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- PDB-3isl: Crystal structure of ureidoglycine-glyoxylate aminotransferase (p... -

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Basic information

Entry
Database: PDB / ID: 3isl
TitleCrystal structure of ureidoglycine-glyoxylate aminotransferase (pucG) from Bacillus subtilis
ComponentsPurine catabolism protein pucG
KeywordsTRANSFERASE / Pyridoxalphosphate / PLP dependent enzymes / purine metabolism / transaminases / aminotransferases / Aminotransferase / Pyridoxal phosphate
Function / homology
Function and homology information


(S)-ureidoglycine-glyoxylate transaminase / allantoin catabolic process / glycine biosynthetic process, by transamination of glyoxylate / serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / purine nucleobase metabolic process / peroxisome
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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 ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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 / (S)-ureidoglycine--glyoxylate transaminase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsCosta, R. / Cendron, L. / Ramazzina, I. / Berni, R. / Peracchi, A. / Percudani, R. / Zanotti, G.
CitationJournal: To be Published
Title: Amino acids from purines in GUT bacteria
Authors: Costa, R. / Cendron, L. / Ramazzina, I. / Berni, R. / Peracchi, A. / Zanotti, G. / Percudani, R.
History
DepositionAug 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / 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_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: Purine catabolism protein pucG
B: Purine catabolism protein pucG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0924
Polymers91,5972
Non-polymers4942
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-33 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.400, 95.990, 101.290
Angle α, β, γ (deg.)90.00, 114.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

21B-548-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein Purine catabolism protein pucG / Ureidoglycine-glyoxylate aminotransferase


Mass: 45798.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: pucG, yurG, BSU32520 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 / References: UniProt: O32148, Transferases
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 30% PEG MME550, 0.1M NaCl, 0.1M Bicine, pH9.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2009 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.05→27.69 Å / Num. all: 54886 / Num. obs: 54886 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6971 / % possible all: 85.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JVO

1jvo


Resolution: 2.06→27.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.713 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.198 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24689 2787 5.1 %RANDOM
Rwork0.19341 ---
obs0.1961 52089 99.51 %-
all-54886 --
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: 28.436 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å2-1.7 Å2
2--2.22 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.06→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6002 0 30 306 6338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9748330
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26523.284268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.524151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.271554
X-RAY DIFFRACTIONr_chiral_restr0.1960.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0151.53836
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74426184
X-RAY DIFFRACTIONr_scbond_it3.21932312
X-RAY DIFFRACTIONr_scangle_it4.7314.52146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1544medium positional0.110.5
1446loose positional0.485
1544medium thermal0.812
1446loose thermal1.2510
LS refinement shellResolution: 2.061→2.115 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 200 -
Rwork0.261 3616 -
obs-3616 94.08 %
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)
10.60420.27750.22710.53250.2190.78260.0004-0.0012-0.06790.06240.0059-0.05970.01780.0422-0.00630.1606-0.02610.01060.11690.01450.145511.1964-14.320111.0999
20.74410.15560.55881.0520.47341.44070.0501-0.2266-0.02410.1202-0.0605-0.0621-0.0345-0.14140.01050.1147-0.0711-0.00720.16570.01160.113520.4435-3.373229.502
34.89980.8176-2.32013.38731.82244.62860.0742-0.0906-0.08610.3658-0.0924-0.55750.39630.0670.01820.1315-0.0325-0.04910.09210.12950.322415.5822-24.344527.8344
40.8466-0.11190.43431.1352-0.09840.8177-0.07180.00140.0572-0.00330.0092-0.0487-0.10960.12690.06260.1947-0.05170.0040.15370.00140.176714.9442-1.65277.7843
52.4269-0.13780.55080.67920.00831.7363-0.2059-0.26530.32410.09870.02090.0716-0.3531-0.16320.18510.23940.0041-0.04960.0683-0.02950.17993.488312.953313.3042
66.3576-4.35470.65429.64070.30077.39680.14480.05510.3838-0.7071-0.4164-0.2245-0.51330.26120.27170.2818-0.1115-0.08950.11940.05960.251210.92519.0635-0.8731
70.6890.00290.27340.5187-0.30750.46830.0066-0.0597-0.00010.071-0.0103-0.0442-0.0584-0.11020.00370.1656-0.02820.01820.14840.00930.1511-4.7393-17.684113.0253
80.4195-0.04810.3271.278-0.25581.83950.0951-0.1972-0.04790.212-0.0656-0.043-0.13440.0473-0.02950.133-0.11330.03020.25150.07110.1157-5.5007-27.344435.0746
95.715-1.25550.16047.2789-2.01290.5648-0.3-0.22040.28240.89120.2515-0.1277-0.2443-0.07720.04850.2944-0.06220.07430.3416-0.10610.1353-1.5175-7.271731.8786
101.0279-0.0885-0.14090.74890.18780.86260.0671-0.126-0.09270.1106-0.04590.10290.0303-0.1546-0.02120.1704-0.05510.0040.18610.04650.1825-10.0349-29.804713.5416
111.5963-0.1613-0.62420.72370.27852.27380.0387-0.2382-0.30330.06550.0127-0.01320.3540.2275-0.05140.1701-0.0341-0.00950.08520.0530.22982.7026-44.379613.4416
128.2896-3.4048-1.75519.84482.00526.39610.1160.2396-0.4886-0.1551-0.0610.29270.1826-0.2212-0.0550.2193-0.0727-0.00380.15290.01930.205-10.0713-50.42913.9175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 70
2X-RAY DIFFRACTION2A71 - 224
3X-RAY DIFFRACTION3A243 - 268
4X-RAY DIFFRACTION4A269 - 313
5X-RAY DIFFRACTION5A314 - 396
6X-RAY DIFFRACTION6A397 - 411
7X-RAY DIFFRACTION7B7 - 63
8X-RAY DIFFRACTION8B64 - 224
9X-RAY DIFFRACTION9B243 - 268
10X-RAY DIFFRACTION10B269 - 313
11X-RAY DIFFRACTION11B314 - 396
12X-RAY DIFFRACTION12B397 - 411

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