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- PDB-8vr3: crystal structure of the Pcryo_0618 aminotransferase from Psychro... -

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Basic information

Entry
Database: PDB / ID: 8vr3
Titlecrystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of its internal aldimine
ComponentsDegT/DnrJ/EryC1/StrS aminotransferase
KeywordsTRANSFERASE / psychrobacter / aminotransferase / aldimine / 2 / 3 / 4-trideoxy-l-arabinose
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 / DegT/DnrJ/EryC1/StrS aminotransferase
Similarity search - Component
Biological speciesPsychrobacter cryohalolentis K5 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,6818
Polymers82,9052
Non-polymers7766
Water9,314517
1
A: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules

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


  • defined by author&software
  • 83.1 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)83,1218
Polymers82,9052
Non-polymers2166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5190 Å2
ΔGint-63 kcal/mol
Surface area27220 Å2
MethodPISA
2
B: DegT/DnrJ/EryC1/StrS aminotransferase
hetero molecules

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


  • defined by author&software
  • 84.2 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)84,2418
Polymers82,9052
Non-polymers1,3366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4120 Å2
ΔGint-33 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.019, 157.970, 130.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 41452.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria)
Gene: Pcryo_0618 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q1QD52

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Non-polymers , 5 types, 523 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-A1ADI / 2,2'-(1,4-diazepane-1,4-diyl)di(ethane-1-sulfonic acid)


Mass: 316.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20N2O6S2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 65.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein incubated with 5 mM UDP and 5 mM PLP. Precipitant: 18-22% PEG 5000, 200 mM tetraethylammonium 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: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 80593 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rsym value: 0.091 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10847 / Rsym value: 0.46 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.65 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.44 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23276 3972 4.9 %RANDOM
Rwork0.19753 ---
obs0.19927 76621 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 45 517 6346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125975
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165815
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6488094
X-RAY DIFFRACTIONr_angle_other_deg0.51.57513422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.258532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.327101071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026885
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021261
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_it2.0872.2132999
X-RAY DIFFRACTIONr_mcbond_other2.0842.2132999
X-RAY DIFFRACTIONr_mcangle_it3.2093.9683753
X-RAY DIFFRACTIONr_mcangle_other3.2093.9693754
X-RAY DIFFRACTIONr_scbond_it3.2342.6672976
X-RAY DIFFRACTIONr_scbond_other3.2342.6662977
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.244.7044337
X-RAY DIFFRACTIONr_long_range_B_refined7.01924.777006
X-RAY DIFFRACTIONr_long_range_B_other7.01924.777007
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.325 259 -
Rwork0.31 5428 -
obs--95.93 %

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