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- PDB-1nfs: STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIM... -

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Basic information

Entry
Database: PDB / ID: 1nfs
TitleSTRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP
ComponentsISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
KeywordsISOMERASE / COMPLEX
Function / homology
Function and homology information


isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / dimethylallyl diphosphate biosynthetic process / isoprenoid biosynthetic process / DNA damage response / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
Isopentenyl-diphosphate delta-isomerase, type 1 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE / : / Isopentenyl-diphosphate Delta-isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsWouters, J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Catalytic Mechanism of Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 as Suggested by Crystal Structures of Complexes with Transition State Analogues ...Title: Catalytic Mechanism of Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 as Suggested by Crystal Structures of Complexes with Transition State Analogues and Irreversible Inhibitors
Authors: Wouters, J. / Oudjama, Y. / Barkley, S.J. / Tricot, C. / Stalon, V. / Droogmans, L. / Poulter, C.D.
History
DepositionDec 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 16, 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_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _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: ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
B: ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9458
Polymers41,2892
Non-polymers6576
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-34 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.982, 71.493, 91.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo molecules in the asymertic unit form the biological assembly

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Components

#1: Protein ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE / DIMETHYLALLYL DIPHOSPHATE ISOMERASE / IPP ISOMERASE / ISOPENTENYL PYROPHOSPHATE ISOMERASE


Mass: 20644.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: Q46822, isopentenyl-diphosphate Delta-isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DED / 2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE


Mass: 249.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H13NO7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.43 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 2000, MANGANESE CHLORIDE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
216 %PEG20001reservoir
3100 mMammonium sulfate1reservoir
410 mM1reservoirMnCl2
5Tris/maleate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.54179 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.96→10 Å / Num. all: 27788 / Num. obs: 23302 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.042 / Net I/σ(I): 9.2
Reflection shellResolution: 1.97→2.08 Å / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 6.3 / % possible all: 94.8
Reflection
*PLUS
Highest resolution: 1.97 Å / Num. measured all: 107068
Reflection shell
*PLUS
% possible obs: 94.8 %

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Processing

Software
NameClassification
MAR345data collection
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HZT

1hzt


Resolution: 1.96→10 Å / Num. parameters: 11935 / Num. restraintsaints: 15429 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 3098 0.2764 %RANDOM
Rwork0.2103 ---
all0.2224 27788 --
obs0.2187 23302 84.6 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2983
Refinement stepCycle: LAST / Resolution: 1.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 32 117 2970
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0.043
X-RAY DIFFRACTIONs_from_restr_planes0.0267
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.97 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.222 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.027
X-RAY DIFFRACTIONs_chiral_restr0.029

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