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- PDB-2fkm: PMM/PGM S108D mutant with alpha-d-glucose 1,6-bisphosphate bound -

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Basic information

Entry
Database: PDB / ID: 2fkm
TitlePMM/PGM S108D mutant with alpha-d-glucose 1,6-bisphosphate bound
ComponentsPhosphomannomutase/phosphoglucomutase
KeywordsISOMERASE / alpha/beta protein / 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, C-terminal domain / Alpha-D-phosphohexomutase superfamily / 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, C-terminal domain / Alpha-D-phosphohexomutase superfamily / 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: 1.9 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 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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 1.5Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 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
X: Phosphomannomutase/phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6523
Polymers50,2471
Non-polymers4052
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.222, 70.356, 84.392
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: 50247.168 Da / Num. of mol.: 1 / Mutation: s108d
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
#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


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50-60% sat Na K tartrate, .1 M Na Hepes pH 7.5 seeding used, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97909 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 4, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 1.9→42.83 Å / Num. all: 33627 / Num. obs: 33583 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.49 % / Rmerge(I) obs: 0.075 / Χ2: 0.99 / Net I/σ(I): 13.9 / Scaling rejects: 1647
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 4 / Num. unique all: 3296 / Χ2: 1.22 / % possible all: 99.4

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.679 / Packing: 0.669
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct99.6 0
Translation4 Å15 Ågeneral99.6 0

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
CNSrefinement
d*TREK9.3LDzdata scaling
PDB_EXTRACT1.701data extraction
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1P5D

1p5d


Resolution: 1.9→42.83 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.169 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.18 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1699 5.1 %RANDOM
Rwork0.203 ---
all0.205 33583 --
obs0.205 33583 99.88 %-
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: 29.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---1.18 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 21 234 3630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223470
X-RAY DIFFRACTIONr_bond_other_d0.0010.023229
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9714728
X-RAY DIFFRACTIONr_angle_other_deg0.76137473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17523.957139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10715539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.741523
X-RAY DIFFRACTIONr_chiral_restr0.0690.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_nbd_refined0.1990.2758
X-RAY DIFFRACTIONr_nbd_other0.1770.23549
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21762
X-RAY DIFFRACTIONr_nbtor_other0.0830.22180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2237
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.218
X-RAY DIFFRACTIONr_mcbond_it0.5521.52890
X-RAY DIFFRACTIONr_mcbond_other0.1091.5932
X-RAY DIFFRACTIONr_mcangle_it0.66823611
X-RAY DIFFRACTIONr_scbond_it1.76641392
X-RAY DIFFRACTIONr_scangle_it2.48461117
LS refinement shellResolution: 1.9→2.003 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.303 223 -
Rwork0.236 4592 -
obs-4815 99.57 %
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)
12.5465-0.8562-1.30211.22280.4880.9949-0.0651-0.27290.11260.10080.1259-0.0881-0.05110.1509-0.0608-0.1081-0.0187-0.0067-0.12080.0008-0.15325.416474.347225.41
20.46010.108-0.14642.2056-0.55840.7607-0.003-0.0372-0.03710.08020.04230.23880.0109-0.0936-0.0393-0.1454-0.00530.0082-0.11320.0038-0.1503-11.387562.968329.9302
36.4394-0.22730.19821.84890.33773.0838-0.0139-0.3832-0.03240.2318-0.04180.0346-0.0314-0.12350.0557-0.12540.00240.0025-0.128-0.0039-0.172-0.731456.017849.6879
Refinement TLS group

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

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A10 - 2569 - 255
22A257 - 368256 - 367
33A369 - 463368 - 462
43B4641

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