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- PDB-1p5g: Enzyme-ligand complex of P. aeruginosa PMM/PGM -

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Basic information

Entry
Database: PDB / ID: 1p5g
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 / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphomannomutase activity / 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / 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, 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
6-O-phosphono-alpha-D-glucopyranose / Phosphomannomutase/phosphoglucomutase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 26, 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 1.3Jun 17, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / struct_conn ...pdbx_distant_solvent_atoms / struct_conn / struct_ref / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_seq_one_letter_code
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 / _chem_comp.type / _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 1.5Aug 16, 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
Revision 1.6Nov 13, 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
Water7,873437
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.591, 74.372, 85.994
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 / Production host: Escherichia coli (E. coli) / Strain (production host): B121(DE3) / References: UniProt: P26276, phosphomannomutase
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC 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.: 437 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
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: 60200 / Num. obs: 59418 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 41.8
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 5.6 / % possible all: 87.7
Reflection shell
*PLUS
% possible obs: 87.7 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K35

1k35


Resolution: 1.61→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.464 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18658 2941 5 %RANDOM
Rwork0.16049 ---
all0.1646 59482 --
obs0.16177 56395 99.79 %-
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: 14.015 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.64 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.61→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 17 437 3877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213616
X-RAY DIFFRACTIONr_bond_other_d0.0020.023359
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9684935
X-RAY DIFFRACTIONr_angle_other_deg0.81737792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795476
X-RAY DIFFRACTIONr_chiral_restr0.0790.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024124
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02726
X-RAY DIFFRACTIONr_nbd_refined0.2120.2747
X-RAY DIFFRACTIONr_nbd_other0.2450.24103
X-RAY DIFFRACTIONr_nbtor_other0.0820.22186
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2348
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.249
X-RAY DIFFRACTIONr_mcbond_it0.7131.52321
X-RAY DIFFRACTIONr_mcangle_it1.28423744
X-RAY DIFFRACTIONr_scbond_it2.04831295
X-RAY DIFFRACTIONr_scangle_it3.2794.51191
LS refinement shellResolution: 1.61→1.695 Å / Rfactor Rfree error: 0.082 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.226 420 -
Rwork0.187 8063 -
obs-8063 14 %
Refinement TLS params.Method: refined / Origin x: -49.7804 Å / Origin y: -18.1648 Å / Origin z: 10.9024 Å
111213212223313233
T0.0076 Å2-0.0028 Å2-0.0061 Å2-0.013 Å20.0083 Å2--0.0079 Å2
L0.1454 °2-0.0077 °20.1311 °2-0.1385 °2-0.0369 °2--0.1098 °2
S0.012 Å °-0.0146 Å °-0.0016 Å °0.0149 Å °0.0125 Å °0.0238 Å °0.0106 Å °-0.0166 Å °-0.0245 Å °
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.19 / 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_deg1.34

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