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- PDB-7l7x: X-ray structure of the Pcryo_0638 aminotransferase from Psychroba... -

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Basic information

Entry
Database: PDB / ID: 7l7x
TitleX-ray structure of the Pcryo_0638 aminotransferase from Psychrobacter cryohalolentis
ComponentsDegT/DnrJ/EryC1/StrS aminotransferase
KeywordsTRANSFERASE / aminotransferase / pyridoxal 5'-phosphate / carbohydrate / deoxysugar
Function / homology
Function and homology information


transaminase activity
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-4RA / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / TETRAMETHYLAMMONIUM ION / DegT/DnrJ/EryC1/StrS aminotransferase
Similarity search - Component
Biological speciesPsychrobacter cryohalolentis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLinehan, M.P. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134643 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar.
Authors: Linehan, M.P. / Thoden, J.B. / Holden, H.M.
History
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: DegT/DnrJ/EryC1/StrS aminotransferase
BBB: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,50720
Polymers89,5562
Non-polymers2,95018
Water23,0591280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-20 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.529, 63.141, 69.853
Angle α, β, γ (deg.)81.747, 78.593, 66.818
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein DegT/DnrJ/EryC1/StrS aminotransferase


Mass: 44778.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5) (bacteria)
Strain: ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5 / Gene: Pcryo_0638 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QD32

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Non-polymers , 6 types, 1298 molecules

#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-4RA / [(2R,3R,4R,5S,6R)-3-acetamido-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 819.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H36N5O20P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TMA / TETRAMETHYLAMMONIUM ION


Mass: 74.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18-22% PEG-8000, 200 mM tetramethylammonium chloride. protein incubated with 1 mM PLP and 5 mM UDP-2-acetamido-4-amino-2,4,6-trideoxy-D-glucose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 202026 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.057 / Net I/σ(I): 7.2
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 36011 / Rsym value: 0.229 / % possible all: 83

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3frk

3frk


Resolution: 1.3→29.957 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.948 / SU ML: 0.037 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1692 10084 4.991 %
Rwork0.1499 191942 -
all0.151 --
obs-202026 92.941 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.478 Å2-0.142 Å20.052 Å2
2---0.374 Å2-0.116 Å2
3----0.067 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6166 0 190 1280 7636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136719
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176025
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.6449191
X-RAY DIFFRACTIONr_angle_other_deg1.4961.57514010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0835853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38723.003343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.467151075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9171534
X-RAY DIFFRACTIONr_chiral_restr0.0820.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021416
X-RAY DIFFRACTIONr_nbd_refined0.2270.21418
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25841
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23194
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2986
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1980.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.215
X-RAY DIFFRACTIONr_nbd_other0.2080.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.243
X-RAY DIFFRACTIONr_mcbond_it1.1941.0973242
X-RAY DIFFRACTIONr_mcbond_other1.1921.0963241
X-RAY DIFFRACTIONr_mcangle_it1.8621.6444073
X-RAY DIFFRACTIONr_mcangle_other1.8621.6454074
X-RAY DIFFRACTIONr_scbond_it2.0211.3033477
X-RAY DIFFRACTIONr_scbond_other2.0211.3043478
X-RAY DIFFRACTIONr_scangle_it3.0521.8775091
X-RAY DIFFRACTIONr_scangle_other3.0511.8775092
X-RAY DIFFRACTIONr_lrange_it5.45115.7218419
X-RAY DIFFRACTIONr_lrange_other5.45115.7238420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3340.2986620.28112210X-RAY DIFFRACTION80.1195
1.334-1.370.2596730.25512404X-RAY DIFFRACTION83.3301
1.37-1.410.2466650.23912489X-RAY DIFFRACTION86.4087
1.41-1.4530.2346760.21312415X-RAY DIFFRACTION88.2143
1.453-1.5010.26310.19112369X-RAY DIFFRACTION90.7188
1.501-1.5540.1886290.17812206X-RAY DIFFRACTION92.3182
1.554-1.6120.1786060.16511940X-RAY DIFFRACTION93.865
1.612-1.6780.1696020.15111669X-RAY DIFFRACTION95.4496
1.678-1.7530.1656130.14411352X-RAY DIFFRACTION96.4608
1.753-1.8380.1565630.13810872X-RAY DIFFRACTION97.0301
1.838-1.9380.1655610.13610504X-RAY DIFFRACTION98.1288
1.938-2.0550.1565320.1389903X-RAY DIFFRACTION98.295
2.055-2.1970.144940.1289338X-RAY DIFFRACTION98.6257
2.197-2.3720.1494320.1218740X-RAY DIFFRACTION98.9642
2.372-2.5990.1494050.1138079X-RAY DIFFRACTION99.1121
2.599-2.9050.1353930.1167281X-RAY DIFFRACTION98.9555
2.905-3.3530.1613140.1266389X-RAY DIFFRACTION98.6025
3.353-4.1040.1482710.135379X-RAY DIFFRACTION97.9712
4.104-5.7940.1412410.1274133X-RAY DIFFRACTION98.3142
5.794-29.9570.2031210.2052270X-RAY DIFFRACTION97.7514

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