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- PDB-2c9j: Structure of the fluorescent protein cmFP512 at 1.35A from Cerian... -

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Basic information

Entry
Database: PDB / ID: 2c9j
TitleStructure of the fluorescent protein cmFP512 at 1.35A from Cerianthus membranaceus
ComponentsGREEN FLUORESCENT PROTEIN FP512
KeywordsLUMINESCENT PROTEIN / FLUORESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE / LUMINESCENCE
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Green fluorescent protein FP512
Function and homology information
Biological speciesCERIANTHUS MEMBRANACEUS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRenzi, F. / Nienhaus, K. / Wiedenmann, J. / Vallone, B. / Nienhaus, G.U.
CitationJournal: Biochemistry / Year: 2006
Title: Exploring Chromophore-Protein Interactions in Fluorescent Protein Cmfp512 from Cerianthus Membranaceus: X-Ray Structure Analysis and Optical Spectroscopy.
Authors: Nienhaus, K. / Renzi, F. / Vallone, B. / Wiedenmann, J. / Nienhaus, G.U.
History
DepositionDec 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _pdbx_validate_polymer_linkage.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
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. THE SHEETS PRESENTED AS "BA" 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. THE SHEETS PRESENTED AS "CA" 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. THE SHEETS PRESENTED AS "DA" 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. THE SHEETS PRESENTED AS "EA" 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. THE SHEETS PRESENTED AS "FA" 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. THE SHEETS PRESENTED AS "GA" 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. THE SHEETS PRESENTED AS "HA" 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

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN FP512
B: GREEN FLUORESCENT PROTEIN FP512
C: GREEN FLUORESCENT PROTEIN FP512
D: GREEN FLUORESCENT PROTEIN FP512
E: GREEN FLUORESCENT PROTEIN FP512
F: GREEN FLUORESCENT PROTEIN FP512
G: GREEN FLUORESCENT PROTEIN FP512
H: GREEN FLUORESCENT PROTEIN FP512


Theoretical massNumber of molelcules
Total (without water)202,6788
Polymers202,6788
Non-polymers00
Water27,7971543
1
E: GREEN FLUORESCENT PROTEIN FP512
F: GREEN FLUORESCENT PROTEIN FP512
G: GREEN FLUORESCENT PROTEIN FP512
H: GREEN FLUORESCENT PROTEIN FP512


Theoretical massNumber of molelcules
Total (without water)101,3394
Polymers101,3394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12210 Å2
ΔGint-65.92 kcal/mol
Surface area29100 Å2
MethodPISA
2
A: GREEN FLUORESCENT PROTEIN FP512
B: GREEN FLUORESCENT PROTEIN FP512
C: GREEN FLUORESCENT PROTEIN FP512
D: GREEN FLUORESCENT PROTEIN FP512


Theoretical massNumber of molelcules
Total (without water)101,3394
Polymers101,3394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-58.54 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.001, 60.108, 125.400
Angle α, β, γ (deg.)83.80, 89.98, 73.85
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.44, -0.896, 0.067), (-0.895, 0.431, -0.115), (0.074, -0.111, -0.991)0.15438, 0.20906, -0.4041
2given(-0.918, 0.017, -0.397), (0.027, -0.994, -0.106), (-0.397, -0.108, 0.912)0.03135, 0.20924, -0.04326
3given(0.366, 0.875, 0.317), (0.872, -0.442, 0.21), (0.324, 0.2, -0.925)0.17915, 0.11729, -0.45336
4given(-0.37, -0.872, -0.32), (-0.775, 0.479, -0.412), (0.512, 0.096, -0.853)26.16197, 8.63111, 61.6986
5given(0.916, -0.018, 0.4), (-0.116, 0.944, 0.308), (-0.383, -0.329, 0.863)26.21752, 8.65356, 62.14501
6given(0.445, 0.893, -0.066), (0.886, -0.449, -0.113), (-0.13, -0.008, -0.991)26.09637, 8.52499, 61.75118
7given(-1, -0.006, 0.001), (0.006, -0.973, 0.231), (0.231, 0.973)26.23363, 8.79598, 62.15709

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Components

#1: Protein
GREEN FLUORESCENT PROTEIN FP512


Mass: 25334.742 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: CHROMOPHORE\: AN IMIDAZOLINONE RING FROM THE CYCLIZATION BETWEEN GLN62 AND GLY64 BACKBONE ATOMS AND COPLANAR TYR63
Source: (gene. exp.) CERIANTHUS MEMBRANACEUS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZQQ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1543 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 30.68 %
Description: DATA WERE SCALED FROM THREE DIFFERENT DATA SETS WITH RESOLUTION 3.2, 1.8 AND 1.35
Crystal growpH: 8.5
Details: 30% PEG 4000, 0.1M TRIS PH 8.5, 0.2M MAGNESIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. obs: 300980 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 1.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.61 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 15171 5 %RANDOM
Rwork0.228 ---
obs0.229 285736 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20.04 Å2-0.04 Å2
2--0.87 Å2-0.09 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.35→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13946 0 0 1543 15489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02214393
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.97119435
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.80451726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38624.182660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.836152354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8851548
X-RAY DIFFRACTIONr_chiral_restr0.0850.21934
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.28335
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.29928
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.21865
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.2119
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.58811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.163213861
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51236341
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2844.55569
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: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 983 -
Rwork0.348 18745 -
obs--80.69 %

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