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- PDB-9vfz: Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in... -

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Basic information

Entry
Database: PDB / ID: 9vfz
TitleCrystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with glucose-1-phosphate
ComponentsPhosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
KeywordsISOMERASE / Metal-binding / Phosphoserine
Function / homology1-O-phosphono-alpha-D-glucopyranose / :
Function and homology information
Biological speciesPhaeodactylibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsShen, Y.W. / Tu, T.
Funding support China, 2items
OrganizationGrant numberCountry
Other government2022YFA0912301 China
National Natural Science Foundation of China (NSFC)U25A20709 China
CitationJournal: To Be Published
Title: In Vitro Design and Optimization of a High-Efficiency Artificial Enzymatic Pathway for Cellulose-to-Starch Conversion
Authors: Shen, Y.W. / Tu, T.
History
DepositionJun 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4113
Polymers64,1271
Non-polymers2842
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.970, 58.966, 99.517
Angle α, β, γ (deg.)90.000, 118.217, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Phosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)


Mass: 64126.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylibacter sp. (bacteria) / Gene: pgm, KDD09_20305 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A959BHL9, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.15 M DL-maleic acid pH 7.0 0.1 M Imidazole pH 7.0 24% v/v polyethylene glycol monomethyl ether 550 3 mM G1P

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 40136 / % possible obs: 99.3 % / Redundancy: 6.48 % / CC1/2: 0.9349 / Net I/σ(I): 8.14
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2967 / CC1/2: 0.6943 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.16 Å / SU ML: 0.3742 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 46.5958 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3586 2024 5.06 %
Rwork0.2724 37945 -
obs0.2769 39969 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 17 53 4251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01434291
X-RAY DIFFRACTIONf_angle_d1.43245820
X-RAY DIFFRACTIONf_chiral_restr0.0726629
X-RAY DIFFRACTIONf_plane_restr0.0096771
X-RAY DIFFRACTIONf_dihedral_angle_d3.83582550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.48131120.47522627X-RAY DIFFRACTION95.67
2-2.060.47791400.41412712X-RAY DIFFRACTION99.2
2.06-2.120.42861210.39022720X-RAY DIFFRACTION98.71
2.12-2.190.45411430.36132701X-RAY DIFFRACTION99.06
2.19-2.260.49121470.36952655X-RAY DIFFRACTION97.36
2.26-2.350.44371380.34862692X-RAY DIFFRACTION98.61
2.35-2.460.41451330.30122744X-RAY DIFFRACTION99.34
2.46-2.590.35681820.29042678X-RAY DIFFRACTION99.17
2.59-2.750.32081630.27472670X-RAY DIFFRACTION98.78
2.75-2.970.3511540.26582755X-RAY DIFFRACTION99.66
2.97-3.270.32761600.27492704X-RAY DIFFRACTION99.48
3.27-3.740.36691340.24862718X-RAY DIFFRACTION98.31
3.74-4.710.31171470.212769X-RAY DIFFRACTION99.56
4.71-49.160.32731500.21842800X-RAY DIFFRACTION98.56
Refinement TLS params.Method: refined / Origin x: 10.0141877041 Å / Origin y: -18.096012326 Å / Origin z: 23.006211665 Å
111213212223313233
T0.490799535257 Å2-0.0406428030088 Å20.0158114078826 Å2-0.239700059458 Å2-0.00194759456728 Å2--0.272336628344 Å2
L0.198765044545 °20.097142277623 °20.295138939222 °2--0.224010188465 °20.286863456751 °2--0.519357705443 °2
S-0.00241676041609 Å °0.0276676971584 Å °-0.00914931562571 Å °-0.178877496717 Å °0.01628650681 Å °0.0216845360549 Å °-0.0904789610717 Å °-0.0235827031328 Å °-0.0146409273456 Å °
Refinement TLS groupSelection details: all

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