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- PDB-8vr5: crystal structure of the Pcryo_0618 aminotransferase from Psychro... -

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Basic information

Entry
Database: PDB / ID: 8vr5
Titlecrystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of PMP and glutamate
ComponentsDegT/DnrJ/EryC1/StrS aminotransferase
KeywordsTRANSFERASE / psychrobacter / aminotransferase / PMP / aldimine
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding / metal ion binding
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-A1ADI / Chem-PDG / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / DegT/DnrJ/EryC1/StrS aminotransferase
Similarity search - Component
Biological speciesPsychrobacter cryohalolentis K5 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBockhaus, N.J. / 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)R35 GM134643 United States
CitationJournal: To Be Published
Title: Biochemical Investigation of the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5
Authors: Bockhaus, N.J. / Dunsirn, M.M. / Thoden, J.B. / Holden, H.M.
History
DepositionJan 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DegT/DnrJ/EryC1/StrS aminotransferase
B: DegT/DnrJ/EryC1/StrS aminotransferase
C: DegT/DnrJ/EryC1/StrS aminotransferase
D: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,41627
Polymers168,4014
Non-polymers3,01523
Water15,439857
1
A: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules

A: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,94618
Polymers84,2012
Non-polymers1,74516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7380 Å2
ΔGint-27 kcal/mol
Surface area27700 Å2
MethodPISA
2
B: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules

B: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,76120
Polymers84,2012
Non-polymers2,56018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6110 Å2
ΔGint-76 kcal/mol
Surface area28400 Å2
MethodPISA
3
C: DegT/DnrJ/EryC1/StrS aminotransferase
D: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0638
Polymers84,2012
Non-polymers8626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-61 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.493, 159.822, 115.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 42100.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria)
Strain: Pcryo_0618 / Gene: Pcryo_0618 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD52

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Non-polymers , 8 types, 880 molecules

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


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1ADI / 2,2'-(1,4-diazepane-1,4-diyl)di(ethane-1-sulfonic acid)


Mass: 316.395 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H20N2O6S2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PDG / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID / N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE


Mass: 378.272 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H19N2O9P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein incubated with 1.0 mM PLP and 5 mM UDP-4-amino-2,3-diacetoamido-2,3,4-trideoxy-L-arabinose. Precipitant: 8-12% PEG 8000, 100 mM magnesium chloride, and 100 mM Homo-PIPES (pH 5)

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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: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 123706 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rsym value: 0.078 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 15159 / Rsym value: 0.34 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.89 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.942 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21348 6297 5.1 %RANDOM
Rwork0.17816 ---
obs0.17998 117412 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.968 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.2→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11583 0 185 857 12625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01211982
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611668
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.64816199
X-RAY DIFFRACTIONr_angle_other_deg0.5081.57326918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72351507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.745556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.119102157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.21867
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022516
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_it2.3112.175998
X-RAY DIFFRACTIONr_mcbond_other2.312.175998
X-RAY DIFFRACTIONr_mcangle_it3.6653.897494
X-RAY DIFFRACTIONr_mcangle_other3.6653.8917495
X-RAY DIFFRACTIONr_scbond_it3.4612.6655984
X-RAY DIFFRACTIONr_scbond_other3.4612.6655985
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6894.6778699
X-RAY DIFFRACTIONr_long_range_B_refined7.24722.3613540
X-RAY DIFFRACTIONr_long_range_B_other7.24722.3713541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 441 -
Rwork0.255 8432 -
obs--98.51 %

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