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- PDB-4quv: Structure of an integral membrane delta(14)-sterol reductase -

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Basic information

Entry
Database: PDB / ID: 4quv
TitleStructure of an integral membrane delta(14)-sterol reductase
ComponentsDelta(14)-sterol reductase
KeywordsOxidoreductase / Membrane protein / Cholesterol Biosynthesis
Function / homology
Function and homology information


Delta14-sterol reductase / Delta14-sterol reductase activity / ergosterol biosynthetic process / sterol biosynthetic process / NADP binding / plasma membrane
Similarity search - Function
Sterol biosynthesis ERG24/DHCR-like / Sterol reductase, conserved site / Ergosterol biosynthesis ERG4/ERG24 family / Sterol reductase family signature 1. / Sterol reductase family signature 2.
Similarity search - Domain/homology
Chem-NDP / Delta(14)-sterol reductase
Similarity search - Component
Biological speciesMethylomicrobium alcaliphilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.743 Å
AuthorsLi, X. / Blobel, G.
CitationJournal: Nature / Year: 2015
Title: Structure of an integral membrane sterol reductase from Methylomicrobium alcaliphilum.
Authors: Li, X. / Roberti, R. / Blobel, G.
History
DepositionJul 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Delta(14)-sterol reductase
B: Delta(14)-sterol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4244
Polymers98,9332
Non-polymers1,4912
Water00
1
A: Delta(14)-sterol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2122
Polymers49,4671
Non-polymers7451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Delta(14)-sterol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2122
Polymers49,4671
Non-polymers7451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area36960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.660, 74.615, 79.549
Angle α, β, γ (deg.)66.00, 90.37, 86.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Delta(14)-sterol reductase


Mass: 49466.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylomicrobium alcaliphilum (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z / Gene: erg, MEALZ_1312 / Production host: Escherichia coli (E. coli) / References: UniProt: G4SW86, Delta14-sterol reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3

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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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris, 0.2 M NH4Ac, 30% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH), pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.74→37.25 Å / Num. all: 63092 / Num. obs: 30541 / % possible obs: 74.8 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.041 / Rsym value: 0.058 / Net I/σ(I): 21.1
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.514 / % possible all: 28.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.743→37.255 Å / SU ML: 0.43 / σ(F): 1.96 / Phase error: 37.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2837 1526 5 %RANDOM
Rwork0.2329 ---
obs0.2355 30541 74.54 %-
all-63092 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.743→37.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 62 0 6490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136736
X-RAY DIFFRACTIONf_angle_d1.6469216
X-RAY DIFFRACTIONf_dihedral_angle_d16.6522297
X-RAY DIFFRACTIONf_chiral_restr0.084975
X-RAY DIFFRACTIONf_plane_restr0.0091104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7434-2.83190.3653530.2509976X-RAY DIFFRACTION28
2.8319-2.93310.3213680.2991327X-RAY DIFFRACTION37
2.9331-3.05050.36291020.29881710X-RAY DIFFRACTION49
3.0505-3.18920.34741070.31492132X-RAY DIFFRACTION60
3.1892-3.35730.32761250.29452568X-RAY DIFFRACTION73
3.3573-3.56750.30981540.26343145X-RAY DIFFRACTION89
3.5675-3.84260.3011760.23973429X-RAY DIFFRACTION97
3.8426-4.22890.28771650.21143474X-RAY DIFFRACTION98
4.2289-4.83970.25381840.18893429X-RAY DIFFRACTION97
4.8397-6.09310.2582100.22353485X-RAY DIFFRACTION98
6.0931-37.25880.27511820.23223340X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.05780.21420.11931.16210.25093.05820.1819-0.7167-1.30860.31810.15590.13820.2445-0.4679-0.34910.43990.0621-0.10060.76690.41880.813-34.995-6.26213.7212
22.9161-0.05740.18892.6286-0.26932.57690.30911.4954-0.3261-0.1914-0.18180.2339-0.08460.1055-0.05220.34880.1652-0.11490.78870.04770.3986-13.31066.4695-13.6064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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