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- PDB-2dho: Crystal structure of human IPP isomerase I in space group P212121 -

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Basic information

Entry
Database: PDB / ID: 2dho
TitleCrystal structure of human IPP isomerase I in space group P212121
ComponentsIsopentenyl-diphosphate delta-isomerase 1
KeywordsISOMERASE / alpha/beta protein
Function / homology
Function and homology information


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 / Activation of gene expression by SREBF (SREBP) / peroxisome / manganese ion binding ...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 / Activation of gene expression by SREBF (SREBP) / peroxisome / manganese ion binding / magnesium ion binding / 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
: / Isopentenyl-diphosphate Delta-isomerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.6 Å
AuthorsZhang, C. / Wei, Z. / Gong, W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structures of human IPP isomerase: new insights into the catalytic mechanism
Authors: Zhang, C. / Liu, L. / Xu, H. / Wei, Z. / Wang, Y. / Lin, Y. / Gong, W.
History
DepositionMar 24, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isopentenyl-diphosphate delta-isomerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,21421
Polymers27,3741
Non-polymers84020
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.019, 62.947, 74.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Isopentenyl-diphosphate delta-isomerase 1 / IPP isomerase 1 / Isopentenyl pyrophosphate isomerase 1 / IPPI1


Mass: 27374.332 Da / Num. of mol.: 1 / Mutation: K157M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q13907, isopentenyl-diphosphate Delta-isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.4M MnCl2, 0.1M Sodium Cacodylate PH6.5, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 33566 / % possible obs: 96.3 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.091 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.66 Å / % possible obs: 68.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.373 / Num. unique obs: 2355 / Χ2: 0.982

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
CrystalCleardata reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→25.79 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.692 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1694 5.1 %RANDOM
Rwork0.173 ---
all0.175 ---
obs-33512 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.506 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 20 306 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221871
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9632554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96725.31994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78315355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.697159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021426
X-RAY DIFFRACTIONr_nbd_refined0.2040.2884
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.221
X-RAY DIFFRACTIONr_mcbond_it0.3861.51118
X-RAY DIFFRACTIONr_mcangle_it0.74321829
X-RAY DIFFRACTIONr_scbond_it1.2583779
X-RAY DIFFRACTIONr_scangle_it1.9274.5711
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 70 -
Rwork0.313 1567 -
obs-1637 64.65 %
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)
12.96114.49224.122212.22988.7127.4049-0.1680.0882-0.2333-0.25240.3942-0.498-0.14980.2735-0.2261-0.01750.00020.044-0.0037-0.0009-0.055916.552925.5612-3.301
22.8518-0.28550.02961.78720.34730.7256-0.0984-0.2638-0.0940.15530.02430.04440.2658-0.02590.07420.01060.010.0329-0.02090.02-0.056117.430816.5741-5.3913
30.91730.4495-1.71722.1028-2.65335.7451-0.04110.029-0.0124-0.0822-0.02460.01960.10580.00490.0657-0.024-0.003-0.0145-0.01670.0022-0.032617.086228.7267-24.0568
42.0135-0.4951.87992.0803-0.7583.3327-0.0492-0.05510.03270.201-0.0118-0.16250.04280.00710.061-0.01350.0007-0.0159-0.04290.0001-0.008127.890629.2279-20.5624
53.36810.0921-0.02820.90910.3482.52340.0253-0.0888-0.02450.03760.00670.05350.0848-0.1636-0.032-0.0202-0.00060.0141-0.03110.0066-0.03659.611327.775-10.091
64.99563.4604-1.50453.7439-1.33741.36350.00580.05630.21070.0120.05690.1996-0.1202-0.1286-0.0627-0.02530.02360.0032-0.021-0.0045-0.037212.980534.0859-16.707
71.42890.70650.00654.8826-0.33731.3078-0.00820.11250.1254-0.1310.04680.3957-0.0353-0.1508-0.0386-0.07810.0027-0.00860.01290.0111-0.044810.610229.7146-22.5217
84.2117-0.4995-0.02061.64830.03450.7633-0.0636-0.106-0.10690.07170.0527-0.0560.09310.02040.0109-0.00770.0024-0.0024-0.03650.0067-0.029924.973616.7705-11.0107
91.7844-0.4889-0.28236.7637-3.66025.0896-0.01660.16560.0354-0.0991-0.0794-0.14360.04460.02920.096-0.0386-0.0188-0.0081-0.0175-0.005-0.027513.246723.844-21.8931
100.92330.50651.26552.13711.13662.60450.0119-0.03570.07930.05440.0106-0.1151-0.0203-0.0146-0.0224-0.0211-0.00940.0064-0.03780.0091-0.041325.019836.9432-23.4847
1112.0712-9.69427.277312.632-9.38611.85090.27610.4673-0.1622-1.0426-0.5306-0.60090.80720.54260.25450.04240.03780.1267-0.0647-0.0025-0.001933.347423.4048-32.6726
125.7544-0.72130.07083.4643-0.01283.33450.08440.1357-0.1522-0.2241-0.0646-0.16420.1680.1832-0.0198-0.01110.02060.0101-0.07380.0116-0.025328.89419.9277-23.9659
136.2159-4.39132.26116.9387-3.23814.98-0.06310.0525-0.2595-0.13860.18140.12990.3939-0.0741-0.11830.0084-0.0243-0.0102-0.0436-0.0129-0.061917.987922.2308-34.492
146.62635.6966-6.21977.0083-7.826119.0763-0.37740.3377-0.1955-0.52710.19520.02850.4918-0.29640.1822-0.0425-0.0482-0.0523-0.0286-0.0157-0.05428.065220.5644-32.2774
1517.5753-6.7187-0.45194.3264-1.29744.4320.15930.4362-0.5701-0.165-0.13230.37960.22540.007-0.0270.0028-0.019-0.0452-0.0735-0.0484-0.018112.216612.0845-22.393
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1113 - 2621 - 34
2227 - 5135 - 59
3352 - 6160 - 69
4462 - 8570 - 93
5586 - 9894 - 106
6699 - 119107 - 127
77120 - 135128 - 143
88136 - 149144 - 157
99150 - 154158 - 162
1010155 - 175163 - 183
1111176 - 188184 - 196
1212189 - 203197 - 211
1313204 - 213212 - 221
1414214 - 221222 - 229
1515222 - 227230 - 235

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