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

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Basic information

Entry
Database: PDB / ID: 4rkp
TitleCrystal Structure of Mevalonate-3-Kinase from Thermoplasma acidophilum (apo form)
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 / phosphotransferase activity, alcohol group as acceptor / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / ATP binding
Similarity search - Function
: / : / Mevalonate-3-kinase, C-terminal domain / : / Diphosphomevalonate decarboxylase-like N-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 / Mevalonate 3-kinase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)75,40612
Polymers74,5572
Non-polymers85010
Water3,243180
1
A: Putative uncharacterized protein Ta1305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6856
Polymers37,2781
Non-polymers4065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein Ta1305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7226
Polymers37,2781
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.490, 62.490, 103.190
Angle α, β, γ (deg.)90.00, 123.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ProComplex condition 68, (Qiagen Cat No. 135468A) 0.1 M Sodium Acetate, pH 5.0, 1.0 M Ammonium Sulfate (2:1 Protein:Reservoir ratio), 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: Oct 25, 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→62.59 Å / Num. all: 54102 / Num. obs: 54102 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.37 % / Biso Wilson estimate: 27.22 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.050.9352.32199.8
2.05-2.110.7832.74199.7
2.11-2.170.6673.24199.8
2.17-2.240.5523.98199.7
2.24-2.310.5084.26199.7
2.31-2.390.3915.46199.8
2.39-2.480.3356.31199.7
2.48-2.580.2887.36199.8
2.58-2.70.2378.86199.8
2.7-2.830.18711.05199.7
2.83-2.980.13814.64199.8
2.98-3.160.10718.59199.5
3.16-3.380.07923.98199.8
3.38-3.650.05930.89199.6
3.65-40.04936.39199.6
4-4.470.0441.71199.5
4.47-5.160.03743.35199.5
5.16-6.320.04139.81199.4
6.32-8.940.03344.82199.6
8.94-62.590.02554.55197.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å62.59 Å
Translation2 Å62.59 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FI4

1fi4


Resolution: 2.1→62.588 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 2341 5 %
Rwork0.1817 --
obs0.1835 46798 99.96 %
all-54093 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.7771 Å2
Refinement stepCycle: LAST / Resolution: 2.1→62.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 47 180 5096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085021
X-RAY DIFFRACTIONf_angle_d1.0136824
X-RAY DIFFRACTIONf_dihedral_angle_d11.1871752
X-RAY DIFFRACTIONf_chiral_restr0.041753
X-RAY DIFFRACTIONf_plane_restr0.005886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1430.30681400.24362650X-RAY DIFFRACTION100
2.143-2.18960.26471340.21652556X-RAY DIFFRACTION100
2.1896-2.24050.25761370.20342596X-RAY DIFFRACTION100
2.2405-2.29660.26791360.21292588X-RAY DIFFRACTION100
2.2966-2.35870.24221370.19832603X-RAY DIFFRACTION100
2.3587-2.42810.27281370.20412591X-RAY DIFFRACTION100
2.4281-2.50640.24211370.20582617X-RAY DIFFRACTION100
2.5064-2.5960.26591370.20722592X-RAY DIFFRACTION100
2.596-2.70.2841370.20182617X-RAY DIFFRACTION100
2.7-2.82290.22051380.20832611X-RAY DIFFRACTION100
2.8229-2.97170.26641360.20342596X-RAY DIFFRACTION100
2.9717-3.15790.27111380.20012610X-RAY DIFFRACTION100
3.1579-3.40170.20161380.1882621X-RAY DIFFRACTION100
3.4017-3.7440.18821380.16862633X-RAY DIFFRACTION100
3.744-4.28560.18021390.14772632X-RAY DIFFRACTION100
4.2856-5.39890.15361390.1452644X-RAY DIFFRACTION100
5.3989-62.61580.18761430.16132700X-RAY DIFFRACTION100

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