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- PDB-1kvk: The Structure of Binary complex between a Mammalian Mevalonate Ki... -

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Basic information

Entry
Database: PDB / ID: 1kvk
TitleThe Structure of Binary complex between a Mammalian Mevalonate Kinase and ATP: Insights into the Reaction Mechanism and Human Inherited Disease
Componentsmevalonate kinase
KeywordsTRANSFERASE / RMK / ATP / GHMP
Function / homology
Function and homology information


Cholesterol biosynthesis / isoprenoid metabolic process / mevalonate kinase / mevalonate kinase activity / regulation of cholesterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol metabolic process / isoprenoid biosynthetic process / sequence-specific mRNA binding / cholesterol biosynthetic process ...Cholesterol biosynthesis / isoprenoid metabolic process / mevalonate kinase / mevalonate kinase activity / regulation of cholesterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol metabolic process / isoprenoid biosynthetic process / sequence-specific mRNA binding / cholesterol biosynthetic process / negative regulation of inflammatory response / peroxisome / negative regulation of translation / mRNA binding / magnesium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-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
ADENOSINE-5'-TRIPHOSPHATE / Mevalonate kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.4 Å
AuthorsFu, Z. / Wang, M. / Potter, D. / Mizioko, H.M. / Kim, J.J.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The Structure of a Binary complex between a Mammalian Mevalonate Kinase and ATP: Insights into the Reaction Mechanism and Human Inherited Disease
Authors: Fu, Z. / Wang, M. / Potter, D. / Mizioko, H.M. / Kim, J.J.
#1: Journal: Structure / Year: 2000
Title: Structure and Mechanism of Homoserine Kinase: Prototype for the GHMP Kinase Superfamily
Authors: Zhou, T. / Daugherty, M. / Grishin, N.V. / Osterman, A.L. / Zhang, H.
History
DepositionJan 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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: mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5643
Polymers42,0331
Non-polymers5312
Water1,13563
1
A: mevalonate kinase
hetero molecules

A: mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1286
Polymers84,0652
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)78.630, 118.700, 42.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein mevalonate kinase / MK


Mass: 42032.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P17256, mevalonate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Hepes, MgCl2, ATP, PEG-5KMME, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 mg/mlprotein1drop
21 mMATP1drop
32 mM1dropMgCl2
4100 mMHEPES1reservoirpH7.5
517.5 %PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.39→65.55 Å / Num. all: 14200 / Num. obs: 14200 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Limit h max: 32 / Limit h min: 0 / Limit k max: 49 / Limit k min: 0 / Limit l max: 16 / Limit l min: 0 / Observed criterion F max: 282198.29 / Observed criterion F min: 0.55
Reflection shellResolution: 2.4→2.49 Å / % possible all: 76.9
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 14000 / Num. measured all: 30833 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 77.8 % / Num. unique obs: 1011 / Num. measured obs: 2653 / Rmerge(I) obs: 0.305

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→65.5 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1215 8.6 %RANDOM
Rwork0.217 ---
all-14200 --
obs-14200 86.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 48.1123 Å2 / ksol: 0.301427 e/Å3
Displacement parametersBiso max: 88.5 Å2 / Biso mean: 43.09 Å2 / Biso min: 9.35 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.42 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→65.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 32 63 2911
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg22.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.99
X-RAY DIFFRACTIONx_mcbond_it1.41.5
X-RAY DIFFRACTIONx_mcangle_it2.352
X-RAY DIFFRACTIONx_scbond_it1.832
X-RAY DIFFRACTIONx_scangle_it2.722.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.490.3567360.33111430.0421588121676.6
2.49-2.590.3841199.30.30311600.0351601127979.9
2.59-2.70.331037.90.29712090.0331622131280.8
2.7-2.850.29810980.26312550.0291600136485.2
2.85-3.020.27512990.22913090.0241623143888.5
3.02-3.260.2711419.50.20813390.0231623148091.1
3.26-3.580.2631379.10.20613700.0221627150792.6
3.58-4.10.2491298.50.19313970.0221626152693.8
4.1-5.170.2291308.40.16914210.021670155192.9
5.17-65.550.2491459.50.21413820.0211770152786.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4atp.paratp.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 60 Å / Num. reflection obs: 14000 / % reflection Rfree: 8 % / Rfactor obs: 0.217 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Lowest resolution: 2.47 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.331 / Num. reflection Rwork: 1011 / Rfactor obs: 0.33

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