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- PDB-8is7: CrtMLIKE with two FsPP molecules. -

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Basic information

Entry
Database: PDB / ID: 8is7
TitleCrtMLIKE with two FsPP molecules.
ComponentsCrtM
KeywordsSTRUCTURAL PROTEIN / dehydrogenase
Function / homology
Function and homology information


carotenoid biosynthetic process / squalene synthase [NAD(P)H] activity / geranylgeranyl diphosphate synthase activity / metal ion binding
Similarity search - Function
Trans-isoprenyl diphosphate synthases, bacterial-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Biological speciesHalobacillus halophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPark, J.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2C300888911 Korea, Republic Of
CitationJournal: To Be Published
Title: CrtMLIKE with two FsPP molecules.
Authors: Park, J.Y.
History
DepositionMar 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CrtM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2386
Polymers32,3681
Non-polymers8705
Water9,314517
1
A: CrtM
hetero molecules

A: CrtM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,47612
Polymers64,7362
Non-polymers1,73910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6730 Å2
ΔGint-78 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.338, 64.469, 171.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CrtM


Mass: 32368.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacillus halophilus (bacteria) / Gene: crtM / Production host: Escherichia coli (E. coli) / References: UniProt: B9UXM0
#2: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris, 30% PEG 4000, 0.2M MgCl2, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 36445 / % possible obs: 94.07 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 30.75
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.303 / Num. unique obs: 1773

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→32.23 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1914 5.47 %
Rwork0.1756 --
obs0.1772 34979 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 43 517 2772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072303
X-RAY DIFFRACTIONf_angle_d1.0353120
X-RAY DIFFRACTIONf_dihedral_angle_d5.265328
X-RAY DIFFRACTIONf_chiral_restr0.051333
X-RAY DIFFRACTIONf_plane_restr0.006406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.2191170.18782102X-RAY DIFFRACTION83
1.64-1.690.2691290.1842142X-RAY DIFFRACTION88
1.69-1.730.24131250.18082215X-RAY DIFFRACTION90
1.73-1.790.22621360.18342285X-RAY DIFFRACTION91
1.79-1.850.22411320.18642298X-RAY DIFFRACTION93
1.85-1.930.26431330.19172310X-RAY DIFFRACTION94
1.93-2.020.2221370.18872348X-RAY DIFFRACTION95
2.02-2.120.22311330.17822374X-RAY DIFFRACTION95
2.12-2.260.19571430.17082431X-RAY DIFFRACTION97
2.26-2.430.20071380.1752432X-RAY DIFFRACTION97
2.43-2.670.1991440.17462453X-RAY DIFFRACTION98
2.67-3.060.20391450.18412492X-RAY DIFFRACTION98
3.06-3.860.1851470.15792533X-RAY DIFFRACTION99
3.86-32.230.18921550.17372650X-RAY DIFFRACTION99

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