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- PDB-6nst: Crystal structure of branched chain amino acid aminotransferase f... -

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Basic information

Entry
Database: PDB / ID: 6nst
TitleCrystal structure of branched chain amino acid aminotransferase from Pseudomonas aeruginosa
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / CSGID / aminostransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / cytosol
Similarity search - Function
Branched-chain amino acid aminotransferase I / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal ...Branched-chain amino acid aminotransferase I / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.136 Å
AuthorsChang, C. / Skarina, T. / Savshenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of branched chain amino acid aminotransferase from Pseudomonas aeruginosa
Authors: Chang, C. / Skarina, T. / Savshenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Branched-chain-amino-acid aminotransferase
B: Branched-chain-amino-acid aminotransferase
C: Branched-chain-amino-acid aminotransferase
D: Branched-chain-amino-acid aminotransferase
E: Branched-chain-amino-acid aminotransferase
F: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,48612
Polymers204,9106
Non-polymers5766
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27790 Å2
ΔGint-262 kcal/mol
Surface area57440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.837, 129.636, 85.787
Angle α, β, γ (deg.)90.000, 114.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Branched-chain-amino-acid aminotransferase / BCAT


Mass: 34151.598 Da / Num. of mol.: 6 / Mutation: L31H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ilvE, PA5013 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O86428, branched-chain-amino-acid transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG3350 25%, ammonium acetate 0.2M, Bis-Tris 0.1 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 28, 2018
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 83927 / % possible obs: 91.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.059 / Rrim(I) all: 0.135 / Χ2: 0.925 / Net I/σ(I): 8.8 / Num. measured all: 342339
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.192.10.41930100.6960.3230.5321.07265.6
2.19-2.232.10.38930460.7340.3050.4981.06466.9
2.23-2.272.10.36530460.760.2820.4641.18167
2.27-2.322.20.31130440.830.2380.3941.13766.2
2.32-2.372.80.28537650.9010.1840.3421.09282.2
2.37-2.423.50.29744430.8990.1750.3471.14496.8
2.42-2.483.60.28644460.8940.1670.3331.09797.6
2.48-2.553.70.26744960.9170.1550.3111.07398.2
2.55-2.623.80.24545020.9210.1410.2841.04998.3
2.62-2.713.90.2444840.9230.1360.2781.05498.1
2.71-2.8140.22544610.9330.1260.2591.06697.1
2.81-2.924.40.2145530.9490.1110.2390.98799.2
2.92-3.054.60.19645400.9640.1010.2210.97499.1
3.05-3.214.80.18245430.9720.0910.2040.95699.4
3.21-3.414.80.15645340.9740.0770.1740.94798.4
3.41-3.685.10.14345920.9780.0690.160.89399.5
3.68-4.055.30.12745780.9840.0590.140.78699.7
4.05-4.635.30.10645620.9870.050.1180.7399
4.63-5.835.40.09946120.990.0450.1090.6399.8
5.83-505.30.09446700.9850.0450.1050.70199.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3u0g

3u0g


Resolution: 2.136→49.919 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 3816 4.83 %
Rwork0.1946 75165 -
obs0.1974 78981 83.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.14 Å2 / Biso mean: 30.742 Å2 / Biso min: 4.15 Å2
Refinement stepCycle: final / Resolution: 2.136→49.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13922 0 30 487 14439
Biso mean--37.95 25.69 -
Num. residues----1794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.136-2.1630.579350.24992172226
2.163-2.19140.3016470.2652988103529
2.1914-2.22150.3181740.25931350142441
2.2215-2.25320.3259960.25451549164547
2.2532-2.28680.30191000.25091601170149
2.2868-2.32260.3425940.24391883197756
2.3226-2.36060.31381150.24572112222764
2.3606-2.40140.291630.22653075323892
2.4014-2.4450.34141540.22443206336095
2.445-2.4920.29011390.23283211335097
2.492-2.54290.2971960.22863217341397
2.5429-2.59820.27731460.22473272341898
2.5982-2.65860.29841480.23283272342098
2.6586-2.72510.32611840.22593220340498
2.7251-2.79880.30521850.2213166335195
2.7988-2.88110.2811480.2223314346299
2.8811-2.97410.29891860.22013279346599
2.9741-3.08040.29821720.22143307347999
3.0804-3.20370.2571420.20893341348399
3.2037-3.34950.23411510.20043298344999
3.3495-3.5260.25071770.1843278345598
3.526-3.74690.22091530.17623345349899
3.7469-4.03610.20871470.159133353482100
4.0361-4.4420.19761640.14573336350099
4.442-5.08430.19451800.14363291347199
5.0843-6.40350.21231860.177533353521100
6.4035-49.9330.21640.17423367353198
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)
10.8795-0.17890.26541.18840.22880.869-0.02970.12760.0847-0.07240.11570.177-0.0947-0.3018-0.02870.13220.00150.01710.2290.110.19637.913626.1428-1.4451
20.59410.36070.11270.3259-0.21821.37350.08350.08160.3534-0.04330.0370.1268-0.2337-0.1454-0.0280.09780.02350.00390.13210.02120.18818.332213.097517.5056
30.33140.05140.14751.1534-0.69270.98190.03090.09050.15290.0568-0.0031-0.0081-0.3006-0.0610.00470.19230.03780.05280.12360.00830.190411.458226.151125.6115
40.47170.2043-0.04180.37850.27331.0659-0.0410.40550.1751-0.37080.18470.2056-0.1976-0.25420.40360.2311-0.1633-0.12580.48250.07450.14940.14062.0853-8.7667
50.6396-0.47590.41320.3631-0.25750.54920.14760.33950.0945-0.3322-0.054-0.03110.05120.0229-0.05980.5323-0.0993-0.0040.53850.02250.147212.3595-0.9062-15.0736
60.6188-0.1144-0.24470.06890.02470.1179-0.09370.09660.0356-0.10570.10470.0980.1026-0.2385-0.0110.1218-0.02890.00060.13130.03480.108721.64691.2121.537
70.84260.25520.55280.27920.11830.3922-0.1310.2247-0.1333-0.19560.07440.00810.2949-0.2265-0.06940.3-0.1350.02110.2755-0.08840.137321.5519-14.5906-6.4372
80.82350.60960.17730.81510.24930.87850.1415-0.22680.06250.1955-0.11390.1055-0.04320.0224-0.00750.2416-0.03280.03020.1539-0.02850.118713.16954.74355.0654
90.3823-0.219-0.39140.20060.08310.54260.0317-0.0545-0.04060.1407-0.04110.03160.03160.0026-0.00470.2316-0.0051-0.01810.15560.00640.112122.4836-0.787843.7985
100.6752-0.6216-0.87450.68820.94811.35060.0871-0.0310.0690.12670.0067-0.0168-0.21390.171-0.01980.2412-0.0132-0.00220.1973-0.05680.148135.805613.108843.8675
110.57670.32730.14630.64660.18190.82110.0314-0.1924-0.06890.2321-0.05890.030.1181-0.07640.00940.27340.00430.00960.11740.01870.07868.5657-22.420145.4149
120.1359-0.0658-0.15570.7343-0.5160.6658-0.0121-0.0943-0.00830.198-0.00380.08070.0293-0.02480.02010.1456-0.00570.01080.1384-0.01210.09538.3616-10.935834.9689
130.19250.0909-0.13321.2565-0.71640.882-0.15980.123-0.1258-0.12310.1182-0.04050.3672-0.10710.01350.1692-0.0792-0.00490.1458-0.00580.13172.0626-19.965219.7029
140.79810.2283-0.0380.4726-0.13130.91730.0645-0.07250.204-0.01970.0439-0.45130.20210.26570.1253-0.039-0.02080.04050.2507-0.07310.403860.95285.677617.8996
150.0955-0.17990.13280.3251-0.24780.3778-0.0562-0.0575-0.08020.03450.0312-0.2048-0.03070.14250.03410.0396-0.00760.01530.1335-0.01380.12739.21535.880910.8255
161.54860.24530.56630.28880.14180.4980.0435-0.03810.2684-0.06760.0749-0.1817-0.27250.12660.05830.0918-0.07430.01630.1352-0.08190.245541.82923.204313.288
171.7234-0.267-0.34072.28640.28850.1413-0.0238-0.2990.00670.0739-0.0132-0.60780.0220.19420.00970.1333-0.00180.03420.20760.01250.372460.8698-13.113510.6678
180.9188-0.18760.10931.00510.26160.59960.01630.0381-0.099-0.0627-0.02-0.20890.12580.1055-0.00410.15690.02790.05050.1097-0.00950.189551.7528-20.48167.2863
190.09120.1448-0.21040.2758-0.28350.5113-0.0311-0.0889-0.0389-0.0380.0085-0.20060.030.12630.0170.09590.0354-0.01340.1688-0.00170.155538.3494-11.472622.9276
200.817-0.1503-0.44750.56750.48040.9124-0.1125-0.0262-0.1179-0.00480.0505-0.11330.18810.04360.0260.14980.04090.03170.07150.00440.105834.0589-28.577420.6946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 126 )A1 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 198 )A127 - 198
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 307 )A199 - 307
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 117 )B2 - 117
5X-RAY DIFFRACTION5chain 'B' and (resid 118 through 139 )B118 - 139
6X-RAY DIFFRACTION6chain 'B' and (resid 140 through 198 )B140 - 198
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 306 )B199 - 306
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 89 )C1 - 89
9X-RAY DIFFRACTION9chain 'C' and (resid 90 through 198 )C90 - 198
10X-RAY DIFFRACTION10chain 'C' and (resid 199 through 307 )C199 - 307
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 89 )D2 - 89
12X-RAY DIFFRACTION12chain 'D' and (resid 90 through 198 )D90 - 198
13X-RAY DIFFRACTION13chain 'D' and (resid 199 through 307 )D199 - 307
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 139 )E1 - 139
15X-RAY DIFFRACTION15chain 'E' and (resid 140 through 198 )E140 - 198
16X-RAY DIFFRACTION16chain 'E' and (resid 199 through 307 )E199 - 307
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 40 )F1 - 40
18X-RAY DIFFRACTION18chain 'F' and (resid 41 through 139 )F41 - 139
19X-RAY DIFFRACTION19chain 'F' and (resid 140 through 198 )F140 - 198
20X-RAY DIFFRACTION20chain 'F' and (resid 199 through 307 )F199 - 307

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