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- PDB-3na5: Crystal structure of a bacterial phosphoglucomutase, an enzyme im... -

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Basic information

Entry
Database: PDB / ID: 3na5
TitleCrystal structure of a bacterial phosphoglucomutase, an enzyme important in the virulence of several human pathogens.
ComponentsPhosphoglucomutase
KeywordsISOMERASE / Phosphoglucomutase / Metal binding
Function / homology
Function and homology information


phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytosol
Similarity search - Function
Phosphoglucomutase, alpha-D-glucose specific / Phosphoglucomutase / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II ...Phosphoglucomutase, alpha-D-glucose specific / Phosphoglucomutase / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMehra-Chaudhary, R. / Beamer, L.J.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens.
Authors: Mehra-Chaudhary, R. / Mick, J. / Tanner, J.J. / Henzl, M.T. / Beamer, L.J.
History
DepositionJun 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglucomutase
B: Phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3266
Polymers121,8592
Non-polymers4674
Water18,3751020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-27 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.466, 105.792, 126.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoglucomutase


Mass: 60929.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: pgm, STM0698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: Q8ZQW9, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1020 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 0.3 M magnesium chloride, 20% PEG 3350,0.1% n-octyl-beta D-gluco-pyranoside , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 21, 2010 / Details: beamline optics
RadiationMonochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→42.27 Å / Num. obs: 120749 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.8
Reflection shellResolution: 1.7→1.7 Å / Redundancy: 3.66 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.03 Å42.27 Å
Translation2.03 Å42.27 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.7LDzdata scaling
MOLREPphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
RefinementMethod to determine structure: REFINEMENT
Starting model: PDB Entry 2FUV

2fuv


Resolution: 1.7→42.27 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.287 / SU ML: 0.073 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 6066 5 %RANDOM
Rwork0.18176 ---
obs0.18355 114594 99.87 %-
all-114594 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.07 Å2
Refine analyzeLuzzati coordinate error free: 0.108 Å / Luzzati sigma a free: 0.106 Å
Refinement stepCycle: LAST / Resolution: 1.7→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8045 0 30 1020 9095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.95511351
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6951114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73724.689354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.866151246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8321539
X-RAY DIFFRACTIONr_chiral_restr0.1240.21280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216439
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6881.55442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15128666
X-RAY DIFFRACTIONr_scbond_it2.05532882
X-RAY DIFFRACTIONr_scangle_it3.2644.52672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 451 -
Rwork0.321 8288 -
obs--99.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64320.2495-0.33820.5288-0.14160.67830.0016-0.0039-0.029-0.0127-0.0419-0.02730.03830.02380.04030.07650.0305-0.0040.08690.00530.058555.094141.542831.9692
20.70090.4653-0.13491.1598-0.2720.7743-0.07680.0506-0.0049-0.08810.07710.00650.02250.0346-0.00030.05430.0120.00630.10660.00810.07368.032150.288417.2938
32.0246-0.93050.24132.4565-0.2071.492-0.02750.3395-0.1776-0.19390.07010.14260.19270.1172-0.04260.0453-0.0531-0.02190.1012-0.01330.036156.777145.0259-1.4824
46.38510.5830.89776.1752-2.47093.22730.06210.1643-0.3122-0.24960.09670.4740.2612-0.2378-0.15870.0167-0.0557-0.02750.13930.02520.081949.569747.9238-1.0074
50.9187-0.0527-0.37360.71650.0180.68310.033-0.06-0.09370.1033-0.08980.10520.07060.00260.05680.1111-0.03220.0220.0994-0.02820.095429.133233.671954.1178
60.4969-0.2777-0.30150.58260.3040.72320.10810.08280.0303-0.0442-0.07060.0341-0.0896-0.0631-0.03740.0893-0.01180.02710.1012-0.01870.07524.563751.038849.3953
70.8157-0.0545-0.02620.76630.30090.8058-0.02540.054-0.0316-0.0197-0.0165-0.0363-0.0628-0.09680.04190.0493-0.00420.030.0714-0.02290.106914.503855.087167.1793
82.62120.53510.3452.0332-0.35630.98930.0475-0.1864-0.15080.2151-0.02910.03240.1409-0.0205-0.01840.06180.00370.00370.06890.01320.100728.47748.450486.2252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 340
2X-RAY DIFFRACTION2A341 - 438
3X-RAY DIFFRACTION3A439 - 506
4X-RAY DIFFRACTION4A507 - 546
5X-RAY DIFFRACTION5B2 - 184
6X-RAY DIFFRACTION6B185 - 309
7X-RAY DIFFRACTION7B310 - 446
8X-RAY DIFFRACTION8B447 - 546

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