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- PDB-4ppj: Crystal structure of Phanta, a weakly fluorescent photochromic GF... -

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Basic information

Entry
Database: PDB / ID: 4ppj
TitleCrystal structure of Phanta, a weakly fluorescent photochromic GFP-like protein. ON state
ComponentsMonomeric Azami Green
KeywordsFLUORESCENT PROTEIN / GFP / chromophore / chromoprotein / photoswitching
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDon Paul, C. / Traore, D.A.K. / Devenish, R.J. / Close, D. / Bell, T. / Bradbury, A. / Wilce, M.C.J. / Prescott, M.
CitationJournal: Plos One / Year: 2015
Title: X-Ray Crystal Structure and Properties of Phanta, a Weakly Fluorescent Photochromic GFP-Like Protein.
Authors: Don Paul, C. / Traore, D.A. / Olsen, S. / Devenish, R.J. / Close, D.W. / Bell, T.D. / Bradbury, A. / Wilce, M.C. / Prescott, M.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Apr 3, 2024Group: 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.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monomeric Azami Green
B: Monomeric Azami Green
C: Monomeric Azami Green
D: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)112,9894
Polymers112,9894
Non-polymers00
Water4,666259
1
A: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2471
Polymers28,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2471
Polymers28,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2471
Polymers28,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2471
Polymers28,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.815, 79.370, 71.001
Angle α, β, γ (deg.)90.00, 102.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A2 - 222
2112B2 - 222
3112C2 - 222
4112D2 - 222

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Components

#1: Protein
Monomeric Azami Green


Mass: 28247.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue DE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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

Crystal growTemperature: 293 K / pH: 7.5
Details: 20% PEG3350, 0.15M MgCl2, 0.1M Tris-HCl pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.97
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→79.37 Å / % possible obs: 98.5 % / Biso Wilson estimate: 54.98 Å2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ECGP123 WITHOUT CHROMOPHORE, WATERS AND SUBSTITUTIONS

Resolution: 2.3→30.68 Å / Cor.coef. Fo:Fc: 0.9355 / Cor.coef. Fo:Fc free: 0.8859 / SU B: 23.352 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.944 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 1669 5.03 %RANDOM
Rwork0.1968 ---
obs0.2001 33166 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.71 Å2
Baniso -1Baniso -2Baniso -3
1-3.6442 Å20 Å24.0001 Å2
2---2.4185 Å20 Å2
3----1.2257 Å2
Refine analyzeLuzzati coordinate error obs: 0.382 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7032 0 0 259 7291
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087220HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.169719HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2519SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes173HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1027HARMONIC5
X-RAY DIFFRACTIONt_it7220HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.3→2.37 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2944 108 4.07 %
Rwork0.2327 2545 -
all0.2355 2653 -
obs--98.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0367-0.402-0.09444.32710.21354.5852-0.15810.2178-0.123-0.2944-0.00330.22360.0154-0.3440.16140.1112-0.00470.0222-0.01420.01280.028430.4460.0462.6
22.33170.8709-1.68215.35331.11218.7527-0.0649-0.0701-0.0770.2825-0.38460.22010.5232-0.97760.44940.0636-0.11160.0870.0983-0.0020.081924.2789-12.40230.289
33.0376-0.56430.68186.4444-3.49329.25360.0079-0.3431-0.25770.621-0.1329-0.0225-0.2290.52140.1250.1042-0.0045-0.02290.258-0.03630.190254.5391-8.08741.046
42.0677-0.2273-0.26463.3462-1.02775.2610.12050.11440.0717-0.3882-0.0549-0.3690.04140.9736-0.06560.11360.02770.0040.3714-0.09970.215860.618-8.27110.385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|220 }A3 - 220
2X-RAY DIFFRACTION2{ B|2 - B|219 }B2 - 219
3X-RAY DIFFRACTION3{ C|2 - C|219 }C2 - 219
4X-RAY DIFFRACTION4{ D|2 - D|220 }D2 - 220

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