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- PDB-4ppl: Crystal structure of eCGP123 H193Q variant at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 4ppl
TitleCrystal structure of eCGP123 H193Q variant at pH 7.5
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: 2.2 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
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_unobs_or_zero_occ_atoms / 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_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
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)112,9854
Polymers112,9854
Non-polymers00
Water14,664814
1
A: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2461
Polymers28,2461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2461
Polymers28,2461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2461
Polymers28,2461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Monomeric Azami Green


Theoretical massNumber of molelcules
Total (without water)28,2461
Polymers28,2461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.560, 83.390, 74.650
Angle α, β, γ (deg.)90.00, 102.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Monomeric Azami Green


Mass: 28246.180 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.: 814 / 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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 293 K / pH: 7.4
Details: 21% PEG 3350, 0.2M MgCl2, 0.1M BTP ph 7.4, 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: 2.2→46.21 Å / % possible obs: 99.2 % / Biso Wilson estimate: 36.57 Å2

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Processing

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

Resolution: 2.2→46.21 Å / Cor.coef. Fo:Fc: 0.9453 / Cor.coef. Fo:Fc free: 0.8697 / SU R Cruickshank DPI: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 2195 5 %RANDOM
Rwork0.19 ---
obs0.1947 43881 99.16 %-
Displacement parametersBiso mean: 60.91 Å2
Baniso -1Baniso -2Baniso -3
1-4.2574 Å20 Å20.3052 Å2
2--2.0727 Å20 Å2
3----6.3301 Å2
Refine analyzeLuzzati coordinate error obs: 0.376 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7030 0 0 814 7844
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017229HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.179748HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2532SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1024HARMONIC5
X-RAY DIFFRACTIONt_it7229HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion20.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion885SEMIHARMONIC5
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_contact8512SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3808 162 5.01 %
Rwork0.3168 3072 -
all0.32 3234 -
obs--99.16 %
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)
10.8326-0.2977-0.36235.8218-0.44333.4394-0.12790.0986-0.0799-0.2036-0.3062-0.60080.00670.30690.43410.2629-0.00440.0777-0.2530.0599-0.22032.9963-4.02214.2891
20.81980.3635-0.50965.238-0.54744.1641-0.0538-0.1912-0.02660.6262-0.2117-0.4215-0.51620.3990.26550.3406-0.0695-0.0177-0.3040.0333-0.3176-3.0174.726133.7078
32.8892-1.6644-1.46234.70130.4084.2479-0.01390.40770.1163-0.34810.3370.48110.1149-0.0949-0.323-0.116-0.0989-0.1871-0.2438-0.0489-0.0265-27.78942.7224-5.8789
42.1373-0.13860.42951.1901-0.56381.6962-0.0461-0.0927-0.13770.19430.10810.53290.0106-0.2673-0.06210.2488-0.04840.1564-0.25360.00690.0378-34.97492.451924.886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 536
2X-RAY DIFFRACTION2{ B|* }B2 - 507
3X-RAY DIFFRACTION3{ C|* }C3 - 499
4X-RAY DIFFRACTION4{ D|* }D3 - 472

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