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- PDB-1r67: Y104A MUTANT OF E.COLI IPP ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 1r67
TitleY104A MUTANT OF E.COLI IPP ISOMERASE
ComponentsIsopentenyl-diphosphate delta-isomerase
KeywordsISOMERASE / COMPLEX Y104A MUTANT
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
Isopentenyl-diphosphate Delta-isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsWouters, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography.
Authors: de Ruyck, J. / Durisotti, V. / Oudjama, Y. / Wouters, J.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5352
Polymers21,5101
Non-polymers241
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.648, 71.648, 61.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-340-

HOH

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Components

#1: Protein Isopentenyl-diphosphate delta-isomerase / IPP isomerase / Isopentenyl pyrophosphate isomerase


Mass: 21510.287 Da / Num. of mol.: 1 / Mutation: Y104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: IDI OR B2889 / Production host: Escherichia coli (E. coli)
References: UniProt: Q46822, isopentenyl-diphosphate Delta-isomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.99 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 2000, MANGANESE CHLORIDE, MAGNESIUM CHLORIDE, AMMONIUM SULFATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 275K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 mg/mlprotein1drop
210-16 %(w/v)PEG2000 MME1reservoirpH4.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9292 / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 11, 2003 / Details: SI CRYSTALS
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92921
20.97981
ReflectionResolution: 1.77→99 Å / Num. obs: 13869 / % possible obs: 89.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.77→1.8 Å / Rmerge(I) obs: 0.161 / % possible all: 93.5
Reflection
*PLUS
Highest resolution: 1.76 Å / Num. obs: 16594 / Num. measured all: 31357 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 1.76 Å / % possible obs: 93.5 % / Rmerge(I) obs: 0.169

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HZT

1hzt


Resolution: 1.77→8 Å / Num. parameters: 5368 / Num. restraintsaints: 5013 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.272 815 5 %RANDOM
Rwork0.1897 ---
all0.2063 16116 --
obs0.1967 13869 90.1 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1285.5
Refinement stepCycle: LAST / Resolution: 1.77→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 1 133 1341
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0273
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.207 / Rfactor Rfree: 0.2356 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.027
X-RAY DIFFRACTIONs_chiral_restr0.04

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