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- PDB-1q54: STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIM... -

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Basic information

Entry
Database: PDB / ID: 1q54
TitleSTRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP
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
4-BROMO-3-HYDROXY-3-METHYL BUTYL DIPHOSPHATE / : / Isopentenyl-diphosphate Delta-isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWouters, J. / Oudjama, Y. / Ghosh, S. / Stalon, V. / Droogmans, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase.
Authors: Wouters, J. / Oudjama, Y. / Ghosh, S. / Stalon, V. / Droogmans, L. / Oldfield, E.
History
DepositionAug 6, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 26, 2003ID: 1N2U
Revision 1.0Aug 26, 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 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)42,0698
Polymers41,2252
Non-polymers8446
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-36 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.830, 71.350, 91.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly corresponds to a dimer

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Components

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


Mass: 20612.324 Da / Num. of mol.: 2 / Mutation: C67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PYL20 / 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-BHI / 4-BROMO-3-HYDROXY-3-METHYL BUTYL DIPHOSPHATE


Mass: 343.003 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13BrO8P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MnCl2, PEG2000, Ammonium Sulfate, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
216 %PEG20001reservoir
3100 mMammonium sulfate1reservoir
410 mM1reservoirpH5.5MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2000 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→10 Å / Num. all: 29014 / Num. obs: 26583 / % possible obs: 95.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 2.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 6.2
Reflection shellResolution: 1.93→2.04 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 4.7 / % possible all: 95

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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: 1.93→10 Å / Num. parameters: 12257 / Num. restraintsaints: 15465 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3212 10 %RANDOM
Rwork0.21 ---
all0.21 29014 --
obs0.21 26583 95.2 %-
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3029.63
Refinement stepCycle: LAST / Resolution: 1.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2819 0 68 175 3062
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.05
X-RAY DIFFRACTIONs_angle_d0.049
X-RAY DIFFRACTIONs_similar_dist0.051
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.102
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21 / Rfactor Rfree: 0.2574 / Rfactor Rwork: 0.2014
Solvent computation
*PLUS
Displacement parameters
*PLUS

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