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- PDB-3h1y: Crystal structure of mannose 6-phosphate isomerase from Salmonell... -

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Basic information

Entry
Database: PDB / ID: 3h1y
TitleCrystal structure of mannose 6-phosphate isomerase from Salmonella typhimurium bound to substrate (f6p)and metal atom (zn)
ComponentsMannose-6-phosphate isomerase
KeywordsISOMERASE / mannose 6-phospaphate isomerase / f6p complex structure / cupin domain
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
6-O-phosphono-beta-D-fructofuranose / Mannose-6-phosphate isomerase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSagurthi, S.R. / Giri, G. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: To be published
Title: Crystal structure of mannose 6-phosphate isomerase from Salmonella typhimurium bound to metal atoms and substrate: Implications for catalytic mechanism
Authors: Sagurthi, S.R. / Giri, G. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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

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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)43,4899
Polymers42,7911
Non-polymers6988
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.890, 92.250, 111.530
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 / Phosphomannose isomerase / PMI / Phosphohexomutase


Mass: 42790.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: AAL20387, manA, pmi, STM1467 / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / References: UniProt: P25081, mannose-6-phosphate isomerase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: micro-bactch under oil / pH: 6.5
Details: 0.1M magnesium acetate, 0.2M sodium cacodylate pH 6.5, 20% PEG 8000, 10mM zinc F6P soaking., Micro-bactch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 13, 2008 / Details: osmic mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 24243 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.09 / Rsym value: 0.03 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.147 / % possible all: 87.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.4.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PMI

1pmi


Resolution: 2.04→28.94 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.23 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23314 1236 5.1 %RANDOM
Rwork0.19212 ---
obs0.19419 23002 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.04→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 41 219 3250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9824198
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11824.962131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84415500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9151514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212337
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_it0.6991.51966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28123153
X-RAY DIFFRACTIONr_scbond_it2.07531126
X-RAY DIFFRACTIONr_scangle_it3.4484.51042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.043→2.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 80 -
Rwork0.218 1645 -
obs--97.07 %

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