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- PDB-4grx: Structure of an omega-aminotransferase from Paracoccus denitrificans -

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Basic information

Entry
Database: PDB / ID: 4grx
TitleStructure of an omega-aminotransferase from Paracoccus denitrificans
ComponentsAminotransferase
KeywordsTRANSFERASE / class III transaminase
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
DELTA-AMINO VALERIC ACID / Aminotransferase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsRausch, C. / Lerchner, A. / Schiefner, A. / Skerra, A.
CitationJournal: Proteins / Year: 2013
Title: Crystal structure of the omega-aminotransferase from Paracoccus denitrificans and its phylogenetic relationship with other class III aminotransferases that have biotechnological potential.
Authors: Rausch, C. / Lerchner, A. / Schiefner, A. / Skerra, A.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,77510
Polymers206,4464
Non-polymers3286
Water4,414245
1
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3875
Polymers103,2232
Non-polymers1643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-98 kcal/mol
Surface area28700 Å2
MethodPISA
2
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3875
Polymers103,2232
Non-polymers1643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-97 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.790, 103.630, 145.430
Angle α, β, γ (deg.)90.000, 98.880, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two dimer A/B and C/D.

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Components

#1: Protein
Aminotransferase


Mass: 51611.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd1222 / Gene: Pden_3984 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21
References: UniProt: A1B956, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DAV / DELTA-AMINO VALERIC ACID


Mass: 118.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25 %(w/v) PEG3350, 0.4 M NaCl, 10 mM urea, 0.1 M Tris/HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2009 / Details: Double Crystal
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 60091 / Num. obs: 60091 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.039 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.31
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.70.5582.76241596386199.6
2.7-2.80.4453.392133455711100
2.8-30.3164.743438189671100
3-3.50.1598.915536414496199.8
3.5-40.07318.09306408106199.6
4-60.04227.994443111693199.8
6-80.03531.17108232873199.7
8-100.02242.4838241030199.6
10-200.01946.093470969186.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU.

3gju

3i5t

3hmu


Resolution: 2.6→19.83 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.1952 / WRfactor Rwork: 0.1511 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8445 / SU B: 22.88 / SU ML: 0.231 / SU R Cruickshank DPI: 0.2489 / SU Rfree: 0.3015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 3063 5.1 %RANDOM
Rwork0.1784 ---
all0.1809 60090 --
obs0.1809 60090 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.11 Å2 / Biso mean: 38.2066 Å2 / Biso min: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å2-0 Å2-0.03 Å2
2---2.41 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14012 0 20 245 14277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914394
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9619530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80451792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64823.313640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.208152272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741596
X-RAY DIFFRACTIONr_chiral_restr0.090.22084
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111112
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 231 -
Rwork0.254 4014 -
all-4245 -
obs--99.81 %
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)
11.92870.48570.01432.4544-0.25731.46360.0094-0.06020.0040.11240.0950.3472-0.2796-0.2256-0.10450.08960.0831-0.02660.17540.05610.2323-2.391435.263764.6429
21.28980.11580.7251.48610.25711.53660.00030.0587-0.0644-0.12630.10820.20520.1648-0.0662-0.10850.1001-0.0034-0.04770.0810.04190.11269.7299.994864.4594
31.7985-1.41580.80951.5434-0.75151.40770.1214-0.0193-0.1136-0.07320.11760.35340.2245-0.2074-0.2390.0536-0.0416-0.03040.20740.0750.2915-2.393912.523665.5347
42.022-0.7707-0.10793.5254-0.75931.6646-0.0538-0.2307-0.10450.31740.14950.5281-0.1376-0.5443-0.09570.04480.019-0.01070.25160.0910.3323-6.504219.890665.6329
50.56120.8496-0.31351.91320.21761.3198-0.14570.139-0.0421-0.43240.1378-0.00120.08330.03780.00790.25960.0558-0.11820.26430.05950.17476.386624.572244.4076
630.4162-2.3577-10.65342.0035-0.24214.8548-0.11241.2537-0.0346-0.60710.28150.25820.0377-0.5144-0.1690.5584-0.1514-0.14420.33140.0180.1440.190930.708938.8075
70.961.26440.18192.16220.65080.38070.03450.0513-0.12310.4882-0.08970.00890.3609-0.15420.05530.580.08140.12620.68510.1640.6649-10.246423.013390.0643
81.82170.0014-0.06970.64720.82742.12410.0076-0.05870.05220.1816-0.00050.3055-0.0011-0.3257-0.00710.19620.11750.09160.12580.08240.3604-0.719441.280176.2684
90.70360.3124-0.01841.80890.46072.1939-0.0317-0.1108-0.03110.3970.0156-0.05-0.11240.20860.01610.15250.0267-0.04120.11570.01770.082122.341531.822785.3046
102.9688-1.26610.26863.34260.94680.4274-0.01290.0561-0.05460.125-0.03090.15990.0335-0.00830.04380.21470.037-0.05820.13820.06640.075514.232538.077572.0596
111.456-0.1788-0.03071.9446-0.61340.31680.0248-0.19540.13670.61930.11840.2578-0.3709-0.1178-0.14320.46070.15570.11910.09920.03460.17887.130140.81991.7314
121.0713-0.19711.18872.8894-2.59453.31690.1651-0.2487-0.24450.47120.25360.325-0.2228-0.4182-0.41880.49610.08730.17940.32560.10620.39960.574431.9918104.4975
131.916-0.58390.48022.8619-0.80943.4913-0.032-0.24170.13210.09350.11210.1788-0.2946-0.2525-0.080.219-0.0019-0.00810.1211-0.05090.1342-25.760461.014122.5101
142.23910.0187-1.18814.29750.58651.90120.04740.2358-0.0828-0.23770.0369-0.6588-0.05380.4632-0.08420.05550.0074-0.05240.4301-0.01190.3779-2.272147.400413.1139
150.89820.30760.13161.4508-0.14932.1223-0.0639-0.0068-0.16670.0290.0012-0.17330.28060.06580.06270.17210.05680.01170.1006-0.01560.1837-25.179229.265413.2472
161.37351.2534-0.55832.13390.37751.2144-0.0642-0.0543-0.1108-0.10090.0464-0.32140.09840.22680.01780.16190.08660.01220.26530.02470.294-12.626636.262517.6866
171.38170.37050.00281.83770.26530.0587-0.07540.1819-0.303-0.48730.1415-0.4377-0.04570.1078-0.06610.23650.07670.01180.494-0.01780.4086-6.667938.724811.2381
181.62171.2759-0.66331.9104-0.25580.66990.0855-0.22850.08650.2367-0.11030.1883-0.0366-0.06360.02480.25190.0366-0.05240.266-0.00510.1419-30.388845.420635.3713
190.9428-0.6214-0.40381.6505-0.63991.3250.0057-0.0094-0.2209-0.5479-0.0391-0.35210.50030.36650.03340.3796-0.00210.10220.6624-0.10090.67823.530345.3241-1.4147
200.7245-0.07560.18380.8970.06751.4473-0.0227-0.03260.11-0.07820.0209-0.1257-0.14630.09420.00190.165-0.03720.03150.1262-0.02550.1497-22.487755.94924.4561
210.85370.1064-0.13071.3487-0.34351.68490.00860.40680.0044-0.32620.0104-0.1108-0.08560.0422-0.0190.3504-0.0030.04120.2478-0.03030.1291-25.508553.0023-15.796
221.0644-0.40730.61031.18180.46810.9802-0.0205-0.01820.0766-0.22730.0656-0.1991-0.27340.1842-0.04510.3166-0.06260.05630.17930.01130.1918-18.770660.99272.1657
230.78130.5291.09341.44151.88822.7840.22250.3558-0.34470.03730.115-0.11140.16090.5122-0.33740.4508-0.00620.13950.6366-0.04760.4559-2.706950.0578-21.3867
240.70290.8508-1.6481.2167-2.37664.72790.19960.1676-0.01910.0433-0.0928-0.0485-0.18580.3852-0.10680.5042-0.00020.22680.9384-0.15890.73095.400555.496-17.8854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 106
2X-RAY DIFFRACTION2A107 - 238
3X-RAY DIFFRACTION3A239 - 301
4X-RAY DIFFRACTION4A302 - 366
5X-RAY DIFFRACTION5A367 - 429
6X-RAY DIFFRACTION6A430 - 453
7X-RAY DIFFRACTION7B5 - 41
8X-RAY DIFFRACTION8B42 - 109
9X-RAY DIFFRACTION9B110 - 282
10X-RAY DIFFRACTION10B283 - 314
11X-RAY DIFFRACTION11B315 - 388
12X-RAY DIFFRACTION12B389 - 453
13X-RAY DIFFRACTION13C5 - 58
14X-RAY DIFFRACTION14C59 - 106
15X-RAY DIFFRACTION15C107 - 265
16X-RAY DIFFRACTION16C266 - 301
17X-RAY DIFFRACTION17C302 - 350
18X-RAY DIFFRACTION18C351 - 453
19X-RAY DIFFRACTION19D5 - 60
20X-RAY DIFFRACTION20D61 - 159
21X-RAY DIFFRACTION21D160 - 283
22X-RAY DIFFRACTION22D284 - 357
23X-RAY DIFFRACTION23D358 - 426
24X-RAY DIFFRACTION24D427 - 453

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