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- PDB-2fkf: Phosphomannomutase/Phosphoglucomutase from Pseudomonas aeruginosa... -

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Basic information

Entry
Database: PDB / ID: 2fkf
TitlePhosphomannomutase/Phosphoglucomutase from Pseudomonas aeruginosa with alpha-D-glucose 1,6-bisphosphate bound
ComponentsPhosphomannomutase/phosphoglucomutase
KeywordsISOMERASE / ALPHA/BETA PROTEIN / PHOSPHOSERINE / ENZYME-METAL COMPLEX / ENZYME-LIGAND COMPLEX
Function / homology
Function and homology information


phosphomannomutase / phosphomannomutase activity / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / alginic acid biosynthetic process / O antigen biosynthetic process / GDP-mannose biosynthetic process / lipopolysaccharide core region biosynthetic process / magnesium ion binding
Similarity search - Function
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 superfamily / 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, 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 superfamily / 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
1,6-di-O-phosphono-alpha-D-glucopyranose / Phosphomannomutase/phosphoglucomutase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRegni, C.A. / Beamer, L.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The reaction of phosphohexomutase from Pseudomonas aeruginosa: structural insights into a simple processive enzyme.
Authors: Regni, C. / Schramm, A.M. / Beamer, L.J.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _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 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphomannomutase/phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7043
Polymers50,2991
Non-polymers4052
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.865, 72.849, 91.258
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 Phosphomannomutase/phosphoglucomutase / PMM / PGM


Mass: 50299.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: algC / Plasmid: PET3-A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P26276, phosphomannomutase, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Sugar ChemComp-G16 / 1,6-di-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE / 1,6-di-O-phosphono-alpha-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose / Glucose 1,6-bisphosphate


Type: D-saccharide / Mass: 339.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O12P2
IdentifierTypeProgram
a-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 50-60% sat Na K tartrate, .1 M Na Hepes pH 7.5 seeding used, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 37917 / Num. obs: 32729 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.076 / Χ2: 1.029
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.47 / Num. unique all: 3246 / Χ2: 0.749 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K35

1k35


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.412 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.18 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1655 5.1 %RANDOM
Rwork0.183 ---
all0.186 32598 --
obs0.2526 32463 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.743 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2---0.05 Å20 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 21 296 3689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223476
X-RAY DIFFRACTIONr_bond_other_d0.0020.023239
X-RAY DIFFRACTIONr_angle_refined_deg1.181.9754742
X-RAY DIFFRACTIONr_angle_other_deg0.77337493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01123.913138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85315.028532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7451523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023947
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02691
X-RAY DIFFRACTIONr_nbd_refined0.2020.2721
X-RAY DIFFRACTIONr_nbd_other0.1770.23335
X-RAY DIFFRACTIONr_nbtor_refined0.170.21763
X-RAY DIFFRACTIONr_nbtor_other0.080.22084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2263
X-RAY DIFFRACTIONr_metal_ion_refined0.1670.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.225
X-RAY DIFFRACTIONr_mcbond_it0.6181.52917
X-RAY DIFFRACTIONr_mcbond_other0.1041.5938
X-RAY DIFFRACTIONr_mcangle_it0.73623625
X-RAY DIFFRACTIONr_scbond_it1.85341390
X-RAY DIFFRACTIONr_scangle_it2.64861116
LS refinement shellResolution: 2→2.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.297 239 -
Rwork0.226 4434 -
obs-4673 99.98 %
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)
11.6744-0.3018-0.34831.75231.12941.4192-0.0758-0.0202-0.15280.11570.1634-0.05020.05230.248-0.0875-0.1620.00380.0312-0.1110.0012-0.178353.324554.59575.8364
23.49452.9189-1.606512.8559-2.99594.19340.4522-0.24060.10521.3392-0.30110.3185-0.54540.2655-0.15110.017-0.04590.0652-0.18030.0001-0.177338.60953.109429.6768
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
119 - 3688 - 367
22369 - 463368 - 462

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