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- PDB-6vpr: Crystal structure of the C-terminal domain of DENR -

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Basic information

Entry
Database: PDB / ID: 6vpr
TitleCrystal structure of the C-terminal domain of DENR
ComponentsDensity-regulated protein
KeywordsTRANSLATION / protein synthesis regulation / translation initiation / translation reinitiation / translation recycling / density regulated protein (DENR)
Function / homology
Function and homology information


translation reinitiation / IRES-dependent viral translational initiation / formation of translation preinitiation complex / ribosome disassembly / translation initiation factor activity / mRNA binding
Similarity search - Function
DENR family, eukaryotes / DENR, C-terminal domain / : / DENR, N-terminal / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain
Similarity search - Domain/homology
ACETATE ION / : / PHOSPHATE ION / L(+)-TARTARIC ACID / Density-regulated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLomakin, I.B. / Steitz, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2020
Title: Crystal structure of the C-terminal domain of DENR.
Authors: Lomakin, I.B. / De, S. / Wang, J. / Borkar, A.N. / Steitz, T.A.
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Density-regulated protein
B: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,21117
Polymers44,2482
Non-polymers1,96315
Water25214
1
A: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0778
Polymers22,1241
Non-polymers9537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Density-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1359
Polymers22,1241
Non-polymers1,0108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.600, 116.600, 75.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Density-regulated protein / DRP / Protein DRP1 / Smooth muscle cell-associated protein 3 / SMAP-3


Mass: 22124.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DENR, DRP1, H14 / Production host: Escherichia coli (E. coli) / References: UniProt: O43583

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Non-polymers , 6 types, 29 molecules

#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M K/Na tartrate, 2.5 M Ammonium Sulfate, 0.1 M tri-Sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.2→100.98 Å / Num. obs: 28988 / % possible obs: 100 % / Redundancy: 20.59 % / Biso Wilson estimate: 75.392 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.173 / Χ2: 1.802 / Net I/σ(I): 11.71 / Num. measured all: 596862 / Scaling rejects: 48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
2.2-2.2619.89712.070.14424012129213112.383100
2.26-2.3220.6410.5140.21434682106210610.7761000.165
2.32-2.3919.4058.1710.3139392203220308.39199.90.196
2.39-2.4621.3976.3570.4942002196319636.511000.326
2.46-2.5421.6334.4230.841600192419234.52899.90.468
2.54-2.6321.413.291.1339266183518343.36999.90.675
2.63-2.7321.1652.3691.5638097180018002.4261000.771
2.73-2.8420.241.3162.8334833172117211.3491000.982
2.84-2.9719.7070.9193.9832418164516450.9431000.95
2.97-3.1121.7070.6126.3934210157615760.6271000.972
3.11-3.2821.4320.37810.0132083149714970.3871000.991
3.28-3.4820.9390.26713.1929545141114110.2731000.994
3.48-3.7219.4720.1619.8825975133413340.1651000.999
3.72-4.0219.6850.11226.0624468124312430.1151000.999
4.02-4.420.8250.08436.5123616113411340.0861000.999
4.4-4.9220.3250.07141.8320894102810280.0731000.999
4.92-5.6918.7640.06941.25171699159150.0711000.999
5.69-6.9621.3080.06149.45164077707700.0631000.998
6.96-9.8520.7660.04458.65123565955950.0451001
9.85-100.9820.0660.0365.1866623333320.0399.71

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→100.98 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 37.46
RfactorNum. reflection% reflection
Rfree0.2877 1501 5.18 %
Rwork0.2237 --
obs0.227 28956 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.15 Å2 / Biso mean: 76.9999 Å2 / Biso min: 40.3 Å2
Refinement stepCycle: final / Resolution: 2.2→100.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 76 15 1442
Biso mean--103.14 69.08 -
Num. residues----171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.270.46311420.435224912633
2.27-2.350.47621460.397924942640
2.35-2.450.41331150.373425022617
2.45-2.560.40531380.351824872625
2.56-2.690.42161430.338724842627
2.7-2.860.30941480.285824712619
2.86-3.080.32961360.270125122648
3.09-3.40.30511380.241224902628
3.4-3.890.27541240.215325182642
3.89-4.90.25911330.183425012634
4.9-100.980.24071380.179825052643

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