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- PDB-2vad: Monomeric red fluorescent protein, DsRed.M1 -

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Basic information

Entry
Database: PDB / ID: 2vad
TitleMonomeric red fluorescent protein, DsRed.M1
ComponentsRED FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / DSRED / GFP-LIKE / MONOMERIC / CHROMOPHORE / LUMINESCENCE / PHOTOPROTEIN
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Red fluorescent protein drFP583
Similarity search - Component
Biological speciesDISCOSOMA SP. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsStrongin, D.E. / Bevis, B. / Khuong, N. / Downing, M.E. / Strack, R.L. / Sundaram, K. / Glick, B.S. / Keenan, R.J.
CitationJournal: Protein Eng.Des.Sel. / Year: 2007
Title: Structural Rearrangements Near the Chromophore Influence the Maturation Speed and Brightness of Dsred Variants.
Authors: Strongin, D.E. / Bevis, B. / Khuong, N. / Downing, M.E. / Strack, R.L. / Sundaram, K. / Glick, B.S. / Keenan, R.J.
History
DepositionAug 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_rmsd_angle / struct_conn
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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RED FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8679
Polymers25,4401
Non-polymers4278
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.892, 62.151, 81.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RED FLUORESCENT PROTEIN / DSRED.M1


Mass: 25440.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DISCOSOMA SP. (sea anemone) / Plasmid: PQE31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B/PREP4 / References: UniProt: Q9U6Y8*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.6
Details: 100 MM HEPES, PH 7.6, 25% PEG3350, 200 MM MGCL2, 5 MM ZNSO4, RT, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 27397 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 43.7
Reflection shellResolution: 1.59→1.65 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZGO

1zgo


Resolution: 1.59→22.34 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3 AND 224-225 ARE DISORDERED AND WERE NOT MODELED. DISORDERED SURFACE SIDECHAINS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1386 5.1 %RANDOM
Rwork0.176 ---
obs0.177 25940 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: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.59→22.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 14 139 1908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221867
X-RAY DIFFRACTIONr_bond_other_d00.021584
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.992509
X-RAY DIFFRACTIONr_angle_other_deg3.7293.0063678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87425.46586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70215305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.579153
X-RAY DIFFRACTIONr_chiral_restr0.10.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022053
X-RAY DIFFRACTIONr_gen_planes_other0.020.02353
X-RAY DIFFRACTIONr_nbd_refined0.20.2288
X-RAY DIFFRACTIONr_nbd_other0.230.21471
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2877
X-RAY DIFFRACTIONr_nbtor_other0.1750.2898
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8981.51088
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5421749
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8073779
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0874.5758
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.63 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.205 103
Rwork0.178 1882

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