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- PDB-1p5d: Enzyme-ligand complex of P. aeruginosa PMM/PGM -

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Basic information

Entry
Database: PDB / ID: 1p5d
TitleEnzyme-ligand complex of P. aeruginosa PMM/PGM
ComponentsPhosphomannomutase
KeywordsISOMERASE / ALPHA/BETA PROTEIN / PHOSPHOHEXOMUTASE / PHOSPHOSERINE / ENZYME-LIGAND COMPLEX / ENZYME-METAL 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-O-phosphono-alpha-D-glucopyranose / Phosphomannomutase/phosphoglucomutase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement followed by regular refinement / Resolution: 1.6 Å
AuthorsRegni, C. / Tipton, P.A. / Beamer, L.J.
CitationJournal: Structure / Year: 2004
Title: Structural basis of diverse substrate recognition by the enzyme PMM/PGM from P. aeruginosa.
Authors: Regni, C. / Naught, L. / Tipton, P.A. / Beamer, L.J.
History
DepositionApr 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Apr 3, 2024Group: 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
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7563
Polymers50,4301
Non-polymers3262
Water8,359464
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.700, 74.193, 84.836
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 / PMM


Mass: 50430.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ALGC OR PA5322 / 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-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC 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.: 464 / 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: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: Na K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Regni, C.A., (2000) Acta Crystallogr, D56, 761.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112-15 mg/mlprotein1drop
210 mMMOPS1droppH7.0
31.4 Msodium potassium tartrate1reservoir
4100 mMsodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2003 / Details: mirrors
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 59165 / Num. obs: 58633 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 32.1
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.8 / % possible all: 98.3
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: rigid body refinement followed by regular refinement
Starting model: PMM/PGM bound to glucose 6-phosphate

Resolution: 1.6→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.4 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.081 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17901 2945 5 %RANDOM
Rwork0.15565 ---
all0.1621 59514 --
obs0.1568 56042 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 17 464 3917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213639
X-RAY DIFFRACTIONr_bond_other_d0.0020.023368
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9684967
X-RAY DIFFRACTIONr_angle_other_deg0.99837816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785478
X-RAY DIFFRACTIONr_chiral_restr0.0850.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024159
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02733
X-RAY DIFFRACTIONr_nbd_refined0.2140.2762
X-RAY DIFFRACTIONr_nbd_other0.2440.24144
X-RAY DIFFRACTIONr_nbtor_other0.0820.22235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2334
X-RAY DIFFRACTIONr_metal_ion_refined0.090.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.235
X-RAY DIFFRACTIONr_mcbond_it0.6921.52327
X-RAY DIFFRACTIONr_mcangle_it1.26823759
X-RAY DIFFRACTIONr_scbond_it2.07831312
X-RAY DIFFRACTIONr_scangle_it3.4424.51208
LS refinement shellResolution: 1.6→1.686 Å / Rfactor Rfree error: 0.212 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.212 411 -
Rwork0.189 7959 -
obs-7959 14 %
Refinement TLS params.Method: refined / Origin x: -49.8146 Å / Origin y: -18.1559 Å / Origin z: 10.6337 Å
111213212223313233
T0.0113 Å2-0.0022 Å2-0.0024 Å2-0.0107 Å20.0015 Å2--0.0009 Å2
L0.226 °20.0101 °20.1163 °2-0.1915 °2-0.0647 °2--0.2182 °2
S0.0086 Å °-0.0143 Å °-0.006 Å °0.0122 Å °0.0097 Å °0.0216 Å °0.0233 Å °-0.0286 Å °-0.0182 Å °
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.39

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