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- PDB-8is6: Apo-CrtMLIKE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8is6
TitleApo-CrtMLIKE
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: 2 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: CrtMKLIKE Apo structure
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


Theoretical massNumber of molelcules
Total (without water)32,3681
Polymers32,3681
Non-polymers00
Water4,197233
1
A: CrtM

A: CrtM


Theoretical massNumber of molelcules
Total (without water)64,7362
Polymers64,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1970 Å2
ΔGint-15 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 64.897, 170.277
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: Feb 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19434 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.991 / Rrim(I) all: 0.134 / Net I/σ(I): 49.33
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 8.3 / Num. unique obs: 981 / CC1/2: 0.978 / Rrim(I) all: 0.481

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.57 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1897 10.01 %
Rwork0.1917 --
obs0.1971 18959 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 0 233 2421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072245
X-RAY DIFFRACTIONf_angle_d0.923049
X-RAY DIFFRACTIONf_dihedral_angle_d11.62302
X-RAY DIFFRACTIONf_chiral_restr0.053331
X-RAY DIFFRACTIONf_plane_restr0.006397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.27771320.18981174X-RAY DIFFRACTION93
2.05-2.10.24441310.20531186X-RAY DIFFRACTION97
2.1-2.160.31441270.19941188X-RAY DIFFRACTION95
2.16-2.230.29351280.21121X-RAY DIFFRACTION93
2.23-2.310.27531330.21461194X-RAY DIFFRACTION95
2.31-2.410.29731370.2031223X-RAY DIFFRACTION98
2.41-2.520.28741340.20131197X-RAY DIFFRACTION98
2.52-2.650.25811330.19351207X-RAY DIFFRACTION98
2.65-2.810.27671370.20851216X-RAY DIFFRACTION98
2.82-3.030.29751370.21261241X-RAY DIFFRACTION99
3.03-3.340.25321400.1911264X-RAY DIFFRACTION100
3.34-3.820.22771390.18011255X-RAY DIFFRACTION99
3.82-4.810.1981400.16461260X-RAY DIFFRACTION98
4.81-42.570.22461490.1971336X-RAY DIFFRACTION99

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