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- PDB-4p76: Cellular response to a crystal-forming protein -

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Basic information

Entry
Database: PDB / ID: 4p76
TitleCellular response to a crystal-forming protein
ComponentsPhotoconvertible fluorescent protein
KeywordsLUMINESCENT PROTEIN
Function / homology
Function and homology information


bioluminescence / metal ion binding
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Photoconvertible fluorescent protein
Similarity search - Component
Biological speciesFavia favus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsTsutsui, H. / Jinno, Y. / Shoda, K. / Tomita, A. / Matsuda, M. / Yamashita, E. / Katayama, H. / Nakagawa, A. / Miyawaki, A.
CitationJournal: Mol.Cell / Year: 2015
Title: A diffraction-quality protein crystal processed as an autophagic cargo
Authors: Tsutsui, H. / Jinno, Y. / Shoda, K. / Tomita, A. / Matsuda, M. / Yamashita, E. / Katayama, H. / Nakagawa, A. / Miyawaki, A.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photoconvertible fluorescent protein
B: Photoconvertible fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6923
Polymers51,6692
Non-polymers231
Water77543
1
A: Photoconvertible fluorescent protein
B: Photoconvertible fluorescent protein
hetero molecules

A: Photoconvertible fluorescent protein
B: Photoconvertible fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3846
Polymers103,3384
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)49.862, 84.426, 118.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYAA3 - 1143 - 112
21SERSERGLYGLYBB3 - 1143 - 112
12PHEPHEARGARGAA118 - 225116 - 223
22PHEPHEPROPROBB118 - 224116 - 222

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.988041, -0.154171, 0.002376), (-0.154153, 0.988027, 0.006332), (-0.003324, 0.00589, -0.999977)6.35911, 0.24793, 59.15041

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Components

#1: Protein Photoconvertible fluorescent protein


Mass: 25834.398 Da / Num. of mol.: 2 / Mutation: Q198S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Favia favus (invertebrata) / Gene: KikGR / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q53UG8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 310 K / Method: vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 11052 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 19.3
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 6.7 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementResolution: 2.9→40.354 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.873 / SU B: 15.092 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 539 4.7 %RANDOM
Rwork0.17445 ---
obs0.17784 11052 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.673 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20 Å2
2--2.42 Å20 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 2.9→40.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 1 43 3609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193657
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9634940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5185438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23424.335173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16615622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7791517
X-RAY DIFFRACTIONr_chiral_restr0.0970.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212815
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0261.7951768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7742.6872204
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.761.8991889
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.38314.6425355
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
881loose positional0.085
866tight thermal1.520.5
881loose thermal2.0210
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 35 -
Rwork0.257 805 -
obs--100 %

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