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- PDB-1pmi: Candida Albicans Phosphomannose Isomerase -

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Basic information

Entry
Database: PDB / ID: 1pmi
TitleCandida Albicans Phosphomannose Isomerase
ComponentsPHOSPHOMANNOSE ISOMERASE
KeywordsISOMERASE / ALDOSE-KETOSE ISOMERASE
Function / homology
Function and homology information


mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / cell wall mannoprotein biosynthetic process / GDP-mannose biosynthetic process / fungal-type cell wall organization / protein glycosylation / carbohydrate metabolic process / zinc ion binding / cytosol
Similarity search - Function
Phosphomannose isomerase type I, C-terminal domain / Phosphomannose Isomerase; domain 2 / Phosphomannose Isomerase, domain 2 / Mannose-6-phosphate isomerase / Phosphomannose isomerase, type I, conserved site / Phosphomannose isomerase type I, catalytic domain / Phosphomannose isomerase type I, helical insertion domain / Phosphomannose isomerase type I, catalytic domain / Phosphomannose isomerase type I, helical insertion domain / Phosphomannose isomerase type I signature 1. ...Phosphomannose isomerase type I, C-terminal domain / Phosphomannose Isomerase; domain 2 / Phosphomannose Isomerase, domain 2 / Mannose-6-phosphate isomerase / Phosphomannose isomerase, type I, conserved site / Phosphomannose isomerase type I, catalytic domain / Phosphomannose isomerase type I, helical insertion domain / Phosphomannose isomerase type I, catalytic domain / Phosphomannose isomerase type I, helical insertion domain / Phosphomannose isomerase type I signature 1. / Phosphomannose isomerase type I signature 2. / Mannose-6-phosphate isomerase, type I / Phosphomannose isomerase type I C-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Mannose-6-phosphate isomerase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsCleasby, A. / Skarzynski, T. / Wonacott, A. / Davies, G.J. / Hubbard, R.E. / Proudfoot, A.E.I. / Wells, T.N.C. / Payton, M.A. / Bernard, A.R.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution.
Authors: Cleasby, A. / Wonacott, A. / Skarzynski, T. / Hubbard, R.E. / Davies, G.J. / Proudfoot, A.E. / Bernard, A.R. / Payton, M.A. / Wells, T.N.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of Candida Albicans Phosphomannose Isomerase
Authors: Tolley, S. / Davies, G. / Hubbard, R.E. / Smith, D.J. / Proudfoot, A.E. / Payton, M.A. / Cleasby, A. / Wonacott, A. / Wells, T.N.
History
DepositionApr 3, 1996Processing site: BNL
Revision 1.0Mar 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOMANNOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8562
Polymers48,7901
Non-polymers651
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.830, 52.920, 85.730
Angle α, β, γ (deg.)90.00, 127.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PHOSPHOMANNOSE ISOMERASE / PMI


Mass: 48790.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P34948, mannose-6-phosphate isomerase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 35 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
220 %(w/v)PEG80001reservoir
3200 mMcalcium acetate1reservoir
425 mMMES1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 45325 / % possible obs: 85 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
Highest resolution: 1.7 Å
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
PROLSQrefinement
MOSFLMdata reduction
RefinementResolution: 1.7→7 Å /
RfactorNum. reflection
Rwork0.184 -
obs-42164
Displacement parametersBiso mean: 24.99 Å2
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 1 322 3754
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0270.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0591
X-RAY DIFFRACTIONp_mcangle_it1.8272
X-RAY DIFFRACTIONp_scbond_it2.9282
X-RAY DIFFRACTIONp_scangle_it4.6163
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1960.3
X-RAY DIFFRACTIONp_multtor_nbd0.2960.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2540.3
X-RAY DIFFRACTIONp_planar_tor4.685
X-RAY DIFFRACTIONp_staggered_tor15.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.26710
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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