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- PDB-1s2t: Crystal Structure Of Apo Phosphoenolpyruvate Mutase -

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Basic information

Entry
Database: PDB / ID: 1s2t
TitleCrystal Structure Of Apo Phosphoenolpyruvate Mutase
ComponentsPhosphoenolpyruvate phosphomutase
KeywordsISOMERASE / phosphoenolpyruvate mutase / PEP mutase / 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: 2 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 / 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
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

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate phosphomutase
B: Phosphoenolpyruvate phosphomutase


Theoretical massNumber of molelcules
Total (without water)65,9092
Polymers65,9092
Non-polymers00
Water11,512639
1
A: Phosphoenolpyruvate phosphomutase
B: Phosphoenolpyruvate phosphomutase

A: Phosphoenolpyruvate phosphomutase
B: Phosphoenolpyruvate phosphomutase


Theoretical massNumber of molelcules
Total (without water)131,8174
Polymers131,8174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area21820 Å2
ΔGint-103 kcal/mol
Surface area41760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.769, 120.882, 88.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsPEP mutase biological unit is a tetramer. The second part of biological assembly can be generated by the two fold axis : 1-x, y, 1/2-z.

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Components

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


Mass: 32954.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mytilus edulis (blue mussel) / Plasmid: PET3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56839, phosphoenolpyruvate mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 45.56 %
Crystal growTemperature: 302 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 302K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 40649 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 6.79 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.136 / % possible all: 85.4

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Processing

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

1pym


Resolution: 2→39.1 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3158 -random
Rwork0.167 ---
obs0.171 39056 94.6 %-
all-41287 --
Refinement stepCycle: LAST / Resolution: 2→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 0 639 5205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5

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