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- PDB-4rks: Crystal Structure of Mevalonate-3-Kinase from Thermoplasma acidop... -

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Basic information

Entry
Database: PDB / ID: 4rks
TitleCrystal Structure of Mevalonate-3-Kinase from Thermoplasma acidophilum (Mevalonate Bound)
ComponentsPutative uncharacterized protein Ta1305
KeywordsTRANSFERASE / mevalonate / mevalonate-3-kinase / mevalonate pyrophosphate decarboxylase / mevalonate diphosphate decarboxylase / mevalonic acid / mevalonate kinase
Function / homology
Function and homology information


mevalonate 3-kinase / isopentenyl diphosphate biosynthetic process, mevalonate pathway / phosphotransferase activity, alcohol group as acceptor / kinase activity / phosphorylation / ATP binding
Similarity search - Function
: / : / Mevalonate-3-kinase, C-terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ACETATE ION / (R)-MEVALONATE / Mevalonate 3-kinase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVinokur, J.M. / Cascio, D. / Sawaya, M.R. / Bowie, J.U.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural analysis of mevalonate-3-kinase provides insight into the mechanisms of isoprenoid pathway decarboxylases.
Authors: Vinokur, J.M. / Korman, T.P. / Sawaya, M.R. / Collazo, M. / Cascio, D. / Bowie, J.U.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 20, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein Ta1305
B: Putative uncharacterized protein Ta1305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,38710
Polymers74,5572
Non-polymers8308
Water3,279182
1
A: Putative uncharacterized protein Ta1305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6184
Polymers37,2781
Non-polymers3393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein Ta1305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7696
Polymers37,2781
Non-polymers4905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.990, 61.190, 103.950
Angle α, β, γ (deg.)90.000, 123.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative uncharacterized protein Ta1305 / Mevalonate-3-Kinase


Mass: 37278.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: Ta1305 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HIN1

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Non-polymers , 5 types, 190 molecules

#2: Chemical ChemComp-MEV / (R)-MEVALONATE / Mevalonic acid


Mass: 147.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ProComplex condition 68, (Quiagen Cat No. 135468A) 0.1 M Sodium Acetate, pH 5.0, 1.0 M Ammonium Sulfate (2:1 Protein:Reservoir ratio), soaked in 65 mM (R)-mevalonate (no mother liquor), ...Details: ProComplex condition 68, (Quiagen Cat No. 135468A) 0.1 M Sodium Acetate, pH 5.0, 1.0 M Ammonium Sulfate (2:1 Protein:Reservoir ratio), soaked in 65 mM (R)-mevalonate (no mother liquor), vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 6, 2013
RadiationMonochromator: CONFOCAL MIRRORS Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→54.87 Å / Num. all: 51669 / Num. obs: 51669 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.37 % / Biso Wilson estimate: 27.26 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Χ2: 0.985 / Net I/σ(I): 20.04
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.543.57275873760197.7
2.05-2.110.4284.59272913709197.7
2.11-2.170.375.26267123631199
2.17-2.240.4284.89237643229189.6
2.24-2.310.19711.5221073060189
2.31-2.390.248.13244783310198.3
2.39-2.480.18210.48237203199198.9
2.48-2.580.16211.75232433125199.1
2.58-2.70.1314.5220112966199.1
2.7-2.830.10617.33213632869199.5
2.83-2.980.08521.75201512711199.3
2.98-3.160.06727.34191782577199.7
3.16-3.380.05432.89179832424199.5
3.38-3.650.04638.55167182280199.6
3.65-40.04144.73150192086198.9
4-4.470.03150.69139081888199.5
4.47-5.160.0351.92123201667199.6
5.16-6.320.0350.37105371429199.5
6.32-8.940.02554.7882111124199.2
8.94-54.870.01961.934306625197.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RKP

4rkp


Resolution: 2→54.855 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2583 5 %RANDOM
Rwork0.1946 ---
obs0.197 51657 97.89 %-
all-51657 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.7 Å2 / Biso mean: 32.6744 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: LAST / Resolution: 2→54.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 50 182 5176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075101
X-RAY DIFFRACTIONf_angle_d0.976913
X-RAY DIFFRACTIONf_chiral_restr0.043754
X-RAY DIFFRACTIONf_plane_restr0.005896
X-RAY DIFFRACTIONf_dihedral_angle_d12.0451824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03850.30591410.23812662280397
2.0385-2.08010.30111440.22762741288599
2.0801-2.12530.32291420.23572697283998
2.1253-2.17480.27631440.24212751289599
2.1748-2.22910.38381290.35412449257889
2.2291-2.28940.40311350.33932557269292
2.2894-2.35680.31091360.26762575271193
2.3568-2.43280.29221430.218127342877100
2.4328-2.51980.25031450.19872746289199
2.5198-2.62070.24881450.20582765291099
2.6207-2.740.28021470.20432793294099
2.74-2.88440.30231450.210327442889100
2.8844-3.06510.25821460.198527802926100
3.0651-3.30170.25551460.194327702916100
3.3017-3.63390.2131490.179128252974100
3.6339-4.15960.19461460.165727732919100
4.1596-5.240.18151480.140628252973100
5.24-54.87580.17371520.151728873039100
Refinement TLS params.Method: refined / Origin x: 33.688 Å / Origin y: 13.2 Å / Origin z: 19.716 Å
111213212223313233
T0.2348 Å2-0.0063 Å2-0.0186 Å2-0.1565 Å2-0.0064 Å2--0.2216 Å2
L0.6606 °2-0.0573 °2-0.3873 °2-0.2047 °2-0.0725 °2--0.915 °2
S-0.0211 Å °-0.0542 Å °0.0365 Å °0.0463 Å °-0.001 Å °0.0224 Å °-0.0532 Å °0.0154 Å °0.0216 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )A2 - 318
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )A401
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )A501 - 599
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )A402 - 403
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )B401
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )B-1 - 318
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )B402
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )B501 - 583
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )B405
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:318 OR RESID 401:401 OR RESID 501:599 OR RESID 402:403 ) ) OR ( CHAIN B AND ( RESID 401:401 OR RESID -1:318 OR RESID 402:402 OR RESID 501:583 OR RESID 405:405 OR RESID 403:404 ) )B403 - 404

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