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

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Basic information

Entry
Database: PDB / ID: 9vga
TitleCrystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with manganese ion
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: 1.82 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)59,5582
Polymers59,5031
Non-polymers551
Water5,332296
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)119,1154
Polymers119,0062
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2440 Å2
ΔGint-19 kcal/mol
Surface area39570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.657, 101.706, 168.361
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-762-

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: phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
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 26% v/v Polyethylene glycol 400 1 mM Mn2+

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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: 1.82→52.73 Å / Num. obs: 45398 / % possible obs: 94.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 8.81 Å2 / CC1/2: 0.953 / Net I/σ(I): 5.1
Reflection shellResolution: 1.82→1.92 Å / Num. unique obs: 4969 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→52.73 Å / SU ML: 0.2734 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 30.2315 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3097 1911 4.44 %
Rwork0.2494 41154 -
obs0.2521 43065 89.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.03 Å2
Refinement stepCycle: LAST / Resolution: 1.82→52.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 1 296 4478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714275
X-RAY DIFFRACTIONf_angle_d0.8715796
X-RAY DIFFRACTIONf_chiral_restr0.0503624
X-RAY DIFFRACTIONf_plane_restr0.0058771
X-RAY DIFFRACTIONf_dihedral_angle_d3.18742549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.3507720.29691624X-RAY DIFFRACTION50.46
1.86-1.920.35211320.29082759X-RAY DIFFRACTION85.13
1.92-1.970.3351280.26222899X-RAY DIFFRACTION90.22
1.97-2.040.30341550.25373075X-RAY DIFFRACTION95.53
2.04-2.110.31991350.25763148X-RAY DIFFRACTION96.76
2.11-2.190.33571500.25323168X-RAY DIFFRACTION97.3
2.19-2.290.31841420.24253003X-RAY DIFFRACTION92.47
2.29-2.410.31951440.25282982X-RAY DIFFRACTION92.79
2.41-2.560.34721340.27833070X-RAY DIFFRACTION93.93
2.56-2.760.36281350.28073084X-RAY DIFFRACTION94.43
2.76-3.040.28851500.26963152X-RAY DIFFRACTION96.32
3.04-3.480.30511490.23063175X-RAY DIFFRACTION96.12
3.48-4.380.26791380.21433025X-RAY DIFFRACTION90.94
4.38-52.730.26811470.22412990X-RAY DIFFRACTION86.75
Refinement TLS params.Method: refined / Origin x: -12.0704291405 Å / Origin y: -11.2688394429 Å / Origin z: -19.5709979869 Å
111213212223313233
T0.00158282423851 Å20.0209864925474 Å20.00153499792934 Å2-0.0354867748358 Å20.00554038619584 Å2--0.0067856910625 Å2
L0.886514725822 °20.333091513693 °2-0.0828606599367 °2-0.811266835101 °2-0.228381513919 °2--0.832075818262 °2
S0.0356402349964 Å °-0.00805358329247 Å °-0.00316139059904 Å °-0.0036078388581 Å °0.0140519599539 Å °0.0915860215811 Å °-0.0351571940087 Å °-0.108773392256 Å °0.0294919396067 Å °
Refinement TLS groupSelection details: all

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