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- PDB-7xnd: Crystal structure of Phosphomevalonate kinase from Silkworm -

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Basic information

Entry
Database: PDB / ID: 7xnd
TitleCrystal structure of Phosphomevalonate kinase from Silkworm
ComponentsPhosphomevalonate kinase
KeywordsBIOSYNTHETIC PROTEIN / kinase / hormone synthesis
Function / homology
Function and homology information


phosphomevalonate kinase activity / phosphomevalonate kinase / isopentenyl diphosphate biosynthetic process, mevalonate pathway / cholesterol biosynthetic process / ATP binding / cytosol
Similarity search - Function
Higher eukaryotic phosphomevalonate kinase / Phosphomevalonate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phosphomevalonate kinase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGuo, P.C. / Zhang, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970468 China
National Natural Science Foundation of China (NSFC)32030103 China
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2022
Title: Structural insights into the substrate binding of phosphomevalonate kinase from the silkworm, Bombyx mori.
Authors: Zhang, H. / Liu, J. / Wang, H. / Fang, H. / Zhao, P. / Xia, Q. / Guo, P.
History
DepositionApr 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Phosphomevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3632
Polymers24,2701
Non-polymers921
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-1 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.070, 54.070, 123.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phosphomevalonate kinase


Mass: 24270.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: MPK_Bm / Production host: Escherichia coli (E. coli) / References: UniProt: A5A7A1, phosphomevalonate kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.8 M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→32.48 Å / Num. obs: 24974 / % possible obs: 99.9 % / Redundancy: 23.2 % / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.068 / Net I/σ(I): 27.1
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 15.6 % / Rmerge(I) obs: 1.236 / Num. unique obs: 1817 / Rpim(I) all: 0.32 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CH4

3ch4


Resolution: 1.6→32.48 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2468 1264 5.076 %
Rwork0.2097 23638 -
all0.212 --
obs-24902 99.872 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 6 64 1459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131418
X-RAY DIFFRACTIONr_bond_other_d0.0340.0181363
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.6421903
X-RAY DIFFRACTIONr_angle_other_deg2.2591.6023142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.96421.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83715275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8511513
X-RAY DIFFRACTIONr_chiral_restr0.090.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021565
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02333
X-RAY DIFFRACTIONr_nbd_refined0.2160.2258
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.21231
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2695
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.253
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.211
X-RAY DIFFRACTIONr_nbd_other0.2980.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.25
X-RAY DIFFRACTIONr_mcbond_it2.9653.067674
X-RAY DIFFRACTIONr_mcbond_other2.9643.065673
X-RAY DIFFRACTIONr_mcangle_it3.8364.576839
X-RAY DIFFRACTIONr_mcangle_other3.8344.579840
X-RAY DIFFRACTIONr_scbond_it4.7983.676744
X-RAY DIFFRACTIONr_scbond_other4.7953.676745
X-RAY DIFFRACTIONr_scangle_it7.2215.2951064
X-RAY DIFFRACTIONr_scangle_other7.2185.2951065
X-RAY DIFFRACTIONr_lrange_it8.23936.1451594
X-RAY DIFFRACTIONr_lrange_other8.24136.1131588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.299980.2811715X-RAY DIFFRACTION99.8898
1.642-1.6870.267940.2711649X-RAY DIFFRACTION99.9427
1.687-1.7350.285890.2671601X-RAY DIFFRACTION99.8818
1.735-1.7890.311960.2621568X-RAY DIFFRACTION99.88
1.789-1.8470.296750.2341537X-RAY DIFFRACTION99.938
1.847-1.9120.255800.2261488X-RAY DIFFRACTION99.6821
1.912-1.9840.228680.211449X-RAY DIFFRACTION100
1.984-2.0650.247910.2041370X-RAY DIFFRACTION100
2.065-2.1570.258790.2071330X-RAY DIFFRACTION99.7875
2.157-2.2620.209530.2071283X-RAY DIFFRACTION100
2.262-2.3840.249580.2041220X-RAY DIFFRACTION99.9218
2.384-2.5280.176590.2021162X-RAY DIFFRACTION99.9182
2.528-2.7020.266640.2081096X-RAY DIFFRACTION99.9139
2.702-2.9180.267460.2051025X-RAY DIFFRACTION100
2.918-3.1950.249530.213965X-RAY DIFFRACTION100
3.195-3.5710.226340.192874X-RAY DIFFRACTION100
3.571-4.1190.202470.199767X-RAY DIFFRACTION100
4.119-5.0360.238340.178673X-RAY DIFFRACTION100
5.036-7.0860.281260.238540X-RAY DIFFRACTION100
7.086-32.480.362200.233326X-RAY DIFFRACTION96.3788

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