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- PDB-4z7y: diphosphomevalonate decarboxylase from the Sulfolobus solfataricu... -

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Basic information

Entry
Database: PDB / ID: 4z7y
Titlediphosphomevalonate decarboxylase from the Sulfolobus solfataricus, space group P21
ComponentsDiphosphomevalonate decarboxylase
KeywordsLYASE / diphosphomevalonate decarboxylase / intersubunit disulfide bond / thermostability / Sulfolobus solfataricus
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
Diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHattori, A. / Unno, H. / Hemmi, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS23580111 Japan
JSPS23108531 Japan
JSPS25108712 Japan
CitationJournal: J.Bacteriol. / Year: 2015
Title: In Vivo Formation of the Protein Disulfide Bond That Enhances the Thermostability of Diphosphomevalonate Decarboxylase, an Intracellular Enzyme from the Hyperthermophilic Archaeon Sulfolobus solfataricus
Authors: Hattori, A. / Unno, H. / Goda, S. / Motoyama, K. / Yoshimura, T. / Hemmi, H.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / struct_ncs_dom_lim
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
Revision 1.4Oct 23, 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: Diphosphomevalonate decarboxylase
B: Diphosphomevalonate decarboxylase
C: Diphosphomevalonate decarboxylase
D: Diphosphomevalonate decarboxylase
E: Diphosphomevalonate decarboxylase
F: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,26612
Polymers221,6906
Non-polymers5766
Water1,45981
1
A: Diphosphomevalonate decarboxylase
B: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0894
Polymers73,8972
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Diphosphomevalonate decarboxylase
D: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0894
Polymers73,8972
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Diphosphomevalonate decarboxylase
F: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0894
Polymers73,8972
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.900, 154.390, 109.969
Angle α, β, γ (deg.)90.00, 114.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 2 - 324 / Label seq-ID: 1 - 323

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.163224, 0.861768, 0.480327), (0.845341, -0.373183, 0.382275), (0.508682, 0.343644, -0.7894)26.04253, -41.28671, 10.72718
3given(-0.99678, -0.076062, -0.025375), (-0.076629, 0.996813, 0.022167), (0.023609, 0.02404, -0.999432)116.73376, 6.86857, 47.54196
4given(-0.225232, 0.840648, -0.492525), (-0.828011, -0.431574, -0.357967), (-0.513486, 0.327191, 0.793271)75.01163, 72.69562, 31.74451
5given(-0.325864, -0.748648, -0.577356), (0.755119, -0.573559, 0.31753), (-0.568866, -0.332501, 0.75222)99.00989, -35.49671, 44.02275
6given(0.304272, -0.788955, 0.533825), (-0.779977, -0.528053, -0.33585), (0.546859, -0.314182, -0.776038)34.51093, 72.52302, 13.76795

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Components

#1: Protein
Diphosphomevalonate decarboxylase / DMD


Mass: 36948.352 Da / Num. of mol.: 6 / Fragment: UNP residues 2-325
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
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 81 / 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

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M sodium acetate, 1.5M ammonium sulfate / PH range: 4.6

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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: Jan 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 78276 / % possible obs: 96.6 % / Redundancy: 3.7 % / Net I/σ(I): 16.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HK2

2hk2


Resolution: 2.7→47.63 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.885 / SU B: 13.227 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.815 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27663 3879 5 %RANDOM
Rwork0.25424 ---
obs0.25535 74370 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.7→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15582 0 30 81 15693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915897
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.96621396
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84351938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39623.95714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.234153030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.27315108
X-RAY DIFFRACTIONr_chiral_restr0.1070.22376
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211676
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.9595.9517770
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.4278.9169702
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5826.2458127
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.68552.20840470
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2587 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A14.43
B13.29
C11.75
D9.6
E13.31
F12.94
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 262 -
Rwork0.315 5464 -
obs--98.78 %

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