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- PDB-5zv0: Crystal structure of E264A mutant of phosphomannose isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 5zv0
TitleCrystal structure of E264A mutant of phosphomannose isomerase from Salmonella typhimurium
ComponentsMannose-6-phosphate isomerase
KeywordsISOMERASE / zinc binding / SUGAR BINDING PROTEIN
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBangera, M. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structural and functional insights into phosphomannose isomerase: the role of zinc and catalytic residues.
Authors: Bangera, M. / Gowda K, G. / Sagurthi, S.R. / Murthy, M.R.N.
History
DepositionMay 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)42,9194
Polymers42,7331
Non-polymers1863
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint11 kcal/mol
Surface area16100 Å2
Unit cell
Length a, b, c (Å)36.270, 91.780, 116.740
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 / Phosphohexomutase / Phosphomannose isomerase / PMI


Mass: 42732.652 Da / Num. of mol.: 1 / Mutation: E264A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: manA, pmi, STM1467 / Production host: Escherichia coli (E. coli) / References: UniProt: P25081, mannose-6-phosphate isomerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.8
Details: 0.1 M Magnesium acetate tetrahydrate, 0.2 M Sodium cacodylate pH 6.8, 20% PEG 8000, 30% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.1→58.37 Å / Num. obs: 21909 / % possible obs: 92.7 % / Redundancy: 9.9 % / Rsym value: 0.109 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.21 Å / Rsym value: 0.26

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H1M

3h1m


Resolution: 2.1→58.37 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.881 / SU B: 12.373 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.232 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27256 1113 5.1 %RANDOM
Rwork0.21274 ---
obs0.21573 20692 92.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.607 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å2-0 Å20 Å2
2--1.03 Å2-0 Å2
3---1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.1→58.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 12 211 3138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192968
X-RAY DIFFRACTIONr_bond_other_d0.0010.022831
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9714038
X-RAY DIFFRACTIONr_angle_other_deg0.70836492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6124.711121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50115453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5811513
X-RAY DIFFRACTIONr_chiral_restr0.0680.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213406
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
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_it0.3270.8541545
X-RAY DIFFRACTIONr_mcbond_other0.3270.8531544
X-RAY DIFFRACTIONr_mcangle_it0.5991.2761926
X-RAY DIFFRACTIONr_mcangle_other0.5991.2771927
X-RAY DIFFRACTIONr_scbond_it0.2730.8941423
X-RAY DIFFRACTIONr_scbond_other0.270.8931423
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4691.3192113
X-RAY DIFFRACTIONr_long_range_B_refined5.7147.5773280
X-RAY DIFFRACTIONr_long_range_B_other5.7147.5863281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 104 -
Rwork0.228 1609 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 6.226 Å / Origin y: 9.773 Å / Origin z: 131.443 Å
111213212223313233
T0.1419 Å2-0.008 Å20.0084 Å2-0.0035 Å2-0.0047 Å2--0.0853 Å2
L1.391 °2-0.2557 °2-0.1321 °2-2.5184 °20.8854 °2--1.8864 °2
S0.031 Å °0.0485 Å °-0.1071 Å °0.1452 Å °-0.0278 Å °0.1508 Å °-0.047 Å °0.0366 Å °-0.0032 Å °

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