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- PDB-4edq: MBP-fusion protein of myosin-binding protein c residues 149-269 -

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Basic information

Entry
Database: PDB / ID: 4edq
TitleMBP-fusion protein of myosin-binding protein c residues 149-269
ComponentsMaltose-binding periplasmic protein,Myosin-binding protein C, cardiac-type chimeric protein
KeywordsTRANSPORT PROTEIN/CONTRACTILE PROTEIN / Cardiac Myosin Binding Protein C / C1 / cMyBPC / TRANSPORT PROTEIN-CONTRACTILE PROTEIN complex
Function / homology
Function and homology information


Striated Muscle Contraction / striated muscle myosin thick filament / myosin filament assembly / cardiac myofibril / A band / ventricular cardiac muscle tissue morphogenesis / structural constituent of muscle / regulation of heart contraction / myosin binding / myofibril ...Striated Muscle Contraction / striated muscle myosin thick filament / myosin filament assembly / cardiac myofibril / A band / ventricular cardiac muscle tissue morphogenesis / structural constituent of muscle / regulation of heart contraction / myosin binding / myofibril / sarcomere organization / detection of maltose stimulus / maltose transport complex / myosin heavy chain binding / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / heart morphogenesis / cardiac muscle contraction / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / regulation of heart rate / sarcomere / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / muscle contraction / structural constituent of cytoskeleton / actin binding / outer membrane-bounded periplasmic space / periplasmic space / cytoskeleton / cell adhesion / DNA damage response / identical protein binding / membrane / metal ion binding
Similarity search - Function
MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Immunoglobulin I-set / Immunoglobulin I-set domain / Bacterial extracellular solute-binding protein / Fibronectin type III domain ...MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Immunoglobulin I-set / Immunoglobulin I-set domain / Bacterial extracellular solute-binding protein / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltotriose / Myosin-binding protein C, cardiac-type / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.641 Å
AuthorsRebowski, G. / Boczkowska, M. / Dominguez, R.
CitationJournal: To be Published
Title: MBP-fusion protein of myosin-binding protein c residues 149-269
Authors: Rebowski, G. / Boczkowska, M. / Dominguez, R.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Myosin-binding protein C, cardiac-type chimeric protein
B: Maltose-binding periplasmic protein,Myosin-binding protein C, cardiac-type chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6344
Polymers107,6262
Non-polymers1,0092
Water23,4201300
1
A: Maltose-binding periplasmic protein,Myosin-binding protein C, cardiac-type chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3172
Polymers53,8131
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein,Myosin-binding protein C, cardiac-type chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3172
Polymers53,8131
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.993, 60.700, 73.314
Angle α, β, γ (deg.)85.73, 79.20, 89.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Maltose-binding periplasmic protein,Myosin-binding protein C, cardiac-type chimeric protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 53812.785 Da / Num. of mol.: 2
Fragment: UNP P0AEX9 residues 27-384 and UNP O70468 residues 149-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Mus musculus (house mouse)
Strain: K12 / Gene: malE, b4034, JW3994 / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9, UniProt: O70468
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1300 / 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: 43.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% PEG 5K MME 0.1 M Bicine pH 9.0 2.9mM 1-s-Nonyl- -D-thioglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9789 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.64→71.81 Å / Num. obs: 106790 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.61
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.4 / % possible all: 94.8

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Processing

Software
NameVersionClassification
JDirectordata collection
PHENIXmodel building
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q26

3q26


Resolution: 1.641→39.277 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 2000 1.87 %
Rwork0.1723 --
obs0.1731 106781 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8737 Å20.6799 Å22.2139 Å2
2--2.5704 Å20.579 Å2
3---1.3033 Å2
Refinement stepCycle: LAST / Resolution: 1.641→39.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7394 0 68 1300 8762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117786
X-RAY DIFFRACTIONf_angle_d1.41210620
X-RAY DIFFRACTIONf_dihedral_angle_d12.852835
X-RAY DIFFRACTIONf_chiral_restr0.1221184
X-RAY DIFFRACTIONf_plane_restr0.0071366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6413-1.68240.27961410.22447405X-RAY DIFFRACTION95
1.6824-1.72780.26451420.21517408X-RAY DIFFRACTION95
1.7278-1.77870.30361410.21477387X-RAY DIFFRACTION95
1.7787-1.83610.27871420.20557459X-RAY DIFFRACTION95
1.8361-1.90170.24391430.1897480X-RAY DIFFRACTION96
1.9017-1.97790.25821440.17527522X-RAY DIFFRACTION96
1.9779-2.06790.20041410.16717462X-RAY DIFFRACTION96
2.0679-2.17690.24371450.16087523X-RAY DIFFRACTION96
2.1769-2.31330.21071420.1657504X-RAY DIFFRACTION96
2.3133-2.49180.21741450.16757545X-RAY DIFFRACTION96
2.4918-2.74250.20571440.16627540X-RAY DIFFRACTION97
2.7425-3.13930.22161440.17067545X-RAY DIFFRACTION97
3.1393-3.95450.20311430.15497512X-RAY DIFFRACTION96
3.9545-39.28830.16671430.17457489X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 27.678 Å / Origin y: 32.4991 Å / Origin z: 65.8872 Å
111213212223313233
T0.103 Å2-0.0027 Å20.0027 Å2-0.1159 Å2-0.0068 Å2--0.1112 Å2
L0.0539 °2-0.0235 °20.0096 °2-0.2408 °2-0.0437 °2--0.0652 °2
S0.0088 Å °0.0112 Å °-0.0093 Å °-0.0019 Å °-0.0089 Å °0.0094 Å °0.0062 Å °0.003 Å °0.0044 Å °
Refinement TLS groupSelection details: all

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