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- PDB-8is9: CrtMLIKE with one FsPP molecule -

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Basic information

Entry
Database: PDB / ID: 8is9
TitleCrtMLIKE with one FsPP molecule
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: 1.59 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 one FsPP molecule
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)32,8395
Polymers32,3681
Non-polymers4714
Water6,395355
1
A: CrtM
hetero molecules

A: CrtM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,67910
Polymers64,7362
Non-polymers9438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5430 Å2
ΔGint-84 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.590, 65.130, 170.940
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.: 1 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
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: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.59→29.19 Å / Num. obs: 38424 / % possible obs: 99.26 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.2
Reflection shellResolution: 1.59→1.9461 Å / Rmerge(I) obs: 1.542 / Num. unique obs: 17258

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→29.19 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 1908 5 %
Rwork0.2005 --
obs0.2017 38147 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 27 355 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082274
X-RAY DIFFRACTIONf_angle_d1.0793086
X-RAY DIFFRACTIONf_dihedral_angle_d6.096317
X-RAY DIFFRACTIONf_chiral_restr0.054333
X-RAY DIFFRACTIONf_plane_restr0.006400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.40381330.38222544X-RAY DIFFRACTION99
1.63-1.670.35371340.32032544X-RAY DIFFRACTION100
1.67-1.720.31231380.27752599X-RAY DIFFRACTION100
1.72-1.780.28261330.24922523X-RAY DIFFRACTION99
1.78-1.840.28621350.23312574X-RAY DIFFRACTION99
1.84-1.920.30391350.25522563X-RAY DIFFRACTION99
1.92-20.2621340.25112541X-RAY DIFFRACTION99
2-2.110.24351380.19942624X-RAY DIFFRACTION100
2.11-2.240.22521320.18972515X-RAY DIFFRACTION98
2.24-2.410.22751370.21922603X-RAY DIFFRACTION99
2.41-2.660.21581360.1972590X-RAY DIFFRACTION100
2.66-3.040.22781390.1992623X-RAY DIFFRACTION100
3.04-3.830.18591390.17932655X-RAY DIFFRACTION100
3.83-29.190.19931450.1692741X-RAY DIFFRACTION99

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