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- PDB-1z4n: Structure of beta-phosphoglucomutase with inhibitor bound alpha-g... -

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Basic information

Entry
Database: PDB / ID: 1z4n
TitleStructure of beta-phosphoglucomutase with inhibitor bound alpha-galactose 1-phosphate cocrystallized with Fluoride
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / Beta-phosphoglucomutase
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 / DNA polymerase; domain 1 ...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
1-O-phosphono-alpha-D-galactopyranose / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsTremblay, L.W. / Zhang, G. / Dai, J. / Dunaway-Mariano, D. / Allen, K.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Chemical Confirmation of a Pentavalent Phosphorane in Complex with beta-Phosphoglucomutase
Authors: Tremblay, L.W. / Zhang, G. / Dai, J. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionMar 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE According to authors, the conflict in the sequence with the database has been mentioned ... SEQUENCE According to authors, the conflict in the sequence with the database has been mentioned in NCBI P71447 for the reference "Quain et al.,1997 Microbiology 143, 855-865". Authors received their clone from the same group.

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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)49,0486
Polymers48,4792
Non-polymers5694
Water7,458414
1
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5243
Polymers24,2401
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5243
Polymers24,2401
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.143, 36.451, 105.119
Angle α, β, γ (deg.)90.00, 94.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 24239.594 Da / Num. of mol.: 2 / Fragment: isomerase
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: Sugar ChemComp-GL1 / 1-O-phosphono-alpha-D-galactopyranose / ALPHA-D-GALACTOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-galactose / 1-O-phosphono-D-galactose / 1-O-phosphono-galactose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
a-D-Galp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.254 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM sodium acetate, 30% PEG 4000, 10 mM magnesium dicloride, 100 mM ammonium fluoride, 50 mM alpha-galactose 1-phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: osmic mirriors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→100 Å / Num. all: 31187 / Num. obs: 31187 / % possible obs: 95.3 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.3
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 5.6 / Num. unique all: 31017 / % possible all: 93

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O08.pdb

1o08


Resolution: 1.97→100 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): -1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2942 10 %random
Rwork0.207 ---
all0.236 29433 --
obs0.236 26391 --
Displacement parametersBiso mean: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1-3.967 Å20 Å20.204 Å2
2---3.169 Å20 Å2
3----0.798 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.97→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 34 414 3700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.69
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4gal.par

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