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- PDB-2wfp: Crystal structure of mannose 6-phosphate isomerase (apo form) fro... -

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Basic information

Entry
Database: PDB / ID: 2wfp
TitleCrystal structure of mannose 6-phosphate isomerase (apo form) from Salmonella typhimurium
ComponentsMANNOSE-6-PHOSPHATE ISOMERASE
KeywordsISOMERASE / APO-STRUCTURE / METAL-BINDING
Function / homology
Function and homology information


mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / GDP-mannose biosynthetic process / carbohydrate metabolic process / zinc ion binding / cytosol
Similarity search - Function
Phosphomannose Isomerase; domain 2 / Phosphomannose Isomerase, domain 2 / Mannose-6-phosphate isomerase / Phosphomannose isomerase, type I, conserved site / Phosphomannose isomerase type I, helical insertion domain / : / Phosphomannose isomerase type I, helical insertion domain / Mannose-6-phosphate isomerase, cupin domain / Phosphomannose isomerase type I signature 1. / Phosphomannose isomerase type I signature 2. ...Phosphomannose Isomerase; domain 2 / Phosphomannose Isomerase, domain 2 / Mannose-6-phosphate isomerase / Phosphomannose isomerase, type I, conserved site / Phosphomannose isomerase type I, helical insertion domain / : / Phosphomannose isomerase type I, helical insertion domain / Mannose-6-phosphate isomerase, cupin domain / Phosphomannose isomerase type I signature 1. / Phosphomannose isomerase type I signature 2. / Mannose-6-phosphate isomerase, type I / Phosphomannose isomerase type I, catalytic domain / Phosphomannose isomerase type I C-terminal / Phosphomannose isomerase type I, catalytic domain / 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 speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.67 Å
AuthorsSagurthi, S.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Crystal Structures of Mannose 6-Phosphate Isomerase from Salmonella Typhimurium Bound to Metal Atoms and Substrate: Implications for Catalytic Mechanism
Authors: Sagurthi, S.R. / Gowda, G. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionApr 13, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MANNOSE-6-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,91517
Polymers42,9221
Non-polymers99316
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.904, 92.470, 111.870
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 MANNOSE-6-PHOSPHATE ISOMERASE / MANNOSE 6-PHOSPHATE ISOMERASE / PHOSPHOMANNOSE ISOMERASE / PMI / PHOSPHOHEXOMUTASE


Mass: 42921.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: LT2 / Plasmid: PRSETC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PLYSIS / References: UniProt: P25081, mannose-6-phosphate isomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.2 Å3/Da / Density % sol: 43.6 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MAGNESIUM ACETATE, 0.2 M SODIUM CACODYLATE PH 6.5, 20% PEG 8000 AND 5% DIOXANE

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MAR345 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS
RadiationMonochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.66→30 Å / Num. obs: 44547 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 19.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 48.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.67→29.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.077 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2233 5 %RANDOM
Rwork0.189 ---
obs0.19 42118 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.67→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 64 372 3400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223145
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9824255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7795407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67324.851134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90515516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2391516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212376
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5851.51984
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11623193
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86131161
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1234.51054
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 164 -
Rwork0.418 2985 -
obs--96.39 %
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)
10.0753-0.04650.03140.267-0.10610.16630.00390.0037-0.0038-0.0055-0.0001-0.00180.0021-0.003-0.0038-0.018-0.00160.0021-0.0074-0.0038-0.01111.846737.020414.0781
20.03170.00010.02050.1202-0.10870.239-0.01090.0129-0.02980.02840.01650.0083-0.0163-0.0199-0.0055-0.0122-0.00250.00350.0017-0.003-0.010913.299834.169517.9563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 391
2X-RAY DIFFRACTION2A1392 - 1407

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