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- PDB-1s2w: Crystal structure of phosphoenolpyruvate mutase in high ionic strength -

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Basic information

Entry
Database: PDB / ID: 1s2w
TitleCrystal structure of phosphoenolpyruvate mutase in high ionic strength
ComponentsPhosphoenolpyruvate phosphomutase
KeywordsISOMERASE / phosphonopyruvate / phosphonate biosynthesis pathway
Function / homology
Function and homology information


phosphoenolpyruvate mutase / phosphoenolpyruvate mutase activity / organic phosphonate biosynthetic process / metal ion binding
Similarity search - Function
Phosphoenolpyruvate phosphomutase, core / Phosphoenolpyruvate phosphomutase / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Phosphoenolpyruvate phosphomutase
Similarity search - Component
Biological speciesMytilus edulis (blue mussel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsLiu, S. / Lu, Z. / Han, Y. / Jia, Y. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O.
CitationJournal: Biochemistry / Year: 2004
Title: Conformational Flexibility of PEP Mutase
Authors: Liu, S. / Lu, Z. / Han, Y. / Jia, Y. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionJan 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT CANNOT BE GENERATED FROM THIS CRYSTAL FORM. THE BIOLOGICAL UNIT IS A TETRAMER, BUT THIS CRYSTAL FORM CONTAINS ONLY DIMERS.
Remark 999SEQUENCE THE AUTHORS INFORMED THAT THEIR SEQUENCE IS CORRECT AT THE POSITIONS WHERE IT CONFLICTS ...SEQUENCE THE AUTHORS INFORMED THAT THEIR SEQUENCE IS CORRECT AT THE POSITIONS WHERE IT CONFLICTS WITH THE SWISS PROT SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate phosphomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0502
Polymers32,9541
Non-polymers961
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphoenolpyruvate phosphomutase
hetero molecules

A: Phosphoenolpyruvate phosphomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1014
Polymers65,9092
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5830 Å2
ΔGint-61 kcal/mol
Surface area21470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.632, 116.556, 72.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTetramer. However, the high ionic strength structure is dimeric.

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Components

#1: Protein Phosphoenolpyruvate phosphomutase / Phosphoenolpyruvate mutase / PEP mutase / PEP phosphomutase


Mass: 32954.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mytilus edulis (blue mussel) / Plasmid: pET 3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56839, phosphoenolpyruvate mutase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 314 K / Method: vapor diffusion, hanging drop / pH: 7
Details: (NH4)2SO4, HEPES, MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 314K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 35608 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 6.47 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.3
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.259 / % possible all: 86.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry code 1pym

1pym


Resolution: 1.69→29.3 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3231 -random
Rwork0.178 ---
obs0.183 32538 88.2 %-
all-36872 --
Refinement stepCycle: LAST / Resolution: 1.69→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 5 270 2295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4

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