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- PDB-2pny: Structure of Human Isopentenyl-diphosphate Delta-isomerase 2 -

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Basic information

Entry
Database: PDB / ID: 2pny
TitleStructure of Human Isopentenyl-diphosphate Delta-isomerase 2
ComponentsIsopentenyl-diphosphate Delta-isomerase 2
KeywordsISOMERASE / Carotenoid biosynthesis / Cholesterol biosynthesis / Isoprene biosynthesis / Lipid synthesis / Peroxisome / Steroid biosynthesis / Sterol biosynthesis / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


isopentenyl diphosphate metabolic process / isopentenyl diphosphate biosynthetic process / isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / dimethylallyl diphosphate biosynthetic process / Cholesterol biosynthesis / isoprenoid biosynthetic process / cholesterol biosynthetic process / peroxisome / hydrolase activity ...isopentenyl diphosphate metabolic process / isopentenyl diphosphate biosynthetic process / isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / dimethylallyl diphosphate biosynthetic process / Cholesterol biosynthesis / isoprenoid biosynthetic process / cholesterol biosynthetic process / peroxisome / hydrolase activity / metal ion binding / cytoplasm / cytosol
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
: / PYROPHOSPHATE 2- / Isopentenyl-diphosphate delta-isomerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsWalker, J.R. / Davis, T. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of the human Isopentenyl-diphosphate Delta-isomerase 2.
Authors: Walker, J.R. / Davis, T. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 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_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_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

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Assembly

Deposited unit
A: Isopentenyl-diphosphate Delta-isomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3737
Polymers28,8261
Non-polymers5476
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.897, 52.815, 96.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isopentenyl-diphosphate Delta-isomerase 2 / IPP isomerase 2 / Isopentenyl pyrophosphate isomerase 2 / IPPI2


Mass: 28825.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Skeletal muscle / Gene: IDI2 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9BXS1, isopentenyl-diphosphate Delta-isomerase

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Non-polymers , 5 types, 193 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein buffer: 10 mg/mL Protein, 0.1 M NaCl, 0.05 M Tris-HCl pH 8.0, 0.001 M TCEP, 0.001 M CaCl2, 0.001 M MgCl2, 0.001 M MnCl2. Precipitant: 2 M Na/K PO4, pH 7.0. Cryoprotectant: 20% ...Details: Protein buffer: 10 mg/mL Protein, 0.1 M NaCl, 0.05 M Tris-HCl pH 8.0, 0.001 M TCEP, 0.001 M CaCl2, 0.001 M MgCl2, 0.001 M MnCl2. Precipitant: 2 M Na/K PO4, pH 7.0. Cryoprotectant: 20% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 19, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 24447 / Num. obs: 24447 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.056 / Net I/σ(I): 36.95
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 9.6 / Num. unique all: 2101 / Rsym value: 0.238 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ICJ

2icj


Resolution: 1.81→24.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.764 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.18203 1202 4.9 %RANDOM
Rwork0.14759 ---
obs0.14931 23192 99.93 %-
all-24394 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.151 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---0.57 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.81→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 29 187 2147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212098
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9662838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42623.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60815378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8821522
X-RAY DIFFRACTIONr_chiral_restr0.1230.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021597
X-RAY DIFFRACTIONr_nbd_refined0.2120.2941
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2189
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.29
X-RAY DIFFRACTIONr_mcbond_it0.9681.51271
X-RAY DIFFRACTIONr_mcangle_it1.31822005
X-RAY DIFFRACTIONr_scbond_it2.5173942
X-RAY DIFFRACTIONr_scangle_it3.5974.5833
LS refinement shellResolution: 1.81→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 81 -
Rwork0.145 1643 -
obs--99.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
121.43476.4268-4.119720.771515.002215.2593-0.2256-0.6937-0.3339-0.31550.0494-0.2499-0.3133-0.00990.17620.0421-0.0333-0.00290.03550.03710.023735.16115.551134.9395
223.65-12.535825.361918.2387-10.91735.07510.1655-0.35040.7093-0.3616-0.5562-0.30340.6875-0.25940.39060.02860.02270.03150.09270.00740.014726.469122.382535.0795
32.2811-0.25460.58354.32342.13247.1037-0.0289-0.0175-0.03910.0792-0.01020.2773-0.0905-0.49880.03910.05540.00950.03940.07890.03840.066517.329723.482122.8648
47.5792-7.9425-8.181421.952216.747913.7342-0.19650.20380.14260.3933-0.11890.2760.6324-0.4090.31540.07280.0005-0.00560.0480.00070.066422.675614.210616.7294
58.87950.4727-5.15494.6463-0.89517.0609-0.1286-0.1751-0.17850.0025-0.0802-0.35080.37190.34160.20880.0590.03540.0130.05560.00160.084136.847111.12718.6843
63.67022.29641.50512.0336-0.14022.5785-0.0015-0.0478-0.06310.20740.0038-0.07680.07360.0499-0.00230.10040.01140.00680.05710.01450.063630.254316.015221.1849
70.5518-0.31770.19391.1528-0.50951.06390.01840.0343-0.0229-0.024-0.0270.030.08530.04930.00860.05720.0059-0.00120.08310.0060.072730.896824.00197.8914
81.03720.137-0.6511.0538-1.70264.04550.0053-0.0058-0.02420.04980.00820.0879-0.05010.0084-0.01340.07640.00690.010.06250.00150.079724.540434.430712.3607
90.37510.32930.093.0728-1.14731.59860.02350.0703-0.0313-0.07290.0255-0.06580.217-0.0188-0.04890.059-0.0102-0.00570.0732-0.01110.089425.584614.76514.7549
103.6443-4.481-1.41216.17152.5112.53920.00550.2212-0.0863-0.0706-0.04770.23660.1138-0.17920.04220.0634-0.0209-0.00360.0711-0.00130.082622.156620.07491.4492
113.9608-0.38590.56651.52580.64110.59510.21950.0493-0.4482-0.12-0.0040.0720.156-0.1565-0.21540.06990.0293-0.03540.0595-0.00010.1216.049826.8889-0.4448
1210.5955-2.99351.23422.54670.14864.16930.31280.5609-0.4888-0.1986-0.23120.07490.1254-0.0403-0.08160.0790.0154-0.00460.061-0.02420.064730.286623.8693-3.7507
131.5907-0.6496-2.04821.89010.05653.9130.041-0.0992-0.03310.0954-0.0452-0.0753-0.07210.13390.00420.0537-0.0047-0.00860.088600.078934.904323.5317.2105
142.7174-1.6150.36341.0421-0.57541.61830.06960.2111-0.0326-0.2198-0.07240.03760.1135-0.07270.00280.0625-0.0103-0.03490.07950.01210.105523.902130.4351-1.8873
152.32070.09311.29322.34620.15272.5173-0.0196-0.04780.0291-0.04810.020.16830.0055-0.2099-0.00040.06990.00640.02520.0790.00710.079815.76132.845112.5775
165.31840.76693.7591.29650.22625.29840.0755-0.03870.19350.0278-0.02810.0622-0.02180.0852-0.04740.07150.00230.02520.05690.00790.069230.387143.94515.5941
172.32430.0089-1.65657.08794.22139.82290.07170.05320.12040.3040.0574-0.2253-0.16040.2616-0.12910.0868-0.0054-0.00460.05570.00780.057633.935644.710217.0519
184.1014-0.2034-3.47520.0595-0.11784.649-0.0148-0.1256-0.10850.03910.0109-0.18660.08930.16410.00390.07590.01110.00140.0647-0.00750.084736.477133.86078.0606
190.5129-1.38950.45159.38344.77216.79270.22680.10060.0411-0.4069-0.1757-0.0293-0.09530.0839-0.05110.09860.00310.04740.0806-0.00270.041135.171636.7223-5.529
201.5168-1.01831.74682.123-0.1074.40620.07020.0747-0.0562-0.16350.0516-0.0263-0.04830.2668-0.12180.06860.00270.04950.0659-0.01270.065140.455324.4504-2.1326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-5 - -114 - 18
2X-RAY DIFFRACTION2AA0 - 519 - 24
3X-RAY DIFFRACTION3AA6 - 1625 - 35
4X-RAY DIFFRACTION4AA17 - 2136 - 40
5X-RAY DIFFRACTION5AA22 - 3241 - 51
6X-RAY DIFFRACTION6AA33 - 4552 - 64
7X-RAY DIFFRACTION7AA46 - 6165 - 80
8X-RAY DIFFRACTION8AA62 - 8381 - 102
9X-RAY DIFFRACTION9AA84 - 99103 - 118
10X-RAY DIFFRACTION10AA100 - 114119 - 133
11X-RAY DIFFRACTION11AA115 - 125134 - 144
12X-RAY DIFFRACTION12AA126 - 133145 - 152
13X-RAY DIFFRACTION13AA134 - 150153 - 169
14X-RAY DIFFRACTION14AA151 - 161170 - 180
15X-RAY DIFFRACTION15AA162 - 171181 - 190
16X-RAY DIFFRACTION16AA172 - 183191 - 202
17X-RAY DIFFRACTION17AA184 - 192203 - 211
18X-RAY DIFFRACTION18AA193 - 205212 - 224
19X-RAY DIFFRACTION19AA206 - 214225 - 233
20X-RAY DIFFRACTION20AA215 - 227234 - 246

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