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- PDB-9v68: Crystal structure of Phaeodactylibacter sp. Phosphoglucomutase -

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Basic information

Entry
Database: PDB / ID: 9v68
TitleCrystal structure of Phaeodactylibacter sp. Phosphoglucomutase
ComponentsPhosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
KeywordsISOMERASE / Metal-binding / Phosphoserine
Function / homology:
Function and homology information
Biological speciesPhaeodactylibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsShen, Y.W. / Tu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionMay 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 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)59,5272
Polymers59,5031
Non-polymers241
Water8,737485
1
A: Phosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)119,0544
Polymers119,0062
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2370 Å2
ΔGint-26 kcal/mol
Surface area39440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.252, 59.314, 96.835
Angle α, β, γ (deg.)90.000, 116.315, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-1007-

HOH

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Components

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


Mass: 59502.793 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
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 6.5 20% v/v polyethylene glycol monomethyl ether 550

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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: 1.58→49.37 Å / Num. obs: 79073 / % possible obs: 96.2 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 13
Reflection shellResolution: 1.58→1.66 Å / Num. unique obs: 9752 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→49.37 Å / SU ML: 0.1482 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.3813 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1836 2000 2.53 %
Rwork0.1636 77038 -
obs0.1641 79038 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.35 Å2
Refinement stepCycle: LAST / Resolution: 1.58→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 1 485 4667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00574275
X-RAY DIFFRACTIONf_angle_d0.77255796
X-RAY DIFFRACTIONf_chiral_restr0.0509624
X-RAY DIFFRACTIONf_plane_restr0.0055771
X-RAY DIFFRACTIONf_dihedral_angle_d2.89612549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.31391090.28644184X-RAY DIFFRACTION73.43
1.62-1.660.24071310.25855062X-RAY DIFFRACTION88.74
1.66-1.710.24241450.22975572X-RAY DIFFRACTION97.86
1.71-1.760.22681460.20895640X-RAY DIFFRACTION98.4
1.76-1.830.22591460.19865632X-RAY DIFFRACTION98.45
1.83-1.90.19821450.18035596X-RAY DIFFRACTION97.84
1.9-1.990.20161460.16735615X-RAY DIFFRACTION98.39
1.99-2.090.18441460.14985638X-RAY DIFFRACTION99.02
2.09-2.220.1671470.14795642X-RAY DIFFRACTION98.7
2.22-2.390.18191460.14815615X-RAY DIFFRACTION97.96
2.39-2.630.19611480.14435709X-RAY DIFFRACTION99.41
2.63-3.010.16931470.14965642X-RAY DIFFRACTION98.39
3.01-3.80.14411490.145753X-RAY DIFFRACTION99.33
3.8-49.370.16551490.15525738X-RAY DIFFRACTION97.23
Refinement TLS params.Method: refined / Origin x: 12.3884262181 Å / Origin y: -17.2863826536 Å / Origin z: 22.4194634902 Å
111213212223313233
T0.140131626317 Å20.00104115212218 Å2-0.00222291737255 Å2-0.0784248911675 Å20.0114101958938 Å2--0.0768469034597 Å2
L0.460729986565 °20.20405797454 °20.114465798255 °2-0.619353407503 °20.171492354218 °2--0.68186850784 °2
S0.00806268164035 Å °-0.0127021384096 Å °0.00253619444543 Å °-0.0559487862063 Å °0.0184349138392 Å °-0.0576835212016 Å °-0.0686672598247 Å °0.0625046635205 Å °-0.0298773403699 Å °
Refinement TLS groupSelection details: all

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