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- PDB-2hk3: Crystal structure of mevalonate diphosphate decarboxylase from St... -

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Basic information

Entry
Database: PDB / ID: 2hk3
TitleCrystal structure of mevalonate diphosphate decarboxylase from Staphylococcus aureus (orthorhombic form)
ComponentsDiphosphomevalonate decarboxylase
KeywordsLYASE / mevalonate diphosphate decarboxylase / diphosphomevalonate decarboxylase / decarboxylase
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / cytosol
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / GHMP kinase, C-terminal domain / GHMP kinase 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 / GHMP kinase, C-terminal domain / GHMP kinase 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsByres, E. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of Trypanosoma brucei and Staphylococcus aureus Mevalonate Diphosphate Decarboxylase Inform on the Determinants of Specificity and Reactivity
Authors: Byres, E. / Alphey, M.S. / Smith, T.K. / Hunter, W.N.
History
DepositionJul 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
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.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphosphomevalonate decarboxylase
B: Diphosphomevalonate decarboxylase


Theoretical massNumber of molelcules
Total (without water)74,7502
Polymers74,7502
Non-polymers00
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-18 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.021, 126.036, 135.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 1 - 327 / Label seq-ID: 5 - 331

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a dimer. There is one biological unit in the asymmetric unit (chains A & B)

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Components

#1: Protein Diphosphomevalonate decarboxylase / / Mevalonate diphosphate decarboxylase


Mass: 37375.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mvaD / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2FJ52, UniProt: Q9FD84*PLUS, diphosphomevalonate decarboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 1.8M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionRedundancy: 7.8 % / Av σ(I) over netI: 5 / Number: 323698 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / D res high: 2.3 Å / D res low: 136.083 Å / Num. obs: 41319 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.2741.7899.510.0860.0866.3
5.147.2710010.0860.0867.5
4.25.1410010.0840.0847.6
3.644.210010.0810.0817.8
3.253.6410010.090.097.9
2.973.2510010.1050.1057.9
2.752.9710010.1290.1298
2.572.7510010.1650.1658
2.422.5710010.2030.2038
2.32.4210010.2440.2448
ReflectionResolution: 2.3→41.77 Å / Num. all: 41319 / Num. obs: 41319 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.4280.24434743759490.244100
2.42-2.5780.2033.64464556000.203100
2.57-2.7580.1654.34225152920.165100
2.75-2.9780.1295.33961049680.129100
2.97-3.257.90.1056.13622145600.105100
3.25-3.647.90.096.63281541540.09100
3.64-4.27.80.0816.72874936960.081100
4.2-5.147.60.0846.32394531380.084100
5.14-7.277.50.0865.91872924980.086100
7.27-41.786.30.0864.8929614640.08699.5

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Phasing

Phasing MRRfactor: 0.41 / Cor.coef. Fo:Fc: 0.696
Highest resolutionLowest resolution
Rotation3 Å41.78 Å
Translation3 Å41.78 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HK2

2hk2


Resolution: 2.3→41.77 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.069 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2079 5 %RANDOM
Rwork0.198 ---
all0.201 41319 --
obs0.198 41319 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.094 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2--0.52 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 0 425 5675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225352
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9487232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31125.116258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.60515956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.1221524
X-RAY DIFFRACTIONr_chiral_restr0.1320.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024040
X-RAY DIFFRACTIONr_nbd_refined0.2360.22628
X-RAY DIFFRACTIONr_nbtor_refined0.30.23663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2464
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.234
X-RAY DIFFRACTIONr_mcbond_it0.9151.53391
X-RAY DIFFRACTIONr_mcangle_it1.51125284
X-RAY DIFFRACTIONr_scbond_it2.50532254
X-RAY DIFFRACTIONr_scangle_it3.9424.51948
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1308MEDIUM POSITIONAL0.090.5
1282LOOSE POSITIONAL0.35
1308MEDIUM THERMAL0.632
1282LOOSE THERMAL1.5110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 138 -
Rwork0.218 2834 -
obs-2972 100 %

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