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

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Basic information

Entry
Database: PDB / ID: 1pcm
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-mannopyranose / Phosphomannomutase/phosphoglucomutase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body followed by regular refinement / Resolution: 1.9 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
DepositionMay 16, 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 1.3Jul 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 / pdbx_struct_conn_angle / 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 / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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 1.4Aug 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 1.5Oct 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
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.648, 74.186, 85.399
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-M6P / 6-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-mannose / 6-O-phosphono-D-mannose / 6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
a-D-Manp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
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: Nov 7, 2002 / 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: 1.9→25 Å / Num. all: 36023 / Num. obs: 35051 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.6 / Net I/σ(I): 21.9
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.4 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.6
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: rigid body followed by regular refinement
Starting model: 1P5G

1p5g


Resolution: 1.9→24.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.045 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20113 1753 5 %RANDOM
Rwork0.1669 ---
all0.16858 35014 --
obs0.1669 33259 97.24 %-
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: 18.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2---0.86 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 17 341 3776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223500
X-RAY DIFFRACTIONr_bond_other_d0.0020.023250
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.974765
X-RAY DIFFRACTIONr_angle_other_deg0.83237534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295454
X-RAY DIFFRACTIONr_chiral_restr0.0830.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023936
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02686
X-RAY DIFFRACTIONr_nbd_refined0.1980.2718
X-RAY DIFFRACTIONr_nbd_other0.2410.23898
X-RAY DIFFRACTIONr_nbtor_other0.0830.22060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.235
X-RAY DIFFRACTIONr_mcbond_it0.61.52255
X-RAY DIFFRACTIONr_mcangle_it1.10623621
X-RAY DIFFRACTIONr_scbond_it1.73531245
X-RAY DIFFRACTIONr_scangle_it2.8754.51144
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.26 258 -
Rwork0.213 4766 -
obs-4766 14.3 %
Refinement TLS params.Method: refined / Origin x: -49.8047 Å / Origin y: -18.2162 Å / Origin z: 10.8582 Å
111213212223313233
T0.0262 Å2-0.0011 Å2-0.0024 Å2-0.0276 Å20.0069 Å2--0.0057 Å2
L0.2428 °2-0.032 °20.1847 °2-0.28 °2-0.0515 °2--0.3045 °2
S0.0052 Å °-0.0147 Å °-0.0129 Å °0.0403 Å °0.0205 Å °0.0326 Å °0.0075 Å °-0.0442 Å °-0.0256 Å °
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 24.9 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.27

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