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- PDB-7qqj: Sucrose phosphorylase from Jeotgalibaca ciconiae -

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Basic information

Entry
Database: PDB / ID: 7qqj
TitleSucrose phosphorylase from Jeotgalibaca ciconiae
ComponentsSucrose phosphorylase
KeywordsTRANSFERASE / sucrose phosphorylase
Function / homology
Function and homology information


sucrose phosphorylase / sucrose phosphorylase activity / :
Similarity search - Function
Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Sucrose phosphorylase
Similarity search - Component
Biological speciesJeotgalibaca ciconiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsUbiparip, Z. / Capra, N. / Rozeboom, H.J. / Desmet, T. / Thunnissen, A.M.W.H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission761030European Union
CitationJournal: To Be Published
Title: Sucrose phosphorylase from Jeotgalibaca ciconiae
Authors: Ubiparip, Z. / Capra, N. / Rozeboom, H.J. / Thunnissen, A.M.W.H. / Desmet, T.
History
DepositionJan 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Sucrose phosphorylase
B: Sucrose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0343
Polymers111,9122
Non-polymers1221
Water5,927329
1
A: Sucrose phosphorylase


Theoretical massNumber of molelcules
Total (without water)55,9561
Polymers55,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sucrose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0782
Polymers55,9561
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.639, 90.828, 96.170
Angle α, β, γ (deg.)90.000, 92.832, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 1 - 474 / Label seq-ID: 1 - 474

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

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

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Components

#1: Protein Sucrose phosphorylase / Sucrose glucosyltransferase


Mass: 55955.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jeotgalibaca ciconiae (bacteria) / Gene: gtfA, EJN90_09285 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S9HEG3, sucrose phosphorylase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein was concentrated to 16 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: ...Details: Protein was concentrated to 16 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 25% PEG 3350, 0.1 M Bis-tris propane, pH 6.5, 50 mM Na/K phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.05→48 Å / Num. obs: 54973 / % possible obs: 98.8 % / Redundancy: 3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.121 / Rrim(I) all: 0.172 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.94-4830.0466510.9940.0460.064
2.05-2.112.80.90842720.3360.8851.269

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Processing

Software
NameVersionClassification
XDSdata scaling
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QQI

7qqi


Resolution: 2.05→48 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.37 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / ESU R: 0.266 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2544 2719 4.948 %
Rwork0.1958 52229 -
all0.199 --
obs-54948 98.669 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.144 Å2
Baniso -1Baniso -2Baniso -3
1-0.944 Å20 Å20.442 Å2
2---0.56 Å20 Å2
3----0.426 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7846 0 8 329 8183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138061
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167433
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.64510918
X-RAY DIFFRACTIONr_angle_other_deg1.281.58217176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42323.254464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5461540
X-RAY DIFFRACTIONr_chiral_restr0.0740.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021865
X-RAY DIFFRACTIONr_nbd_refined0.2020.21657
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.27099
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23867
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23795
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2377
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0740.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.249
X-RAY DIFFRACTIONr_nbd_other0.2430.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.216
X-RAY DIFFRACTIONr_mcbond_it2.593.0643787
X-RAY DIFFRACTIONr_mcbond_other2.5913.0633785
X-RAY DIFFRACTIONr_mcangle_it3.684.5894729
X-RAY DIFFRACTIONr_mcangle_other3.684.5894730
X-RAY DIFFRACTIONr_scbond_it3.2513.4924274
X-RAY DIFFRACTIONr_scbond_other3.253.4924275
X-RAY DIFFRACTIONr_scangle_it4.995.0866189
X-RAY DIFFRACTIONr_scangle_other4.995.0866190
X-RAY DIFFRACTIONr_lrange_it6.46236.0359166
X-RAY DIFFRACTIONr_lrange_other6.4535.9729126
X-RAY DIFFRACTIONr_ncsr_local_group_10.1060.0515550
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.106390.05007
12BX-RAY DIFFRACTIONLocal ncs0.106390.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1030.3012040.3013848X-RAY DIFFRACTION99.3868
2.103-2.1610.3372160.2883786X-RAY DIFFRACTION99.6514
2.161-2.2230.3021800.2593721X-RAY DIFFRACTION99.8209
2.223-2.2920.3151950.2433518X-RAY DIFFRACTION99.3578
2.292-2.3670.2721650.2153502X-RAY DIFFRACTION99.4036
2.367-2.450.2641830.2143324X-RAY DIFFRACTION99.1518
2.45-2.5420.2741940.2143193X-RAY DIFFRACTION99.1511
2.542-2.6460.2791810.2043047X-RAY DIFFRACTION98.4146
2.646-2.7640.2931460.1872980X-RAY DIFFRACTION98.4257
2.764-2.8980.2691230.1952841X-RAY DIFFRACTION98.2759
2.898-3.0550.2311090.1762767X-RAY DIFFRACTION99.2409
3.055-3.240.2261240.1672568X-RAY DIFFRACTION99.4826
3.24-3.4640.2491130.1852432X-RAY DIFFRACTION99.3365
3.464-3.7410.2481280.1642218X-RAY DIFFRACTION98.4887
3.741-4.0970.1961040.1522021X-RAY DIFFRACTION97.1651
4.097-4.580.205930.1541851X-RAY DIFFRACTION97.006
4.58-5.2860.2151000.1631602X-RAY DIFFRACTION95.9955
5.286-6.4690.28640.2151390X-RAY DIFFRACTION97.1925
6.469-9.1280.277620.2161045X-RAY DIFFRACTION95.5134
9.128-480.236350.233575X-RAY DIFFRACTION91.1809

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