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- PDB-1s2v: Crystal structure of phosphoenolpyruvate mutase complexed with Mg(II) -

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Basic information

Entry
Database: PDB / ID: 1s2v
TitleCrystal structure of phosphoenolpyruvate mutase complexed with Mg(II)
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: 2.1 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: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
C: Phosphoenolpyruvate phosphomutase
D: Phosphoenolpyruvate phosphomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9158
Polymers131,8174
Non-polymers974
Water16,862936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21200 Å2
ΔGint-121 kcal/mol
Surface area39810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.517, 86.469, 104.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer. The second dimer(molecules C and D) formed a tetramer with the first dimer (molecule A and B) in the asymmetric unit by the operation: x-1/2,-y+1/2,-z+1.

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Components

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


Mass: 32954.344 Da / Num. of mol.: 4
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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 936 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 298 K / pH: 7.5
Details: PEG 4000, glycerol, HEPES, MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.984
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 62612 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Redundancy: 5.99 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.238 / % possible all: 91.1

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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: 2.1→38 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4315 -RANDOM
Rwork0.185 ---
obs0.185 52982 81.3 %-
all-65613 --
Refinement stepCycle: LAST / Resolution: 2.1→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8884 0 4 936 9824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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