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- PDB-3fm9: Analysis of the Structural Determinants Underlying Discrimination... -

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Basic information

Entry
Database: PDB / ID: 3fm9
TitleAnalysis of the Structural Determinants Underlying Discrimination between Substrate and Solvent in beta-Phosphoglucomutase Catalysis
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / HAD superfamily / phosphoaspartate / induced fit / domain movement
Function / homology
Function and homology information


beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / molecular replacement / Resolution: 2.7 Å
AuthorsFinci, L. / Lahiri, S. / Peisach, E. / Allen, K.N.
Citation
Journal: Biochemistry / Year: 2009
Title: Analysis of the structural determinants underlying discrimination between substrate and solvent in beta-phosphoglucomutase catalysis.
Authors: Dai, J. / Finci, L. / Zhang, C. / Lahiri, S. / Zhang, G. / Peisach, E. / Allen, K.N. / Dunaway-Mariano, D.
#1: Journal: Science / Year: 2003
Title: The pentacovalent phosphorous intermediate of a phosphoryl transfer reaction
Authors: Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2602
Polymers24,2361
Non-polymers241
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.478, 57.656, 77.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-phosphoglucomutase / / Beta-PGM


Mass: 24235.605 Da / Num. of mol.: 1 / Mutation: T16P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: L0001, LL0429, pgmB / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.5 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.001M DTT, 0.01M MgCl2, 25% PEG 3350, 0.2M NaCl, 0.1M bisTris pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 12, 2007
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 7122 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.151 / Χ2: 1.547 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.85.40.5617001.02399.2
2.8-2.915.50.4076951.08499.7
2.91-3.045.70.337001.2999.2
3.04-3.25.60.2716891.34199.7
3.2-3.45.70.1957111.47499.7
3.4-3.665.60.1586921.54399.4
3.66-4.035.60.1287051.67399.3
4.03-4.625.50.1117271.96699.9
4.62-5.815.50.1057261.92499.5
5.81-5050.0917772.15197.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å39.6 Å
Translation2.7 Å39.6 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: PDB ENTRY 1ZOL
Resolution: 2.7→39.598 Å / FOM work R set: 0.783 / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.28 678 10 %random
Rwork0.208 ---
obs0.216 7122 94.98 %-
all-7456 --
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.428 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 86.79 Å2 / Biso mean: 32.56 Å2 / Biso min: 8.74 Å2
Baniso -1Baniso -2Baniso -3
1--4.927 Å20 Å20 Å2
2---2.746 Å2-0 Å2
3---7.673 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 1 62 1769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.03

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