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- PDB-3rq1: Crystal Structure of Aminotransferase Class I and II from Veillon... -

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Basic information

Entry
Database: PDB / ID: 3rq1
TitleCrystal Structure of Aminotransferase Class I and II from Veillonella parvula
ComponentsAminotransferase class I and II
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta structure / cytosol
Function / homology
Function and homology information


amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aspartate/other aminotransferase / 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 ...Aspartate/other aminotransferase / 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
2-OXOGLUTARIC ACID / OXALOACETATE ION / Aminotransferase class I and II
Similarity search - Component
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKim, Y. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Aminotransferase Class I and II from Veillonella parvula
Authors: Kim, Y. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase class I and II
B: Aminotransferase class I and II
C: Aminotransferase class I and II
D: Aminotransferase class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,43419
Polymers186,9384
Non-polymers1,49615
Water7,963442
1
A: Aminotransferase class I and II
C: Aminotransferase class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,46512
Polymers93,4692
Non-polymers99610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-36 kcal/mol
Surface area28300 Å2
MethodPISA
2
B: Aminotransferase class I and II
D: Aminotransferase class I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9687
Polymers93,4692
Non-polymers4995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-31 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.991, 81.057, 106.395
Angle α, β, γ (deg.)102.40, 101.37, 102.95
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aminotransferase class I and II


Mass: 46734.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_1105 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BM21 magic / References: UniProt: D1BN29

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Non-polymers , 5 types, 457 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H3O5
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium citrate, 20 % (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 84494 / Num. obs: 84494 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 39.74 Å2 / Rsym value: 0.087 / Net I/σ(I): 8.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 3916 / Rsym value: 0.421 / % possible all: 88.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→42.397 Å / SU ML: 0.35 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.21 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 4223 5.01 %random
Rwork0.19 ---
all0.194 84252 --
obs0.194 84252 96.43 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.574 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso mean: 56.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.9534 Å2-7.41 Å22.9848 Å2
2--14.1771 Å23.6243 Å2
3----12.2237 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12748 0 98 442 13288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413331
X-RAY DIFFRACTIONf_angle_d1.69818055
X-RAY DIFFRACTIONf_dihedral_angle_d16.5174875
X-RAY DIFFRACTIONf_chiral_restr0.1351954
X-RAY DIFFRACTIONf_plane_restr0.0092379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1997-2.22470.3411910.29151981207271
2.2247-2.25080.37841290.2822486261589
2.2508-2.27830.36041150.28152534264992
2.2783-2.30710.35551370.2722653279094
2.3071-2.33750.35871300.25642592272295
2.3375-2.36950.33491780.26152622280095
2.3695-2.40340.36081440.23792653279797
2.4034-2.43920.32111410.23622723286497
2.4392-2.47730.29011410.22542681282297
2.4773-2.5180.32251350.232692282798
2.518-2.56140.29811320.23692707283997
2.5614-2.60790.34141390.232694283398
2.6079-2.65810.31531580.21452739289798
2.6581-2.71230.26951520.21072676282898
2.7123-2.77130.29421420.20852745288798
2.7713-2.83580.30141260.20932685281198
2.8358-2.90670.30651310.21222754288598
2.9067-2.98520.28391430.22182709285298
2.9852-3.0730.32551370.21022713285098
3.073-3.17220.29911360.21912706284298
3.1722-3.28550.26261740.20432726290099
3.2855-3.4170.26141450.18742715286099
3.417-3.57250.25371600.17912689284999
3.5725-3.76070.24071460.16842762280899
3.7607-3.99620.20731620.14382721288399
3.9962-4.30440.21471420.14152756289899
4.3044-4.73710.1821300.14442735286599
4.7371-5.42140.26261440.15742749289399
5.4214-6.82570.27461360.1992747288399
6.8257-42.40460.21761470.17982684283197
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)
10.38460.11530.28470.4108-0.15550.2798-0.13480.00110.05980.07970.0676-0.0057-0.2137-0.05690.02320.30450.00650.03650.1730.00210.2071-14.62-5.6733105.672
20.2784-0.0844-0.22770.2438-0.1930.5955-0.08350.063-0.0566-0.12790.0196-0.0846-0.07450.20790.00190.2115-0.00580.02580.3013-0.07950.2816-13.3175-27.202792.9531
30.5928-0.2923-0.16690.6312-0.09020.6562-0.0817-0.21730.08390.2621-0.10590.0391-0.18550.09260.06670.24540.05540.03540.27850.02670.3626-33.1288-22.0343108.9122
40.3587-0.2597-0.37650.11880.27360.3556-0.02650.028-0.1891-0.06250.05610.07050.050.0264-0.02490.2631-0.0122-0.03180.24890.00430.3876-28.0691-31.9008101.3536
50.1181-0.1415-0.22420.14510.25520.42460.09920.35640.0337-0.2618-0.00330.0478-0.045-0.0807-0.04210.259-0.0137-0.03750.359-0.0420.3259-22.4413-26.440685.4436
60.43690.1286-0.17390.22430.2170.34690.0343-0.2517-0.22210.0917-0.0410.0485-0.00010.11470.00020.26280.0823-0.03610.38650.05450.3975-10.4014-25.4733116.9578
70.27150.05030.08110.3424-0.06770.8493-0.00950.0647-0.18840.0750.0427-0.014-0.2412-0.22710.11250.3781-0.2217-0.11250.3556-0.03140.24191.8599-80.814124.3442
80.36350.2197-0.01660.19-0.0520.03490.3402-0.5034-0.13740.17120.0004-0.0075-0.24560.6525-0.12910.4466-0.2051-0.02130.6554-0.11870.352916.6969-67.9784137.967
91.47350.10170.60220.0505-0.04611.22520.68330.16230.48520.28680.10550.1792-0.1680.17710.14590.5173-0.14710.19420.2765-0.00880.4102-3.4127-57.9006131.9118
100.82930.0263-0.13550.31310.40421.13340.62390.2490.39730.11160.21690.1818-0.61920.05510.21010.52910.01370.28570.34020.20820.5145-1.8393-52.1814123.1379
111.47510.10491.13521.8925-0.56382.10960.6755-0.45360.43010.29090.12460.2993-0.3240.06860.59130.619-0.16840.31630.426-0.16840.3747-2.0456-57.464142.7901
120.09540.06110.06090.09930.13070.69970.2677-0.20780.0563-0.0011-0.1567-0.1340.07070.2738-0.04770.3115-0.15790.05080.4413-0.09980.34816.9132-65.2311115.7681
131.75-0.095-1.43750.306-0.15951.4344-0.37630.3952-0.1649-0.2597-0.00370.0812-0.0279-0.1359-0.12970.2545-0.1702-0.03980.6334-0.00810.2476-26.4508-22.197874.3133
140.4090.27140.25260.26090.03870.8744-0.02880.3724-0.2281-0.13720.0663-0.0805-0.18910.5342-0.06370.28870.00140.05250.5005-0.10930.3644-3.0349-16.791179.2559
150.5150.0164-0.02920.4585-0.45811.0583-0.03250.21080.0803-0.10070.15060.0331-0.1512-0.0234-0.05060.3132-0.03050.00390.29840.01780.2265-20.07553.320480.5813
160.6703-0.1074-0.11591.0004-0.4190.1935-0.18010.5513-0.1249-0.44940.0409-0.20550.04490.06370.01460.37-0.11030.1130.6516-0.06050.2642-12.2186-8.043669.3301
170.2251-0.09750.13290.34430.16130.69050.3111-0.32080.06890.15630.10440.2966-0.08740.07290.28740.7496-0.09560.35050.79370.07840.5668-7.9802-63.0386153.2828
180.52940.365-0.37870.5411-0.26780.78460.1489-0.2155-0.01480.1407-0.1056-0.0366-0.18590.396-0.01670.2568-0.0169-0.03270.38080.04370.2422-2.3185-79.6071143.9681
190.37270.3775-0.23280.3671-0.12690.38180.01980.00730.07330.25850.16330.221-0.0422-0.1618-0.06870.42380.0490.07180.310.07340.3261-22.2231-83.944151.8688
200.95850.2101-0.91760.67830.11940.9481-0.0575-0.0801-0.04780.4021-0.03970.05070.01780.37340.05240.3357-0.03660.00990.33690.0410.227-10.4074-89.2207146.3805
210.84330.2979-0.56030.4204-0.01640.30770.3439-0.7119-0.15120.358-0.26650.0966-0.09850.28770.07690.4711-0.16930.01560.83120.05770.2447-4.4202-77.4695158.6166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:32)
2X-RAY DIFFRACTION2chain 'A' and (resseq 33:119)
3X-RAY DIFFRACTION3chain 'A' and (resseq 120:172)
4X-RAY DIFFRACTION4chain 'A' and (resseq 173:268)
5X-RAY DIFFRACTION5chain 'A' and (resseq 269:313)
6X-RAY DIFFRACTION6chain 'A' and (resseq 314:415)
7X-RAY DIFFRACTION7chain 'B' and (resseq 2:32)
8X-RAY DIFFRACTION8chain 'B' and (resseq 33:79)
9X-RAY DIFFRACTION9chain 'B' and (resseq 80:143)
10X-RAY DIFFRACTION10chain 'B' and (resseq 144:268)
11X-RAY DIFFRACTION11chain 'B' and (resseq 269:313)
12X-RAY DIFFRACTION12chain 'B' and (resseq 314:415)
13X-RAY DIFFRACTION13chain 'C' and (resseq 2:32)
14X-RAY DIFFRACTION14chain 'C' and (resseq 33:79)
15X-RAY DIFFRACTION15chain 'C' and (resseq 80:277)
16X-RAY DIFFRACTION16chain 'C' and (resseq 278:414)
17X-RAY DIFFRACTION17chain 'D' and (resseq 2:48)
18X-RAY DIFFRACTION18chain 'D' and (resseq 49:143)
19X-RAY DIFFRACTION19chain 'D' and (resseq 144:195)
20X-RAY DIFFRACTION20chain 'D' and (resseq 196:277)
21X-RAY DIFFRACTION21chain 'D' and (resseq 278:411)

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