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- PDB-7xdr: Crystal structure of a glucosylglycerol phosphorylase from Marino... -

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Basic information

Entry
Database: PDB / ID: 7xdr
TitleCrystal structure of a glucosylglycerol phosphorylase from Marinobacter adhaerens
ComponentsGlucosylglycerol phosphorylase
KeywordsBIOSYNTHETIC PROTEIN / phosphorylase
Function / homology
Function and homology information


glucosylglycerol phosphorylase (configuration-retaining) / glucosylglycerol metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / glycosyltransferase 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
Glucosylglycerol phosphorylase
Similarity search - Component
Biological speciesMarinobacter adhaerens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWei, H.L. / Li, Q. / Yang, J.G. / Liu, W.D. / Sun, Y.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2022
Title: Protein Engineering of Glucosylglycerol Phosphorylase Facilitating Efficient and Highly Regio- and Stereoselective Glycosylation of Polyols in a Synthetic System.
Authors: Zhang, T. / Liu, P. / Wei, H. / Sun, X. / Zeng, Y. / Zhang, X. / Cai, Y. / Cui, M. / Ma, H. / Liu, W. / Sun, Y. / Yang, J.
History
DepositionMar 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Glucosylglycerol phosphorylase
B: Glucosylglycerol phosphorylase
C: Glucosylglycerol phosphorylase
D: Glucosylglycerol phosphorylase
E: Glucosylglycerol phosphorylase
F: Glucosylglycerol phosphorylase
G: Glucosylglycerol phosphorylase
H: Glucosylglycerol phosphorylase
I: Glucosylglycerol phosphorylase
J: Glucosylglycerol phosphorylase
K: Glucosylglycerol phosphorylase
L: Glucosylglycerol phosphorylase
M: Glucosylglycerol phosphorylase
N: Glucosylglycerol phosphorylase
O: Glucosylglycerol phosphorylase
P: Glucosylglycerol phosphorylase
Q: Glucosylglycerol phosphorylase
R: Glucosylglycerol phosphorylase


Theoretical massNumber of molelcules
Total (without water)987,89018
Polymers987,89018
Non-polymers00
Water30,7701708
1
A: Glucosylglycerol phosphorylase
B: Glucosylglycerol phosphorylase
C: Glucosylglycerol phosphorylase
D: Glucosylglycerol phosphorylase
G: Glucosylglycerol phosphorylase
R: Glucosylglycerol phosphorylase


Theoretical massNumber of molelcules
Total (without water)329,2976
Polymers329,2976
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-41 kcal/mol
Surface area96140 Å2
MethodPISA
2
E: Glucosylglycerol phosphorylase
K: Glucosylglycerol phosphorylase
L: Glucosylglycerol phosphorylase

H: Glucosylglycerol phosphorylase

M: Glucosylglycerol phosphorylase

N: Glucosylglycerol phosphorylase


Theoretical massNumber of molelcules
Total (without water)329,2976
Polymers329,2976
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area15200 Å2
ΔGint-45 kcal/mol
Surface area96340 Å2
MethodPISA
3
F: Glucosylglycerol phosphorylase
J: Glucosylglycerol phosphorylase
O: Glucosylglycerol phosphorylase

I: Glucosylglycerol phosphorylase

Q: Glucosylglycerol phosphorylase

P: Glucosylglycerol phosphorylase


Theoretical massNumber of molelcules
Total (without water)329,2976
Polymers329,2976
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
crystal symmetry operation2_756-x+2,y+1/2,-z+11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area15030 Å2
ΔGint-47 kcal/mol
Surface area96400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.267, 185.174, 257.619
Angle α, β, γ (deg.)90.000, 101.560, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 321 or (resid 322...
21(chain B and (resid 2 through 321 or (resid 322...
31(chain C and (resid 2 through 321 or (resid 322...
41(chain D and (resid 2 through 321 or (resid 322...
51(chain E and (resid 2 through 321 or (resid 322...
61(chain F and resid 2 through 480)
71(chain G and (resid 2 through 321 or (resid 322...
81(chain H and (resid 2 through 321 or (resid 322...
91(chain I and (resid 2 through 321 or (resid 322...
101(chain J and (resid 2 through 321 or (resid 322...
111(chain K and (resid 2 through 321 or (resid 322...
121(chain L and (resid 2 through 321 or (resid 322...
131(chain M and (resid 2 through 321 or (resid 322...
141(chain N and (resid 2 through 321 or (resid 322...
151(chain O and (resid 2 through 321 or (resid 322...
161(chain P and (resid 2 through 321 or (resid 322...
171(chain Q and (resid 2 through 321 or (resid 322...
181(chain R and (resid 2 through 321 or (resid 322...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUMETMET(chain A and (resid 2 through 321 or (resid 322...AA2 - 3212 - 321
12ARGARGARGARG(chain A and (resid 2 through 321 or (resid 322...AA322 - 323322 - 323
13METMETCYSCYS(chain A and (resid 2 through 321 or (resid 322...AA1 - 4801 - 480
14METMETCYSCYS(chain A and (resid 2 through 321 or (resid 322...AA1 - 4801 - 480
15METMETCYSCYS(chain A and (resid 2 through 321 or (resid 322...AA1 - 4801 - 480
16METMETCYSCYS(chain A and (resid 2 through 321 or (resid 322...AA1 - 4801 - 480
21LEULEUMETMET(chain B and (resid 2 through 321 or (resid 322...BB2 - 3212 - 321
22ARGARGARGARG(chain B and (resid 2 through 321 or (resid 322...BB322 - 323322 - 323
23METMETCYSCYS(chain B and (resid 2 through 321 or (resid 322...BB1 - 4801 - 480
24METMETCYSCYS(chain B and (resid 2 through 321 or (resid 322...BB1 - 4801 - 480
25METMETCYSCYS(chain B and (resid 2 through 321 or (resid 322...BB1 - 4801 - 480
26METMETCYSCYS(chain B and (resid 2 through 321 or (resid 322...BB1 - 4801 - 480
31LEULEUMETMET(chain C and (resid 2 through 321 or (resid 322...CC2 - 3212 - 321
32ARGARGARGARG(chain C and (resid 2 through 321 or (resid 322...CC322 - 323322 - 323
33METMETCYSCYS(chain C and (resid 2 through 321 or (resid 322...CC1 - 4801 - 480
34METMETCYSCYS(chain C and (resid 2 through 321 or (resid 322...CC1 - 4801 - 480
35METMETCYSCYS(chain C and (resid 2 through 321 or (resid 322...CC1 - 4801 - 480
36METMETCYSCYS(chain C and (resid 2 through 321 or (resid 322...CC1 - 4801 - 480
41LEULEUMETMET(chain D and (resid 2 through 321 or (resid 322...DD2 - 3212 - 321
42ARGARGARGARG(chain D and (resid 2 through 321 or (resid 322...DD322 - 323322 - 323
43METMETCYSCYS(chain D and (resid 2 through 321 or (resid 322...DD1 - 4801 - 480
44METMETCYSCYS(chain D and (resid 2 through 321 or (resid 322...DD1 - 4801 - 480
51LEULEUMETMET(chain E and (resid 2 through 321 or (resid 322...EE2 - 3212 - 321
52ARGARGARGARG(chain E and (resid 2 through 321 or (resid 322...EE322 - 323322 - 323
53LEULEUCYSCYS(chain E and (resid 2 through 321 or (resid 322...EE2 - 4802 - 480
54LEULEUCYSCYS(chain E and (resid 2 through 321 or (resid 322...EE2 - 4802 - 480
61LEULEUCYSCYS(chain F and resid 2 through 480)FF2 - 4802 - 480
71LEULEUMETMET(chain G and (resid 2 through 321 or (resid 322...GG2 - 3212 - 321
72ARGARGARGARG(chain G and (resid 2 through 321 or (resid 322...GG322 - 323322 - 323
73LEULEUCYSCYS(chain G and (resid 2 through 321 or (resid 322...GG2 - 4802 - 480
74LEULEUCYSCYS(chain G and (resid 2 through 321 or (resid 322...GG2 - 4802 - 480
81LEULEUMETMET(chain H and (resid 2 through 321 or (resid 322...HH2 - 3212 - 321
82ARGARGARGARG(chain H and (resid 2 through 321 or (resid 322...HH322 - 323322 - 323
83METMETCYSCYS(chain H and (resid 2 through 321 or (resid 322...HH1 - 4801 - 480
84METMETCYSCYS(chain H and (resid 2 through 321 or (resid 322...HH1 - 4801 - 480
85METMETCYSCYS(chain H and (resid 2 through 321 or (resid 322...HH1 - 4801 - 480
86METMETCYSCYS(chain H and (resid 2 through 321 or (resid 322...HH1 - 4801 - 480
91LEULEUMETMET(chain I and (resid 2 through 321 or (resid 322...II2 - 3212 - 321
92ARGARGARGARG(chain I and (resid 2 through 321 or (resid 322...II322 - 323322 - 323
93METMETCYSCYS(chain I and (resid 2 through 321 or (resid 322...II1 - 4801 - 480
94METMETCYSCYS(chain I and (resid 2 through 321 or (resid 322...II1 - 4801 - 480
95METMETCYSCYS(chain I and (resid 2 through 321 or (resid 322...II1 - 4801 - 480
96METMETCYSCYS(chain I and (resid 2 through 321 or (resid 322...II1 - 4801 - 480
101LEULEUMETMET(chain J and (resid 2 through 321 or (resid 322...JJ2 - 3212 - 321
102ARGARGARGARG(chain J and (resid 2 through 321 or (resid 322...JJ322 - 323322 - 323
103METMETCYSCYS(chain J and (resid 2 through 321 or (resid 322...JJ1 - 4801 - 480
104METMETCYSCYS(chain J and (resid 2 through 321 or (resid 322...JJ1 - 4801 - 480
105METMETCYSCYS(chain J and (resid 2 through 321 or (resid 322...JJ1 - 4801 - 480
106METMETCYSCYS(chain J and (resid 2 through 321 or (resid 322...JJ1 - 4801 - 480
111LEULEUMETMET(chain K and (resid 2 through 321 or (resid 322...KK2 - 3212 - 321
112ARGARGARGARG(chain K and (resid 2 through 321 or (resid 322...KK322 - 323322 - 323
113METMETCYSCYS(chain K and (resid 2 through 321 or (resid 322...KK1 - 4801 - 480
114METMETCYSCYS(chain K and (resid 2 through 321 or (resid 322...KK1 - 4801 - 480
121LEULEUMETMET(chain L and (resid 2 through 321 or (resid 322...LL2 - 3212 - 321
122ARGARGARGARG(chain L and (resid 2 through 321 or (resid 322...LL322 - 323322 - 323
123METMETCYSCYS(chain L and (resid 2 through 321 or (resid 322...LL1 - 4801 - 480
124METMETCYSCYS(chain L and (resid 2 through 321 or (resid 322...LL1 - 4801 - 480
125METMETCYSCYS(chain L and (resid 2 through 321 or (resid 322...LL1 - 4801 - 480
126METMETCYSCYS(chain L and (resid 2 through 321 or (resid 322...LL1 - 4801 - 480
131LEULEUMETMET(chain M and (resid 2 through 321 or (resid 322...MM2 - 3212 - 321
132ARGARGARGARG(chain M and (resid 2 through 321 or (resid 322...MM322 - 323322 - 323
133METMETCYSCYS(chain M and (resid 2 through 321 or (resid 322...MM1 - 4801 - 480
134METMETCYSCYS(chain M and (resid 2 through 321 or (resid 322...MM1 - 4801 - 480
135METMETCYSCYS(chain M and (resid 2 through 321 or (resid 322...MM1 - 4801 - 480
136METMETCYSCYS(chain M and (resid 2 through 321 or (resid 322...MM1 - 4801 - 480
141LEULEUMETMET(chain N and (resid 2 through 321 or (resid 322...NN2 - 3212 - 321
142ARGARGARGARG(chain N and (resid 2 through 321 or (resid 322...NN322 - 323322 - 323
143METMETCYSCYS(chain N and (resid 2 through 321 or (resid 322...NN1 - 4801 - 480
144METMETCYSCYS(chain N and (resid 2 through 321 or (resid 322...NN1 - 4801 - 480
145METMETCYSCYS(chain N and (resid 2 through 321 or (resid 322...NN1 - 4801 - 480
146METMETCYSCYS(chain N and (resid 2 through 321 or (resid 322...NN1 - 4801 - 480
151LEULEUMETMET(chain O and (resid 2 through 321 or (resid 322...OO2 - 3212 - 321
152ARGARGARGARG(chain O and (resid 2 through 321 or (resid 322...OO322 - 323322 - 323
153METMETCYSCYS(chain O and (resid 2 through 321 or (resid 322...OO1 - 4801 - 480
154METMETCYSCYS(chain O and (resid 2 through 321 or (resid 322...OO1 - 4801 - 480
161LEULEUMETMET(chain P and (resid 2 through 321 or (resid 322...PP2 - 3212 - 321
162ARGARGARGARG(chain P and (resid 2 through 321 or (resid 322...PP322 - 323322 - 323
163METMETCYSCYS(chain P and (resid 2 through 321 or (resid 322...PP1 - 4801 - 480
164METMETCYSCYS(chain P and (resid 2 through 321 or (resid 322...PP1 - 4801 - 480
165METMETCYSCYS(chain P and (resid 2 through 321 or (resid 322...PP1 - 4801 - 480
166METMETCYSCYS(chain P and (resid 2 through 321 or (resid 322...PP1 - 4801 - 480
171LEULEUMETMET(chain Q and (resid 2 through 321 or (resid 322...QQ2 - 3212 - 321
172ARGARGARGARG(chain Q and (resid 2 through 321 or (resid 322...QQ322 - 323322 - 323
173METMETCYSCYS(chain Q and (resid 2 through 321 or (resid 322...QQ1 - 4801 - 480
174METMETCYSCYS(chain Q and (resid 2 through 321 or (resid 322...QQ1 - 4801 - 480
175METMETCYSCYS(chain Q and (resid 2 through 321 or (resid 322...QQ1 - 4801 - 480
176METMETCYSCYS(chain Q and (resid 2 through 321 or (resid 322...QQ1 - 4801 - 480
181LEULEUMETMET(chain R and (resid 2 through 321 or (resid 322...RR2 - 3212 - 321
182ARGARGARGARG(chain R and (resid 2 through 321 or (resid 322...RR322 - 323322 - 323
183METMETCYSCYS(chain R and (resid 2 through 321 or (resid 322...RR1 - 4801 - 480
184METMETCYSCYS(chain R and (resid 2 through 321 or (resid 322...RR1 - 4801 - 480
185METMETCYSCYS(chain R and (resid 2 through 321 or (resid 322...RR1 - 4801 - 480
186METMETCYSCYS(chain R and (resid 2 through 321 or (resid 322...RR1 - 4801 - 480

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Components

#1: Protein
Glucosylglycerol phosphorylase / GGoP / 2-O-alpha-D-glucopyranosylglycerol:phosphate alpha-D-glucosyltransferase / 2-O-alpha-D- ...GGoP / 2-O-alpha-D-glucopyranosylglycerol:phosphate alpha-D-glucosyltransferase / 2-O-alpha-D-glucosylglycerol phosphorylase (retaining)


Mass: 54882.793 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter adhaerens (bacteria) / Strain: DSM 23420 / HP15 / Gene: gtfA, HP15_2853 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E4PMA5, glucosylglycerol phosphorylase (configuration-retaining)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1708 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG8000, MgAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2022
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→33.4 Å / Num. obs: 363096 / % possible obs: 99.6 % / Redundancy: 6.776 % / Biso Wilson estimate: 43.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.128 / Χ2: 0.895 / Net I/σ(I): 12.73 / Num. measured all: 4861714
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.556.7930.7892.127762341163831142650.8040.85498.2
2.55-2.726.9030.5263.317535731092821091660.9090.56999.9
2.72-2.947.0710.3645.047196161019331017750.950.39299.8
2.94-3.226.8260.2327.9563880793723935820.9770.25199.8
3.22-3.66.7790.13414.0757385584753846470.9910.14699.9
3.6-4.156.6920.08821.8350002474862747250.9950.09699.8
4.15-5.086.2560.06329.2439454763184630690.9960.06999.8
5.08-7.146.6890.05731.1932768249031489850.9970.06199.9
7.14-33.46.4970.03839.6317737627493273010.9990.04199.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S9V

6s9v


Resolution: 2.4→33.4 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.56 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 35798 4.99 %
Rwork0.1939 344959 -
obs0.1961 363085 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.48 Å2 / Biso mean: 49.2491 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: final / Resolution: 2.4→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms69488 0 0 1708 71196
Biso mean---43.98 -
Num. residues----8638
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A26154X-RAY DIFFRACTION8.048TORSIONAL
12B26154X-RAY DIFFRACTION8.048TORSIONAL
13C26154X-RAY DIFFRACTION8.048TORSIONAL
14D26154X-RAY DIFFRACTION8.048TORSIONAL
15E26154X-RAY DIFFRACTION8.048TORSIONAL
16F26154X-RAY DIFFRACTION8.048TORSIONAL
17G26154X-RAY DIFFRACTION8.048TORSIONAL
18H26154X-RAY DIFFRACTION8.048TORSIONAL
19I26154X-RAY DIFFRACTION8.048TORSIONAL
110J26154X-RAY DIFFRACTION8.048TORSIONAL
111K26154X-RAY DIFFRACTION8.048TORSIONAL
112L26154X-RAY DIFFRACTION8.048TORSIONAL
113M26154X-RAY DIFFRACTION8.048TORSIONAL
114N26154X-RAY DIFFRACTION8.048TORSIONAL
115O26154X-RAY DIFFRACTION8.048TORSIONAL
116P26154X-RAY DIFFRACTION8.048TORSIONAL
117Q26154X-RAY DIFFRACTION8.048TORSIONAL
118R26154X-RAY DIFFRACTION8.048TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.490.325817920.272339703576299
2.49-2.590.299217980.2493438336181100
2.59-2.710.296418000.24083453936339100
2.71-2.850.296918250.23763449136316100
2.85-3.030.302618110.23773445136262100
3.03-3.260.29318080.23513450536313100
3.26-3.590.251518130.20753451336326100
3.59-4.110.223118310.18213458836419100
4.11-5.170.181318060.14973463536441100
5.17-33.40.188618420.15643488436726100

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