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

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Basic information

Entry
Database: PDB / ID: 4rkz
TitleCrystal Structure of Mevalonate-3-Kinase from Thermoplasma acidophilum (Mevalonate 3-Phosphate/ADP 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 / 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
Chem-3S4 / ADENOSINE-5'-DIPHOSPHATE / Mevalonate 3-kinase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 14, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)75,8259
Polymers74,5572
Non-polymers1,2687
Water72140
1
A: Putative uncharacterized protein Ta1305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0304
Polymers37,2781
Non-polymers7513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein Ta1305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7955
Polymers37,2781
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.370, 61.060, 103.550
Angle α, β, γ (deg.)90.00, 122.95, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRCHAIN AAA2 - 31821 - 337
2GLYGLYCHAIN BBB-1 - 31818 - 337

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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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-3S4 / (3R)-5-hydroxy-3-methyl-3-(phosphonooxy)pentanoic acid


Mass: 228.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O7P
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
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 5 mM mevalonate 3-phosphate and ADP generated ...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 5 mM mevalonate 3-phosphate and ADP generated enzymatically, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→86.891 Å / Num. all: 34215 / Num. obs: 34215 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 53.03 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 15.04
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.360.633.18199.4
2.36-2.420.4854199.5
2.42-2.490.4174.54199.1
2.49-2.570.3715.58199.3
2.57-2.660.2897.08199.6
2.66-2.750.2468.33199.4
2.75-2.850.1910.19199.3
2.85-2.970.14412.28199.4
2.97-3.10.10914.69199.4
3.1-3.250.08816.62198.5
3.25-3.430.07420.8199.6
3.43-3.640.06523.91199.5
3.64-3.890.05826.38199
3.89-4.20.05427.89198.8
4.2-4.60.0528.87199.6
4.6-5.140.04729.09197.5
5.14-5.940.04931.09199.4
5.94-7.270.0531.52199
7.27-10.290.05331.02197.6
10.29-54.430.05633.7198.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1555refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RKP

4rkp


Resolution: 2.3→86.891 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 3418 10 %
Rwork0.2015 --
obs0.2063 34194 99.44 %
all-34194 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.1158 Å2
Refinement stepCycle: LAST / Resolution: 2.3→86.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 75 40 4862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034923
X-RAY DIFFRACTIONf_angle_d0.6726701
X-RAY DIFFRACTIONf_dihedral_angle_d12.011688
X-RAY DIFFRACTIONf_chiral_restr0.025747
X-RAY DIFFRACTIONf_plane_restr0.002855
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A2794X-RAY DIFFRACTIONTORSIONAL
12B2794X-RAY DIFFRACTIONTORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33290.41781420.31951283X-RAY DIFFRACTION100
2.3329-2.36770.35411390.30931259X-RAY DIFFRACTION100
2.3677-2.40470.36691440.29271317X-RAY DIFFRACTION99
2.4047-2.44410.39341400.28441252X-RAY DIFFRACTION99
2.4441-2.48630.33751400.28171257X-RAY DIFFRACTION100
2.4863-2.53150.3181420.26011282X-RAY DIFFRACTION99
2.5315-2.58020.31721390.25321242X-RAY DIFFRACTION99
2.5802-2.63290.33121430.25121286X-RAY DIFFRACTION100
2.6329-2.69010.32051410.23541275X-RAY DIFFRACTION100
2.6901-2.75270.31271430.24811286X-RAY DIFFRACTION99
2.7527-2.82160.27611430.24051280X-RAY DIFFRACTION100
2.8216-2.89780.31981420.24941282X-RAY DIFFRACTION100
2.8978-2.98310.27971390.23831250X-RAY DIFFRACTION99
2.9831-3.07940.27191460.22161313X-RAY DIFFRACTION100
3.0794-3.18950.28761410.24161272X-RAY DIFFRACTION99
3.1895-3.31720.28531410.22891269X-RAY DIFFRACTION99
3.3172-3.46820.24441440.21591295X-RAY DIFFRACTION100
3.4682-3.6510.25641420.20111273X-RAY DIFFRACTION100
3.651-3.87980.2331430.19011293X-RAY DIFFRACTION100
3.8798-4.17930.23631430.17061284X-RAY DIFFRACTION99
4.1793-4.59990.20161430.1571283X-RAY DIFFRACTION100
4.5999-5.26540.19931430.16741291X-RAY DIFFRACTION98
5.2654-6.63350.26141460.19121314X-RAY DIFFRACTION100
6.6335-86.95260.18691490.16871338X-RAY DIFFRACTION99

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