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- PDB-6k67: Application of anti-helix antibodies in protein structure determi... -

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Basic information

Entry
Database: PDB / ID: 6k67
TitleApplication of anti-helix antibodies in protein structure determination (9011-3LRH)
Components
  • 3LRH introbody
  • Engineered calmodulin
KeywordsSTRUCTURAL PROTEIN / antibody / protein design
Function / homology
Function and homology information


negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding ...negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein serine/threonine kinase activity / spindle microtubule / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / myelin sheath / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLee, J.O. / Jin, M.S. / Kim, J.W. / Kim, S. / Lee, H. / Cho, G.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2014R1A2A1A10050436 Korea, Republic Of
National Research Foundation (Korea)NRF-2017M3A9F6029753 Korea, Republic Of
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Application of antihelix antibodies in protein structure determination.
Authors: Kim, J.W. / Kim, S. / Lee, H. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O.
History
DepositionJun 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3LRH introbody
B: Engineered calmodulin
C: 3LRH introbody
D: Engineered calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9378
Polymers51,7774
Non-polymers1604
Water4,288238
1
A: 3LRH introbody
B: Engineered calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9694
Polymers25,8892
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-38 kcal/mol
Surface area10240 Å2
MethodPISA
2
C: 3LRH introbody
D: Engineered calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9694
Polymers25,8892
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-24 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.298, 115.298, 93.275
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 3LRH introbody


Mass: 14203.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Engineered calmodulin


Mass: 11685.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP25*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 50% PEG 400, 0.2M CaCl2, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33481 / % possible obs: 99.7 % / Redundancy: 5.1 % / Rpim(I) all: 0.043 / Net I/σ(I): 27.3
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 3373 / Rpim(I) all: 0.26

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LRH, 2W73

3lrh

2w73


Resolution: 1.95→27.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.074 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1712 5.1 %RANDOM
Rwork0.20266 ---
obs0.20441 31710 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.547 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.21 Å20 Å2
2---0.41 Å20 Å2
3---1.34 Å2
Refinement stepCycle: 1 / Resolution: 1.95→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 4 238 3146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132954
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172661
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.6393996
X-RAY DIFFRACTIONr_angle_other_deg1.471.5786203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32623.973146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36315495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8591514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4383.6181528
X-RAY DIFFRACTIONr_mcbond_other3.4363.6141527
X-RAY DIFFRACTIONr_mcangle_it4.6615.4041903
X-RAY DIFFRACTIONr_mcangle_other4.665.4081904
X-RAY DIFFRACTIONr_scbond_it4.6954.1021426
X-RAY DIFFRACTIONr_scbond_other4.6944.1071427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9575.9462094
X-RAY DIFFRACTIONr_long_range_B_refined8.72343.9833329
X-RAY DIFFRACTIONr_long_range_B_other8.44543.6433270
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 109 -
Rwork0.302 2287 -
obs--96.5 %

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