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- PDB-5gme: Crystal structure of Sulfolobus solfataricus Diphosphomevalonate ... -

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Basic information

Entry
Database: PDB / ID: 5gme
TitleCrystal structure of Sulfolobus solfataricus Diphosphomevalonate decarboxylase in complex with ADP
ComponentsDiphosphomevalonate decarboxylase
KeywordsLYASE / Sulfolobus solfataricus / Diphosphomevalonate decarboxylase / ADP
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / ATP binding / cytosol
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-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'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Chem-DP6 / Diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsUnno, H. / Hemmi, H. / Hattori, A.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A Single Amino Acid Mutation Converts (R)-5-Diphosphomevalonate Decarboxylase into a Kinase
Authors: Motoyama, K. / Unno, H. / Hattori, A. / Takaoka, T. / Ishikita, H. / Kawaide, H. / Yoshimura, T. / Hemmi, H.
History
DepositionJul 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 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: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3546
Polymers37,0801
Non-polymers1,2755
Water4,630257
1
A: Diphosphomevalonate decarboxylase
hetero molecules

A: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,70812
Polymers74,1592
Non-polymers2,54910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6630 Å2
ΔGint-92 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.289, 151.289, 104.422
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1004-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Diphosphomevalonate decarboxylase / DMD


Mass: 37079.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO2989 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97UL5, diphosphomevalonate decarboxylase

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-DP6 / (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID


Mass: 308.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O10P2
#3: 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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6 / Details: 0.1M sodium acetate, 1.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→27.8 Å / Num. obs: 50337 / % possible obs: 99.8 % / Redundancy: 15.2 % / Net I/σ(I): 23

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4Z7C

4z7c


Resolution: 1.7→27.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.607 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20204 2551 5.1 %RANDOM
Rwork0.16893 ---
obs0.1706 47643 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.579 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 78 257 2932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192724
X-RAY DIFFRACTIONr_bond_other_d0.0030.022604
X-RAY DIFFRACTIONr_angle_refined_deg2.5931.9983680
X-RAY DIFFRACTIONr_angle_other_deg1.25636009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42523.95119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9115505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1721518
X-RAY DIFFRACTIONr_chiral_restr0.1850.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02605
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9532.4331295
X-RAY DIFFRACTIONr_mcbond_other2.9332.431294
X-RAY DIFFRACTIONr_mcangle_it3.8213.6371617
X-RAY DIFFRACTIONr_mcangle_other3.8253.641618
X-RAY DIFFRACTIONr_scbond_it4.4223.031427
X-RAY DIFFRACTIONr_scbond_other4.4173.0311420
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6214.3322052
X-RAY DIFFRACTIONr_long_range_B_refined8.6321.1363348
X-RAY DIFFRACTIONr_long_range_B_other8.59520.6393224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 190 -
Rwork0.209 3503 -
obs--100 %

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