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- PDB-6n0x: Crystal structure of Anaerolinea thermophila mevalonate 5-phospha... -

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Basic information

Entry
Database: PDB / ID: 6n0x
TitleCrystal structure of Anaerolinea thermophila mevalonate 5-phosphate decarboxylase complexed with (R)-MVAP
ComponentsDiphosphomevalonate decarboxylase
KeywordsLYASE
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / 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 kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PMV / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesAnaerolinea thermophila
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsNoel, J.P. / Thomas, S.T. / Louie, G.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)EEC-0813570 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase.
Authors: Thomas, S.T. / Louie, G.V. / Lubin, J.W. / Lundblad, V. / Noel, J.P.
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)215,83712
Polymers214,4686
Non-polymers1,3696
Water36,5522029
1
A: Diphosphomevalonate decarboxylase
E: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9464
Polymers71,4892
Non-polymers4562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-29 kcal/mol
Surface area23970 Å2
MethodPISA
2
B: Diphosphomevalonate decarboxylase
F: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9464
Polymers71,4892
Non-polymers4562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-28 kcal/mol
Surface area23900 Å2
MethodPISA
3
C: Diphosphomevalonate decarboxylase
D: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9464
Polymers71,4892
Non-polymers4562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-27 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.600, 135.630, 105.700
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Diphosphomevalonate decarboxylase


Mass: 35744.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerolinea thermophila (strain DSM 14523 / JCM 11388 / NBRC 100420 / UNI-1) (bacteria)
Strain: DSM 14523 / JCM 11388 / NBRC 100420 / UNI-1 / Gene: mvaD, ANT_19910 / Production host: Escherichia coli (E. coli)
References: UniProt: E8N6F3, diphosphomevalonate decarboxylase
#2: Chemical
ChemComp-PMV / (3R)-3-HYDROXY-3-METHYL-5-(PHOSPHONOOXY)PENTANOIC ACID / PHOSPHOMEVALONATE


Mass: 228.137 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2029 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M acetic acid pH 4.5 3-5% PEG 20,000 0.3 M ammonium acetate 5 mM (R)-MVAP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→37.57 Å / Num. obs: 361184 / % possible obs: 90.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.3
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.84 / Num. unique obs: 11325 / % possible all: 57.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
MOSFLM7.1.0data reduction
Aimless0.2.7data scaling
MOLREP11.2.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HK2

2hk2


Resolution: 1.44→37.566 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.54 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.1961 18015 5.02 %
Rwork0.1722 --
obs0.1734 359162 89.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.44→37.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14647 0 84 2029 16760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115052
X-RAY DIFFRACTIONf_angle_d1.17320500
X-RAY DIFFRACTIONf_dihedral_angle_d17.3845429
X-RAY DIFFRACTIONf_chiral_restr0.0782367
X-RAY DIFFRACTIONf_plane_restr0.012622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.45640.38863450.40087100X-RAY DIFFRACTION56
1.4564-1.47350.38043750.38827356X-RAY DIFFRACTION58
1.4735-1.49150.39224250.36967673X-RAY DIFFRACTION61
1.4915-1.51030.38084080.3568135X-RAY DIFFRACTION64
1.5103-1.53020.34314600.33678643X-RAY DIFFRACTION68
1.5302-1.55120.32124830.3169310X-RAY DIFFRACTION74
1.5512-1.57330.32755030.30219269X-RAY DIFFRACTION74
1.5733-1.59680.31354890.28239324X-RAY DIFFRACTION74
1.5968-1.62180.29045480.262810682X-RAY DIFFRACTION84
1.6218-1.64840.25726180.247412195X-RAY DIFFRACTION97
1.6484-1.67680.25546450.239112227X-RAY DIFFRACTION97
1.6768-1.70730.25096950.234612194X-RAY DIFFRACTION97
1.7073-1.74010.25666570.225812415X-RAY DIFFRACTION98
1.7401-1.77560.23666550.210912478X-RAY DIFFRACTION99
1.7756-1.81430.2456510.199412521X-RAY DIFFRACTION99
1.8143-1.85650.21576760.187612535X-RAY DIFFRACTION99
1.8565-1.90290.21926970.184212491X-RAY DIFFRACTION99
1.9029-1.95430.19746800.178612562X-RAY DIFFRACTION99
1.9543-2.01180.19726860.170312538X-RAY DIFFRACTION100
2.0118-2.07680.19346560.161712662X-RAY DIFFRACTION100
2.0768-2.1510.1716440.159712696X-RAY DIFFRACTION100
2.151-2.23710.18426940.155212540X-RAY DIFFRACTION100
2.2371-2.33890.1866570.149312667X-RAY DIFFRACTION100
2.3389-2.46220.18296780.150312658X-RAY DIFFRACTION100
2.4622-2.61640.19236310.152812662X-RAY DIFFRACTION100
2.6164-2.81840.17446800.149312694X-RAY DIFFRACTION100
2.8184-3.10190.17156780.156212647X-RAY DIFFRACTION100
3.1019-3.55040.17546630.154612720X-RAY DIFFRACTION100
3.5504-4.4720.1616670.135812757X-RAY DIFFRACTION100
4.472-37.5790.17476710.160812796X-RAY DIFFRACTION99

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