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- PDB-8is8: CrtMLIKE with two GsPP molecules -

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Basic information

Entry
Database: PDB / ID: 8is8
TitleCrtMLIKE with two GsPP molecules
ComponentsCrtM
KeywordsSTRUCTURAL PROTEIN / dehydrogenase
Function / homology
Function and homology information


carotenoid biosynthetic process / : / farnesyltranstransferase activity
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
GERANYL S-THIOLODIPHOSPHATE / CrtM
Similarity search - Component
Biological speciesHalobacillus halophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 GsPP 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

Downloads & links

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Assembly

Deposited unit
A: CrtM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1026
Polymers32,3681
Non-polymers7335
Water2,342130
1
A: CrtM
hetero molecules

A: CrtM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,20312
Polymers64,7362
Non-polymers1,46710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6080 Å2
ΔGint-78 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.297, 64.793, 170.702
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-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O6P2S / 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.: 130 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
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: 2.3→50 Å / Num. obs: 23872 / % possible obs: 97.94 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 43.76
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.283 / Num. unique obs: 1199

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.68 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1252 9.97 %
Rwork0.1947 --
obs0.1995 12555 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 41 130 2347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012265
X-RAY DIFFRACTIONf_angle_d1.093082
X-RAY DIFFRACTIONf_dihedral_angle_d6.865319
X-RAY DIFFRACTIONf_chiral_restr0.05334
X-RAY DIFFRACTIONf_plane_restr0.006401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.30521350.20331207X-RAY DIFFRACTION96
2.39-2.50.28121330.21571215X-RAY DIFFRACTION97
2.5-2.630.28881370.19971231X-RAY DIFFRACTION98
2.63-2.80.29651380.2031245X-RAY DIFFRACTION98
2.8-3.010.25071370.22481238X-RAY DIFFRACTION98
3.01-3.310.2661420.19661272X-RAY DIFFRACTION99
3.31-3.790.23581380.19041269X-RAY DIFFRACTION98
3.79-4.780.19831410.16311271X-RAY DIFFRACTION98
4.78-42.680.21961510.20461355X-RAY DIFFRACTION98

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