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- PDB-2hke: Mevalonate diphosphate decarboxylase from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 2hke
TitleMevalonate diphosphate decarboxylase from Trypanosoma brucei
ComponentsDiphosphomevalonate decarboxylase, putative
KeywordsLYASE / mevalonate diphosphate decarboxylase / diphosphomevalonate decarboxylase / decarboxylase
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / phosphorylation / cholesterol biosynthetic process / kinase activity / cilium / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsByres, E. / Alphey, M.S. / Hunter, W.N.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of Trypanosoma brucei and Staphylococcus aureus Mevalonate Diphosphate Decarboxylase Inform on the Determinants of Specificity and Reactivity
Authors: Byres, E. / Alphey, M.S. / Smith, T.K. / Hunter, W.N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: A preliminary crystallographic analysis of the putative mevalonate diphosphate decarboxylase from Trypanosoma brucei.
Authors: Byres, E. / Martin, D.M.A. / Hunter, W.N.
History
DepositionJul 4, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Diphosphomevalonate decarboxylase, putative
B: Diphosphomevalonate decarboxylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4678
Polymers83,8912
Non-polymers5766
Water12,827712
1
A: Diphosphomevalonate decarboxylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2334
Polymers41,9451
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diphosphomevalonate decarboxylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2334
Polymers41,9451
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.463, 168.666, 54.850
Angle α, β, γ (deg.)90.00, 118.78, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B)

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Components

#1: Protein Diphosphomevalonate decarboxylase, putative / Mevalonate diphosphate decarboxylase


Mass: 41945.258 Da / Num. of mol.: 2 / Mutation: D92E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: 427, bloodstream form / Gene: mdd (CDS:Tb10.05.0010) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q388P2, diphosphomevalonate decarboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 22% PEG 8000, 180mM ammonium sulfate, 100mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionRedundancy: 6.1 % / Av σ(I) over netI: 4.3 / Number: 455415 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / D res high: 1.8 Å / D res low: 168.665 Å / Num. obs: 74805 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.6942.1798.610.0920.0925.7
4.025.6910010.0790.0796.2
3.294.0299.910.0710.0716.3
2.853.2999.810.0810.0816.3
2.552.8599.610.1070.1076.3
2.322.5599.410.1430.1436.3
2.152.3299.210.190.196.1
2.012.1598.710.2620.2626
1.92.0198.310.4010.4015.9
1.81.99810.6580.6585.8
ReflectionResolution: 1.8→42.18 Å / Num. all: 74800 / Num. obs: 74805 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 4.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.95.80.6581.162870108040.65898
1.9-2.015.90.4011.660357102440.40198.3
2.01-2.1560.26225788696640.26298.7
2.15-2.326.10.193.25523590140.1999.2
2.32-2.556.30.1434.65220383380.14399.4
2.55-2.856.30.1075.94792275860.10799.6
2.85-3.296.30.0817.64219666680.08199.8
3.29-4.026.30.0718.13570956770.07199.9
4.02-5.696.20.0797.42734844100.079100
5.69-42.175.70.0926.51368924000.09298.6

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Phasing

Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 74755
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.48-10057.60.2509
6.8-9.4858.60.804887
5.58-6.866.70.7691155
4.84-5.5861.90.8481352
4.34-4.8457.70.8641515
3.96-4.3454.60.8791678
3.67-3.9652.90.8761806
3.44-3.6752.60.8691972
3.24-3.4451.50.8642084
3.08-3.2447.70.8642228
2.93-3.0851.50.8562306
2.81-2.93550.8532411
2.7-2.8152.20.8392493
2.6-2.756.10.8432591
2.51-2.668.80.8322712
2.43-2.5171.50.8252800
2.36-2.4366.30.8422843
2.3-2.3651.60.8522985
2.23-2.352.20.8563009
2.18-2.2360.40.8613108
2.13-2.1853.40.8653185
2.08-2.13560.863267
2.03-2.0854.50.8673303
1.99-2.0358.30.8713416
1.95-1.99680.8443433
1.91-1.9561.10.8463553
1.88-1.91510.853564
1.84-1.8853.30.8323652
1.8-1.8460.90.7724938

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
DM4.2phasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FI4

1fi4


Resolution: 1.8→42.18 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.543 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3767 5 %RANDOM
Rwork0.166 ---
all0.168 74800 --
obs0.168 74800 98.96 %-
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: 24.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-0.82 Å2
2--1.02 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5820 0 30 712 6562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225944
X-RAY DIFFRACTIONr_bond_other_d0.0010.024103
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9828037
X-RAY DIFFRACTIONr_angle_other_deg0.922310072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96524.483232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.062151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0411530
X-RAY DIFFRACTIONr_chiral_restr0.0950.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021132
X-RAY DIFFRACTIONr_nbd_refined0.2130.21225
X-RAY DIFFRACTIONr_nbd_other0.1980.24368
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22973
X-RAY DIFFRACTIONr_nbtor_other0.0890.23143
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2602
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.248
X-RAY DIFFRACTIONr_mcbond_it1.4131.54837
X-RAY DIFFRACTIONr_mcbond_other0.2631.51507
X-RAY DIFFRACTIONr_mcangle_it1.59526092
X-RAY DIFFRACTIONr_scbond_it2.77632504
X-RAY DIFFRACTIONr_scangle_it3.8974.51943
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 267 -
Rwork0.223 5199 -
obs-5466 97.55 %

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