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- PDB-6n0z: Crystal structure of Anaerolinea thermophila mevalonate 5-phospha... -

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Basic information

Entry
Database: PDB / ID: 6n0z
TitleCrystal structure of Anaerolinea thermophila mevalonate 5-phosphate decarboxylase N20K H194M mutant complexed with (R)-MVAPP
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-DP6 / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesAnaerolinea thermophila
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)216,36512
Polymers214,5176
Non-polymers1,8496
Water31,5981754
1
A: Diphosphomevalonate decarboxylase
E: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1224
Polymers71,5062
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-33 kcal/mol
Surface area24840 Å2
MethodPISA
2
B: Diphosphomevalonate decarboxylase
F: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1224
Polymers71,5062
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-31 kcal/mol
Surface area25510 Å2
MethodPISA
3
C: Diphosphomevalonate decarboxylase
D: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1224
Polymers71,5062
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-34 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.800, 138.090, 105.130
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Diphosphomevalonate decarboxylase


Mass: 35752.770 Da / Num. of mol.: 6 / Mutation: D20K, H194M
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-DP6 / (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID


Mass: 308.117 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1754 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
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)-MVAPP

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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: Aug 26, 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: 1.95→46.03 Å / Num. obs: 131416 / % possible obs: 79 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2 % / Rmerge(I) obs: 0.624 / Num. unique obs: 10659 / % possible all: 65.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
MOSFLM7.1.1data reduction
Aimless0.3.11data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HK2

2hk2


Resolution: 1.95→45.567 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5
RfactorNum. reflection% reflection
Rfree0.2023 6583 5.01 %
Rwork0.1674 --
obs0.1691 131340 78.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→45.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14847 0 108 1754 16709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715287
X-RAY DIFFRACTIONf_angle_d0.86520824
X-RAY DIFFRACTIONf_dihedral_angle_d17.8755576
X-RAY DIFFRACTIONf_chiral_restr0.0522390
X-RAY DIFFRACTIONf_plane_restr0.0072665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.32071680.2613457X-RAY DIFFRACTION65
1.9722-1.99540.30642060.24743430X-RAY DIFFRACTION65
1.9954-2.01970.26931810.24473429X-RAY DIFFRACTION65
2.0197-2.04530.30941940.22823358X-RAY DIFFRACTION65
2.0453-2.07220.26611700.21413422X-RAY DIFFRACTION65
2.0722-2.10060.25121820.21323380X-RAY DIFFRACTION65
2.1006-2.13060.28291750.19923373X-RAY DIFFRACTION64
2.1306-2.16240.23091670.19943379X-RAY DIFFRACTION64
2.1624-2.19620.25241880.1963388X-RAY DIFFRACTION65
2.1962-2.23220.22841910.18213302X-RAY DIFFRACTION63
2.2322-2.27070.21921700.193330X-RAY DIFFRACTION64
2.2707-2.3120.24251810.18743350X-RAY DIFFRACTION63
2.312-2.35640.21791650.18593416X-RAY DIFFRACTION65
2.3564-2.40450.22892370.19034020X-RAY DIFFRACTION77
2.4045-2.45680.22861870.18744059X-RAY DIFFRACTION76
2.4568-2.51390.2392050.18584036X-RAY DIFFRACTION76
2.5139-2.57680.22742160.18773957X-RAY DIFFRACTION76
2.5768-2.64650.23341890.17693970X-RAY DIFFRACTION75
2.6465-2.72430.2172400.17373904X-RAY DIFFRACTION75
2.7243-2.81230.21371950.17044104X-RAY DIFFRACTION77
2.8123-2.91280.19372640.18055057X-RAY DIFFRACTION96
2.9128-3.02940.21972690.17645253X-RAY DIFFRACTION100
3.0294-3.16720.20573090.1665245X-RAY DIFFRACTION100
3.1672-3.33410.20052870.16655283X-RAY DIFFRACTION100
3.3341-3.5430.16492540.16055308X-RAY DIFFRACTION100
3.543-3.81640.18222830.14985264X-RAY DIFFRACTION100
3.8164-4.20020.17692770.13285301X-RAY DIFFRACTION100
4.2002-4.80740.1532580.12025334X-RAY DIFFRACTION100
4.8074-6.05460.17552900.15125277X-RAY DIFFRACTION100
6.0546-45.57970.15232850.14865371X-RAY DIFFRACTION100

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