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- PDB-8isa: CrtMLIKE with one GsPP molecule -

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Basic information

Entry
Database: PDB / ID: 8isa
TitleCrtMLIKE with one GsPP 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
GERANYL S-THIOLODIPHOSPHATE / CrtM
Similarity search - Component
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 GsPP 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

Downloads & links

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Assembly

Deposited unit
A: CrtM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6982
Polymers32,3681
Non-polymers3301
Water7,512417
1
A: CrtM
hetero molecules

A: CrtM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3974
Polymers64,7362
Non-polymers6612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3930 Å2
ΔGint-13 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.410, 59.940, 168.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-473-

HOH

21A-742-

HOH

31A-815-

HOH

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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.: 1 / Source method: obtained synthetically / Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
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→29.97 Å / Num. obs: 34754 / % possible obs: 99.13 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.49
Reflection shellResolution: 1.5901→1.8563 Å / Rmerge(I) obs: 0.237 / Num. unique obs: 12766

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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→29.97 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 1724 5 %
Rwork0.1752 --
obs0.1764 34460 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 19 417 2606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072241
X-RAY DIFFRACTIONf_angle_d0.9863044
X-RAY DIFFRACTIONf_dihedral_angle_d11.657310
X-RAY DIFFRACTIONf_chiral_restr0.053330
X-RAY DIFFRACTIONf_plane_restr0.006394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.640.22671440.18642727X-RAY DIFFRACTION100
1.64-1.690.22411420.17942701X-RAY DIFFRACTION100
1.69-1.750.2011410.18362676X-RAY DIFFRACTION99
1.75-1.820.2391400.17962662X-RAY DIFFRACTION98
1.82-1.90.20661430.17532710X-RAY DIFFRACTION100
1.9-20.19491430.17732722X-RAY DIFFRACTION100
2-2.130.22791430.17022709X-RAY DIFFRACTION99
2.13-2.290.19371440.16262733X-RAY DIFFRACTION99
2.29-2.520.20221430.17162725X-RAY DIFFRACTION100
2.52-2.890.20651430.17582713X-RAY DIFFRACTION98
2.89-3.640.19921470.1732788X-RAY DIFFRACTION100
3.64-29.970.17181510.17972870X-RAY DIFFRACTION98

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