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- PDB-5zt4: Crystal structure of H99A mutant of phosphomannose isomerase from... -

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Basic information

Entry
Database: PDB / ID: 5zt4
TitleCrystal structure of H99A 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: 1.7 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 1, 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)43,1588
Polymers42,7241
Non-polymers4347
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint22 kcal/mol
Surface area16270 Å2
Unit cell
Length a, b, c (Å)36.220, 91.660, 116.230
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: 42723.621 Da / Num. of mol.: 1 / Mutation: H99A
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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
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 8000,5% 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: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.7→32.35 Å / Num. obs: 43599 / % possible obs: 100 % / Redundancy: 12.7 % / Rsym value: 0.095 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.79 Å / Rsym value: 0.795

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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: 1.7→32.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.895 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21552 2189 5 %RANDOM
Rwork0.18003 ---
obs0.18183 41332 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0 Å20 Å2
2---1.07 Å20 Å2
3---2.34 Å2
Refinement stepCycle: 1 / Resolution: 1.7→32.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 28 284 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193055
X-RAY DIFFRACTIONr_bond_other_d0.0010.022925
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9724150
X-RAY DIFFRACTIONr_angle_other_deg0.86336717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11325.039127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72315474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1441513
X-RAY DIFFRACTIONr_chiral_restr0.110.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213514
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02673
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_it1.341.5141580
X-RAY DIFFRACTIONr_mcbond_other1.3391.5131579
X-RAY DIFFRACTIONr_mcangle_it1.9682.2621973
X-RAY DIFFRACTIONr_mcangle_other1.9672.2631974
X-RAY DIFFRACTIONr_scbond_it2.2021.7581475
X-RAY DIFFRACTIONr_scbond_other2.1871.7581475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2072.5322175
X-RAY DIFFRACTIONr_long_range_B_refined5.92313.7513481
X-RAY DIFFRACTIONr_long_range_B_other5.92613.7563482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 155 -
Rwork0.26 2986 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 6.0913 Å / Origin y: 9.6591 Å / Origin z: 130.8562 Å
111213212223313233
T0.0413 Å2-0.0015 Å2-0.0003 Å2-0.0038 Å20.0046 Å2--0.0203 Å2
L1.1088 °2-0.2089 °2-0.0372 °2-1.8444 °20.5504 °2--1.1221 °2
S0.0292 Å °-0.041 Å °-0.0691 Å °0.1133 Å °-0.0242 Å °0.0747 Å °-0.015 Å °0.009 Å °-0.0051 Å °

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