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- PDB-1lvh: The Structure of Phosphorylated beta-phosphoglucomutase from Lact... -

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Basic information

Entry
Database: PDB / ID: 1lvh
TitleThe Structure of Phosphorylated beta-phosphoglucomutase from Lactoccocus lactis to 2.3 angstrom resolution
Componentsbeta-phosphoglucomutase
KeywordsISOMERASE / HAD superfamily / phosphoaspartate / aspartylphosphate
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 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily ...Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / : / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
Citation
Journal: Biochemistry / Year: 2002
Title: Caught in the act: the structure of phosphorylated beta-phosphoglucomutase from Lactococcus lactis.
Authors: Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary X-ray diffraction studies of beta-phosphoglucomutase from Lactococcus lactus
Authors: Lahiri, S.D. / Zhang, G. / Radstrom, P. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionMay 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _struct_conn_type.id / _struct_ref_seq_dif.details
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-phosphoglucomutase
B: beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6884
Polymers48,6392
Non-polymers492
Water4,666259
1
A: beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3442
Polymers24,3201
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3442
Polymers24,3201
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.667, 92.776, 111.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein beta-phosphoglucomutase


Mass: 24319.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: PGMB / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 16% PEG 3350, 0.15M Ammonium Floride, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6.5
Details: Lahiri, S.D., (2002) Acta Crystallogr., Sect.D, 58, 324.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium fluoride1reservoir
220 %(w/v)PEG33501reservoirpH6.5
315 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9792369, 0.9790073, 0.96112713
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2001 / Details: Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97923691
20.97900731
30.961127131
ReflectionResolution: 2.3→50 Å / Num. all: 25469 / Num. obs: 25469 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1746 / Rsym value: 0.191 / % possible all: 60.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 23862 / % possible obs: 91 % / Num. measured all: 420727
Reflection shell
*PLUS
% possible obs: 60.8 % / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→42.89 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: maximum likelihood target using amplitudes and phase probability distributions
RfactorNum. reflection% reflectionSelection details
Rfree0.2857 2390 -RANDOM
Rwork0.2435 ---
all0.2477 25463 --
obs0.2477 24135 94.8 %-
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--12.45 Å20 Å2
3----13.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 2 259 3684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.318 333 -
Rwork0.255 --
obs-3378 81 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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