527-0.09220.2002-0.1543-0.3746-0.09330.01610.0199-0.02550.099-0.0728-0.0877-37.678.80818.566
32.6178-0.569-1.00282.5988-0.11821.99060.01740.0702-0.03860.2305-0.04860.2786-0.1415-0.30040.03120.02680.0193-0.0322-0.0351-0.0645-0.0098-23.729-36.25255.666
45.06590.1658-1.13371.9137-0.2481.9290.35210.18970.3217-0.0434-0.0417-0.2379-0.19470.3718-0.3103-0.0117-0.0077-0.04230.1515-0.11130.06698.479-27.64452.589
54.1197-0.0488-0.55421.6265-0.14211.10780.2097-0.06440.3329-0.0207-0.0594-0.2264-0.16120.3543-0.1503-0.0012-0.0422-0.05340.0217-0.0736-0.03878.66644.14851.531
62.4552-0.6523-0.75242.7637-0.24461.6781-0.0251-0.0950.01240.32070.02960.2824-0.04-0.2048-0.0044-0.0242-0.0187-0.022-0.1089-0.0495-0.1664-23.26935.58654.425
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 39216 - 404
22BB-1 - 39211 - 404
33CC2 - 39214 - 404
44DD1 - 39013 - 402
55EE-1 - 39111 - 403
66FF3 - 39115 - 403

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