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- PDB-7b0m: Sugar transaminase from a metagenome collected from troll oil fie... -

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Basic information

Entry
Database: PDB / ID: 7b0m
TitleSugar transaminase from a metagenome collected from troll oil field production water
ComponentsSugar aminotransferase
KeywordsTRANSFERASE / aminotransferase / thermostability / catalysis
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, LLPSF_NHT_00031 family / 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
DI(HYDROXYETHYL)ETHER / Sugar aminotransferase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsLittlechild, J.A. / De Rose, S.A. / Isupov, M.N. / Sayer, C. / Karki, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L002035/1 United Kingdom
CitationJournal: To Be Published
Title: Sugar transaminases from hot environments
Authors: James, P. / Littlechild, J.A. / De Rose, S.A. / Isupov, M.N. / Karki, S. / Tabji, A.B. / Garcia-Moyano, A. / Birkeland, N.K.
History
DepositionNov 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Sugar aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,19211
Polymers42,3071
Non-polymers88510
Water6,233346
1
AAA: Sugar aminotransferase
hetero molecules

AAA: Sugar aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,38522
Polymers84,6152
Non-polymers1,77020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area8440 Å2
ΔGint19 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.405, 76.405, 134.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11AAA-676-

HOH

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Components

#1: Protein Sugar aminotransferase


Mass: 42307.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A5Q0MTV0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.2
Details: 0.2 M Lithium Sulfate,0.1 M Phosphate, 20% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.43→59.37 Å / Num. obs: 84599 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 8.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.9
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 8.3 % / Rmerge(I) obs: 2.873 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4170 / CC1/2: 0.282 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BN1

3bn1


Resolution: 1.43→59.37 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.565 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1973 4195 4.963 %
Rwork0.1651 80337 -
all0.167 --
obs-84532 99.969 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 34.673 Å2
Baniso -1Baniso -2Baniso -3
1-0.465 Å20.232 Å20 Å2
2--0.465 Å20 Å2
3----1.508 Å2
Refinement stepCycle: LAST / Resolution: 1.43→59.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 58 346 3331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133204
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173133
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.654342
X-RAY DIFFRACTIONr_angle_other_deg1.4791.5777288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.523.775151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28115583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7321512
X-RAY DIFFRACTIONr_chiral_restr0.1080.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02686
X-RAY DIFFRACTIONr_nbd_refined0.2250.2620
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22923
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21566
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0590.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.219
X-RAY DIFFRACTIONr_nbd_other0.1930.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2230.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_mcbond_it5.9338.4841526
X-RAY DIFFRACTIONr_mcbond_other5.9078.4741525
X-RAY DIFFRACTIONr_mcangle_it6.11114.2371919
X-RAY DIFFRACTIONr_mcangle_other6.11814.2551920
X-RAY DIFFRACTIONr_scbond_it8.5510.0351678
X-RAY DIFFRACTIONr_scbond_other8.54810.041679
X-RAY DIFFRACTIONr_scangle_it10.26215.9762400
X-RAY DIFFRACTIONr_scangle_other10.2615.9812401
X-RAY DIFFRACTIONr_lrange_it9.78663.7414065
X-RAY DIFFRACTIONr_lrange_other9.75463.32913737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.4670.3453540.3575843X-RAY DIFFRACTION99.9677
1.467-1.5070.3643250.3315711X-RAY DIFFRACTION99.9669
1.507-1.5510.2842770.315554X-RAY DIFFRACTION100
1.551-1.5990.3052640.2955444X-RAY DIFFRACTION99.965
1.599-1.6510.2632760.2445248X-RAY DIFFRACTION100
1.651-1.7090.2662490.2245097X-RAY DIFFRACTION100
1.709-1.7730.2332730.2084902X-RAY DIFFRACTION100
1.773-1.8460.2342530.1894698X-RAY DIFFRACTION99.9596
1.846-1.9280.2232400.1814576X-RAY DIFFRACTION100
1.928-2.0220.2072170.1824339X-RAY DIFFRACTION99.9781
2.022-2.1310.221850.1784196X-RAY DIFFRACTION100
2.131-2.260.2021950.1743906X-RAY DIFFRACTION100
2.26-2.4160.1911930.1493719X-RAY DIFFRACTION99.9744
2.416-2.6090.1861500.1513501X-RAY DIFFRACTION100
2.609-2.8580.1671630.1413200X-RAY DIFFRACTION100
2.858-3.1950.1831390.152913X-RAY DIFFRACTION100
3.195-3.6870.1651470.1492562X-RAY DIFFRACTION99.8526
3.687-4.5130.1441190.1242205X-RAY DIFFRACTION100
4.513-6.3670.1751200.1441707X-RAY DIFFRACTION99.8361
6.367-59.370.29560.1751017X-RAY DIFFRACTION99.1682

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