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- PDB-4rbn: The crystal structure of Nitrosomonas europaea sucrose synthase: ... -

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Basic information

Entry
Database: PDB / ID: 4rbn
TitleThe crystal structure of Nitrosomonas europaea sucrose synthase: Insights into the evolutionary origin of sucrose metabolism in prokaryotes
ComponentsSucrose synthase:Glycosyl transferases group 1
KeywordsTRANSFERASE / Sucrose Synthase / Rossmann Fold / glucosyltransferase / NDP-glucose / D-fructose / NDP / Sucrose / cytosol
Function / homology
Function and homology information


sucrose synthase / sucrose synthase activity / sucrose metabolic process
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1230 / Nuclear Transport Factor 2; Chain: A, - #330 / Sucrose synthase, plant/cyanobacteria / Sucrose synthase / Sucrose synthase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Nuclear Transport Factor 2; Chain: A, / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1230 / Nuclear Transport Factor 2; Chain: A, - #330 / Sucrose synthase, plant/cyanobacteria / Sucrose synthase / Sucrose synthase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Nuclear Transport Factor 2; Chain: A, / Four Helix Bundle (Hemerythrin (Met), subunit A) / Roll / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsWu, R. / Asencion Diez, M.D. / Figueroa, C.M. / Machtey, M. / Iglesias, A.A. / Ballicora, M.A. / Liu, D.
CitationJournal: J.Bacteriol. / Year: 2015
Title: The Crystal Structure of Nitrosomonas europaea Sucrose Synthase Reveals Critical Conformational Changes and Insights into Sucrose Metabolism in Prokaryotes.
Authors: Wu, R. / Asencion Diez, M.D. / Figueroa, C.M. / Machtey, M. / Iglesias, A.A. / Ballicora, M.A. / Liu, D.
History
DepositionSep 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sucrose synthase:Glycosyl transferases group 1
C: Sucrose synthase:Glycosyl transferases group 1
B: Sucrose synthase:Glycosyl transferases group 1
D: Sucrose synthase:Glycosyl transferases group 1


Theoretical massNumber of molelcules
Total (without water)363,8734
Polymers363,8734
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-19 kcal/mol
Surface area124990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.899, 236.899, 213.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Sucrose synthase:Glycosyl transferases group 1


Mass: 90968.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: ss2, NE1214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q820M5, sucrose synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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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: 4.75 Å3/Da / Density % sol: 74.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 5% Tacsimate pH 5.0, 5% (w/v) PEG 3350, and 0.1 M sodium citrate pH 5.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.05→72.883 Å / Num. obs: 126170 / % possible obs: 97.9 %
Reflection shellHighest resolution: 3.05 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→68.387 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 6336 5.02 %
Rwork0.176 --
obs0.1786 126123 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→68.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25390 0 0 205 25595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125989
X-RAY DIFFRACTIONf_angle_d1.53735229
X-RAY DIFFRACTIONf_dihedral_angle_d18.4379645
X-RAY DIFFRACTIONf_chiral_restr0.113825
X-RAY DIFFRACTIONf_plane_restr0.0074616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.08470.36612190.29334015X-RAY DIFFRACTION99
3.0847-3.1210.3362110.27114033X-RAY DIFFRACTION99
3.121-3.15910.32592040.26094027X-RAY DIFFRACTION99
3.1591-3.1990.3241890.25534037X-RAY DIFFRACTION99
3.199-3.24110.32462120.25323990X-RAY DIFFRACTION99
3.2411-3.28550.29992170.25014044X-RAY DIFFRACTION98
3.2855-3.33250.3391920.24374022X-RAY DIFFRACTION99
3.3325-3.38220.26181980.22934028X-RAY DIFFRACTION99
3.3822-3.43510.27382280.21614010X-RAY DIFFRACTION98
3.4351-3.49140.25852380.2053958X-RAY DIFFRACTION98
3.4914-3.55160.29661960.20774000X-RAY DIFFRACTION98
3.5516-3.61620.27732530.20113986X-RAY DIFFRACTION98
3.6162-3.68570.24282070.1853989X-RAY DIFFRACTION98
3.6857-3.76090.21642230.17324026X-RAY DIFFRACTION98
3.7609-3.84270.23732170.1693965X-RAY DIFFRACTION98
3.8427-3.93210.24872300.17523985X-RAY DIFFRACTION98
3.9321-4.03040.22021970.164017X-RAY DIFFRACTION98
4.0304-4.13940.19862050.15354004X-RAY DIFFRACTION98
4.1394-4.26110.20262270.14883946X-RAY DIFFRACTION98
4.2611-4.39870.21062130.1494003X-RAY DIFFRACTION98
4.3987-4.55580.19371960.1484040X-RAY DIFFRACTION98
4.5558-4.73820.21522010.14463974X-RAY DIFFRACTION98
4.7382-4.95380.18442090.1413937X-RAY DIFFRACTION97
4.9538-5.21490.18592150.14153972X-RAY DIFFRACTION97
5.2149-5.54150.21771750.14853981X-RAY DIFFRACTION97
5.5415-5.96910.20151980.16353950X-RAY DIFFRACTION96
5.9691-6.56940.24132120.17623964X-RAY DIFFRACTION97
6.5694-7.51890.20722100.16273957X-RAY DIFFRACTION97
7.5189-9.46910.16272190.14063976X-RAY DIFFRACTION97
9.4691-68.4040.19372250.17313951X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1309-0.03550.00690.09920.00160.15060.0577-0.04890.1067-0.01510.01510.05650.0995-0.18350.2276-0.2299-0.0958-0.11380.1371-0.09740.0936-35.599395.7354-25.9995
20.0617-0.0029-0.00920.10770.01690.0059-0.04720.0292-0.02010.2783-0.13450.23820.157-0.1144-0.17960.1324-0.2920.19690.2677-0.1180.1665-49.453887.7537-9.1623
30.1121-0.0395-0.02360.04540.00630.06320.0679-0.1740.02990.08010.0734-0.03510.03010.12680.2331-0.0736-0.0027-0.28760.1509-0.06180.07659.441299.1363-2.685
40.0334-0.02210.03850.0676-0.03180.0476-0.0666-0.04090.08830.21270.05110.0057-0.06620.04060.00490.14810.0854-0.19940.2911-0.2356-0.00365.0716107.601418.6032
50.1251-0.02610.01730.1507-0.01720.13770.0699-0.00570.09190.01490.0183-0.14170.08450.20220.2187-0.14460.0205-0.02190.18930.13070.168527.855597.5485-39.8488
60.0526-0.00220.01540.0503-0.01110.0157-0.0255-0.02670.0016-0.1759-0.1106-0.17550.10810.0701-0.15750.10660.18040.12190.28380.17320.208342.814789.7254-56.1806
70.12450.060.01910.0272-0.00860.068-0.01330.25680.0542-0.09090.0764-0.01560.0294-0.10610.08210.0007-0.0524-0.15870.23780.08940.1103-17.168997.1264-63.3761
80.03240.02350.0314-0.00920.00970.0386-0.05260.00660.054-0.088-0.003-0.0242-0.02960.0156-0.06390.147-0.1738-0.18440.36650.17960.0092-13.695105.0982-86.9987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 483 )
2X-RAY DIFFRACTION2chain 'A' and (resid 484 through 792 )
3X-RAY DIFFRACTION3chain 'C' and (resid 4 through 483 )
4X-RAY DIFFRACTION4chain 'C' and (resid 484 through 792 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 483 )
6X-RAY DIFFRACTION6chain 'B' and (resid 484 through 792 )
7X-RAY DIFFRACTION7chain 'D' and (resid 4 through 522 )
8X-RAY DIFFRACTION8chain 'D' and (resid 523 through 792 )

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