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- PDB-4ppk: Crystal structure of eCGP123 T69V variant at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 4ppk
TitleCrystal structure of eCGP123 T69V variant at pH 7.5
ComponentsMonomeric Azami Green
KeywordsFLUORESCENT PROTEIN / GFP / chromophore / 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 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 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...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_main_chain_plane / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)113,0174
Polymers113,0174
Non-polymers00
Water10,467581
1
A: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2541
Polymers28,2541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2541
Polymers28,2541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2541
Polymers28,2541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2541
Polymers28,2541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Monomeric Azami Green
B: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)56,5082
Polymers56,5082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area18010 Å2
MethodPISA
6
C: Monomeric Azami Green
D: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)56,5082
Polymers56,5082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-8 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.980, 81.330, 73.930
Angle α, β, γ (deg.)90.00, 107.64, 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 - 220
2112B2 - 220
3112C2 - 220
4112D2 - 220

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Components

#1: Protein
Monomeric Azami Green


Mass: 28254.225 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 / Water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 1.85 Å3/Da / Density % sol: 33.52 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 20% PEG3350, 0.1M 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→50 Å / % possible obs: 98.6 % / Biso Wilson estimate: 30.82 Å2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ECGP123 WITHOUT CHROMOPHORE, WATERS AND SUBSTITUTIONS

Resolution: 2→38.26 Å / Cor.coef. Fo:Fc: 0.9382 / Cor.coef. Fo:Fc free: 0.9038 / SU B: 7.428 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 2752 5 %RANDOM
Rwork0.1938 ---
obs0.197 55026 98.73 %-
all-55029 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.2556 Å20 Å20.7219 Å2
2--2.1586 Å20 Å2
3----3.4142 Å2
Refine analyzeLuzzati coordinate error obs: 0.301 Å
Refinement stepCycle: LAST / Resolution: 2→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7062 0 0 581 7643
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097338HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.139888HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2582SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1048HARMONIC5
X-RAY DIFFRACTIONt_it7338HARMONIC20
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→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 205 5.01 %
Rwork0.2204 3890 -
all0.2219 4095 -
obs--98.73 %
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)
12.1145-0.1103-0.01331.18910.07230.64070.05890.24840.1039-0.1391-0.0355-0.25810.00260.0897-0.0234-0.0244-0.01850.052-0.04530.0107-0.05521.67664.002931.4218
23.03111.0569-0.02812.8862-0.10220.6285-0.04580.1995-0.1567-0.28410.01950.07340.0282-0.04210.0263-0.0288-0.0102-0.0094-0.1044-0.0261-0.0804-7.5967-6.233331.3089
32.59460.3866-0.08321.16190.021.1199-0.0964-0.1812-0.00820.27690.090.13260.0151-0.10330.00640.12110.06480.05280.05070.032-0.0834-10.7926-2.223663.2499
42.681-0.31290.36270.7645-0.23061.2789-0.087-0.3394-0.07220.16560.0968-0.1495-0.01890.0674-0.00980.08730.0547-0.04390.035-0.0103-0.054820.7994-1.447363.5929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 460
2X-RAY DIFFRACTION2{ B|* }B2 - 428
3X-RAY DIFFRACTION3{ C|* }C3 - 439
4X-RAY DIFFRACTION4{ D|* }D2 - 454

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