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- PDB-9vg8: Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in... -

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Basic information

Entry
Database: PDB / ID: 9vg8
TitleCrystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with magnesium ion
ComponentsPhosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)
KeywordsISOMERASE / Metal-binding / Phosphoserine
Biological speciesPhaeodactylibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 13, 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)59,5272
Polymers59,5031
Non-polymers241
Water4,810267
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 area2360 Å2
ΔGint-25 kcal/mol
Surface area39640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.850, 168.980, 59.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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: 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.: 267 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 6.0, 24% v/v Polyethylene glycol 400 1 mM Mg2+

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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: 1.65→84.49 Å / Num. obs: 64621 / % possible obs: 86.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 6.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.2
Reflection shellResolution: 1.65→1.74 Å / Num. unique obs: 7269 / CC1/2: 0.745

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→84.49 Å / SU ML: 0.3466 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 31.285 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 1759 3.07 %
Rwork0.2214 55532 -
obs0.2227 57291 76.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.96 Å2
Refinement stepCycle: LAST / Resolution: 1.65→84.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 1 267 4449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634275
X-RAY DIFFRACTIONf_angle_d0.80945796
X-RAY DIFFRACTIONf_chiral_restr0.0522624
X-RAY DIFFRACTIONf_plane_restr0.0054771
X-RAY DIFFRACTIONf_dihedral_angle_d2.82142549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.8485530.8351521X-RAY DIFFRACTION27.81
1.7-1.750.6231910.59062838X-RAY DIFFRACTION51.42
1.75-1.810.48911140.39013816X-RAY DIFFRACTION68.95
1.81-1.870.48171290.31634132X-RAY DIFFRACTION74.95
1.87-1.950.32531370.27434375X-RAY DIFFRACTION87.26
1.95-2.030.3241300.22153814X-RAY DIFFRACTION89.17
2.03-2.140.296990.22793432X-RAY DIFFRACTION61.96
2.14-2.280.22831280.20394010X-RAY DIFFRACTION72.12
2.28-2.450.24221690.19525215X-RAY DIFFRACTION93.68
2.45-2.70.23141670.19095309X-RAY DIFFRACTION95.15
2.7-3.090.21321770.18755527X-RAY DIFFRACTION98.29
3.09-3.890.19791810.16395655X-RAY DIFFRACTION99.44
3.89-84.490.18051840.15535888X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 12.0997613359 Å / Origin y: 22.5890832326 Å / Origin z: 14.577401359 Å
111213212223313233
T0.0763003011832 Å20.00555238390238 Å2-0.0118972281625 Å2-0.0848843485288 Å2-0.00553197164471 Å2--0.0830859562631 Å2
L0.465869265016 °20.250533616764 °2-0.168354531162 °2-0.701740556464 °2-0.29973530181 °2--0.531828133321 °2
S-0.00083563954228 Å °-0.0134834002068 Å °-0.0121169244515 Å °0.0230919089586 Å °-0.026037936737 Å °-0.0754990195981 Å °0.0166820478113 Å °0.0539724936659 Å °0.00533007232368 Å °
Refinement TLS groupSelection details: all

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