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- PDB-1m1b: Crystal Structure of Phosphoenolpyruvate Mutase Complexed with Su... -

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Basic information

Entry
Database: PDB / ID: 1m1b
TitleCrystal Structure of Phosphoenolpyruvate Mutase Complexed with Sulfopyruvate
ComponentsPHOSPHOENOLPYRUVATE PHOSPHOMUTASE
KeywordsISOMERASE / phosphoenolpyruvate mutase / PEP mutase / sulfopyruvate
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
SULFOPYRUVATE / Phosphoenolpyruvate phosphomutase
Similarity search - Component
Biological speciesMytilus edulis (blue mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLiu, S. / Lu, Z. / Jia, Y. / Dunaway-Mariano, D. / Herzberg, O.
CitationJournal: Biochemistry / Year: 2002
Title: Dissociative phosphoryl transfer in PEP mutase catalysis: structure of the enzyme/sulfopyruvate complex and kinetic properties of mutants.
Authors: Liu, S. / Lu, Z. / Jia, Y. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionJun 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2946
Polymers65,9092
Non-polymers3854
Water4,630257
1
A: PHOSPHOENOLPYRUVATE PHOSPHOMUTASE
B: PHOSPHOENOLPYRUVATE PHOSPHOMUTASE
hetero molecules

A: PHOSPHOENOLPYRUVATE PHOSPHOMUTASE
B: PHOSPHOENOLPYRUVATE PHOSPHOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,58712
Polymers131,8174
Non-polymers7708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area22910 Å2
ΔGint-124 kcal/mol
Surface area37430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.024, 130.441, 90.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SPV / SULFOPYRUVATE


Mass: 168.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, glycerol, magnesium chloride, Hepes, sulfopyruvate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 8 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 %(w/v)PEG70001reservoir
215 %glycerol1reservoir
35 mM1reservoirMgCl2
4100 mMHEPES1reservoirpH7.0-8.0
59 mg/mlprotein1drop
65 mMS-pyr1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 25, 2001 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→26.5 Å / Num. all: 25261 / Num. obs: 21045 / % possible obs: 83.3 % / Observed criterion σ(F): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.8
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 3.7 / % possible all: 64.9
Reflection
*PLUS
Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 64.9 % / Rmerge(I) obs: 0.244

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Processing

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

1pym


Resolution: 2.25→26.5 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1380 -RANDOM
Rwork0.179 ---
obs0.185 20235 78.9 %-
all-25651 --
Refinement stepCycle: LAST / Resolution: 2.25→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 22 257 4827
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.46
Refinement
*PLUS
% reflection Rfree: 6 % / Rfactor obs: 0.185 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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