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- PDB-7b0d: Sugar transaminase from Archaeoglobus veneficus -

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Basic information

Entry
Database: PDB / ID: 7b0d
TitleSugar transaminase from Archaeoglobus veneficus
ComponentsGlutamine--scyllo-inositol transaminase
KeywordsTRANSFERASE / aminotransferase / thermostability / catalysis
Function / homology
Function and homology information


glutamine-scyllo-inositol transaminase / glutamine-scyllo-inositol transaminase activity / : / polysaccharide biosynthetic process / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glutamine--scyllo-inositol transaminase
Similarity search - Component
Biological speciesArchaeoglobus veneficus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsJames, P. / Littlechild, J.A. / De Rose, S.A. / Isupov, M.N.
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 19, 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 / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine--scyllo-inositol transaminase
B: Glutamine--scyllo-inositol transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,79330
Polymers91,6002
Non-polymers2,19328
Water13,061725
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-68 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.227, 105.953, 111.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 0 - 367 / Label seq-ID: 28 - 395

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamine--scyllo-inositol transaminase / Sugar transaminase


Mass: 45799.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus veneficus (strain DSM 11195 / SNP6) (archaea)
Strain: DSM 11195 / SNP6 / Gene: Arcve_0555 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F2KQE6, glutamine-scyllo-inositol transaminase

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Non-polymers , 6 types, 753 molecules

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


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: PO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.2 / Details: 0.1 M phosphate/citrate 20 % w/v PEG 6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.27→49.29 Å / Num. obs: 212879 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Redundancy: 5 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.3
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.352 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 9242 / CC1/2: 0.305 / % possible all: 87

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Processing

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

3nyu


Resolution: 1.27→49.287 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.139 / SU B: 0.838 / SU ML: 0.034 / Average fsc free: 0.913 / Average fsc work: 0.9172 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1747 10625 4.993 %
Rwork0.1516 202153 -
all0.153 --
obs-212778 97.585 %
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: 21.446 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0 Å2
2--0.078 Å20 Å2
3---0.232 Å2
Refinement stepCycle: LAST / Resolution: 1.27→49.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 129 725 6836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177150
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.65310159
X-RAY DIFFRACTIONr_angle_other_deg1.3771.58316743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16751018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11723.079432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.353151461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6951548
X-RAY DIFFRACTIONr_chiral_restr0.0840.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021698
X-RAY DIFFRACTIONr_nbd_refined0.220.21411
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.26376
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23241
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.23109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2547
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.242
X-RAY DIFFRACTIONr_nbd_other0.2030.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1580.21
X-RAY DIFFRACTIONr_mcbond_it2.6734.8693300
X-RAY DIFFRACTIONr_mcbond_other2.654.8643294
X-RAY DIFFRACTIONr_mcangle_it3.7588.2194201
X-RAY DIFFRACTIONr_mcangle_other3.7598.2244202
X-RAY DIFFRACTIONr_scbond_it4.8946.334080
X-RAY DIFFRACTIONr_scbond_other4.796.3094041
X-RAY DIFFRACTIONr_scangle_it6.62210.0885806
X-RAY DIFFRACTIONr_scangle_other6.55410.0475747
X-RAY DIFFRACTIONr_lrange_it7.87538.00831284
X-RAY DIFFRACTIONr_lrange_other7.87137.98131256
X-RAY DIFFRACTIONr_ncsr_local_group_10.1170.0513530
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.116790.05008
12BX-RAY DIFFRACTIONLocal ncs0.116790.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.3030.3166890.31413336X-RAY DIFFRACTION87.755
1.303-1.3390.3027140.29113855X-RAY DIFFRACTION93.6251
1.339-1.3770.2766980.26213896X-RAY DIFFRACTION95.9942
1.377-1.420.2637270.24113721X-RAY DIFFRACTION98.3861
1.42-1.4660.2227450.21413541X-RAY DIFFRACTION99.5263
1.466-1.5180.2126900.19313051X-RAY DIFFRACTION99.6519
1.518-1.5750.1936590.18212555X-RAY DIFFRACTION99.1298
1.575-1.6390.1986480.16912042X-RAY DIFFRACTION98.3111
1.639-1.7120.1846600.15311652X-RAY DIFFRACTION99.5875
1.712-1.7960.1725820.14411179X-RAY DIFFRACTION99.6864
1.796-1.8930.1575380.13710716X-RAY DIFFRACTION99.8049
1.893-2.0080.165350.13410083X-RAY DIFFRACTION99.7932
2.008-2.1460.165000.1339468X-RAY DIFFRACTION99.1939
2.146-2.3180.1424520.1238624X-RAY DIFFRACTION96.8623
2.318-2.5390.1534310.1258175X-RAY DIFFRACTION99.6295
2.539-2.8380.1513940.1277394X-RAY DIFFRACTION99.2355
2.838-3.2770.1613420.1346576X-RAY DIFFRACTION99.3537
3.277-4.0110.1382730.1185550X-RAY DIFFRACTION98.1791
4.011-5.6650.162150.1394202X-RAY DIFFRACTION94.928
5.665-49.280.2641330.2212537X-RAY DIFFRACTION98.8157

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