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- PDB-6pfp: Crystal Structure of Amino Acids 1473-1536 of Human Beta Cardiac ... -

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Basic information

Entry
Database: PDB / ID: 6pfp
TitleCrystal Structure of Amino Acids 1473-1536 of Human Beta Cardiac Myosin Fused to Gp7 and Eb1
ComponentsMyosin-7 fused to GP7 and EB1
KeywordsMOTOR PROTEIN / Myosin Rod / Myosin / Coiled-Coil / Gp7 / Eb1
Function / homology
Function and homology information


viral scaffold / virion assembly / DNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / EB1-like C-terminal motif / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Capsid assembly scaffolding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsAndreas, M.P. / Korkmaz, E.N. / Kirsch, C.J. / Hargreaves, M.D. / Kieffer, D.J. / Ajay, G. / Cui, Q. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R21 HL111237 United States
CitationJournal: To Be Published
Title: A Complete Model of the Cardiac Myosin Rod
Authors: Andreas, M.P. / Korkmaz, E.N. / Kirsch, C.J. / Hargreaves, M. / Kieffer, D.J. / Ajay, G. / Cui, Q. / Rayment, I.
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-7 fused to GP7 and EB1
B: Myosin-7 fused to GP7 and EB1
C: Myosin-7 fused to GP7 and EB1
D: Myosin-7 fused to GP7 and EB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,82213
Polymers76,7814
Non-polymers1,0419
Water5,603311
1
A: Myosin-7 fused to GP7 and EB1
B: Myosin-7 fused to GP7 and EB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0778
Polymers38,3902
Non-polymers6876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-112 kcal/mol
Surface area20600 Å2
MethodPISA
2
C: Myosin-7 fused to GP7 and EB1
D: Myosin-7 fused to GP7 and EB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7455
Polymers38,3902
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-111 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.107, 59.304, 86.548
Angle α, β, γ (deg.)81.790, 86.420, 89.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Myosin-7 fused to GP7 and EB1


Mass: 19195.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH7, MYHCB / Production host: Escherichia coli (E. coli) / References: UniProt: P13848*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystals grew from 1:1 mixture of 18 mg/ml protein solution with 37% (w/v) 2-methyl-2,4-pentanediol (MPD), 80 mM magnesium sulfate, 100 mM sodium acetate. Protein solution contained 10 mM 4- ...Details: Crystals grew from 1:1 mixture of 18 mg/ml protein solution with 37% (w/v) 2-methyl-2,4-pentanediol (MPD), 80 mM magnesium sulfate, 100 mM sodium acetate. Protein solution contained 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) pH 7.6, and 0.2 mM tris(2-carboxyethyl)phosphine (TCEP).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 35454 / % possible obs: 95.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.05 / Rrim(I) all: 0.106 / Χ2: 0.857 / Net I/σ(I): 7.1 / Num. measured all: 128524
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.242.70.30614990.940.1720.3530.74383.8
2.24-2.282.80.2816430.9310.1580.3230.83186.4
2.28-2.322.80.2516930.9410.1420.2890.80989.6
2.32-2.372.90.24416370.9410.1370.2810.78890.4
2.37-2.422.90.22216900.9520.1320.260.87790.7
2.42-2.483.40.23218490.9610.1280.2660.82297.3
2.48-2.543.60.21117590.9680.1150.2410.84397.9
2.54-2.613.70.18418450.9780.0990.210.81998.6
2.61-2.693.90.19118510.9690.1030.2180.8698.6
2.69-2.773.90.16617930.9720.0890.190.85198.8
2.77-2.873.90.13418550.9820.0720.1530.89497.5
2.87-2.993.70.11217900.9860.0610.1280.95695.9
2.99-3.124.10.10718310.9850.0560.1210.92199.2
3.12-3.294.10.09918300.9850.0530.1130.92699.3
3.29-3.4940.09218460.9780.050.1050.96898.3
3.49-3.763.90.07617850.9850.0420.0870.98496.7
3.76-4.143.90.06718530.9890.0370.0770.91997.8
4.14-4.7440.06418070.9920.0330.0730.84399
4.74-5.973.90.06817910.9940.0340.0760.7395.6
5.97-5040.06218070.9880.0380.0730.64297.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INOH

Resolution: 2.2→37.177 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.01
RfactorNum. reflection% reflection
Rfree0.2454 1660 5.01 %
Rwork0.1936 --
obs0.1962 33162 89.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.99 Å2 / Biso mean: 41.3123 Å2 / Biso min: 7.82 Å2
Refinement stepCycle: final / Resolution: 2.2→37.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5133 0 69 311 5513
Biso mean--44.77 40.08 -
Num. residues----624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.26480.3309990.21381890198964
2.2648-2.33790.2431150.21712056217170
2.3379-2.42150.25291170.21552246236377
2.4215-2.51840.30221290.21692551268088
2.5184-2.6330.28471550.2192802295795
2.633-2.77180.31741400.2192833297398
2.7718-2.94530.24281490.19952837298696
2.9453-3.17260.28911520.20472924307699
3.1726-3.49170.23121570.19342887304499
3.4917-3.99650.22621510.16732810296197
3.9965-5.03310.2091510.16032901305299
5.0331-37.18210.22331450.20842765291094

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