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- PDB-2g3o: The 2.1A crystal structure of copGFP -

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Basic information

Entry
Database: PDB / ID: 2g3o
TitleThe 2.1A crystal structure of copGFP
Componentsgreen fluorescent protein 2
KeywordsLUMINESCENT PROTEIN / beta-barrel / chromophore / GFP
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 2
Function and homology information
Biological speciesPontellina plumata (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWilmann, P.G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The 2.1A crystal structure of copGFP, a representative member of the copepod clade within the green fluorescent protein superfamily
Authors: Wilmann, P.G. / Battad, J. / Petersen, J. / Wilce, M.C.J. / Dove, S. / Devenish, R.J. / Prescott, M. / Rossjohn, J.
History
DepositionFeb 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: green fluorescent protein 2
B: green fluorescent protein 2
C: green fluorescent protein 2
D: green fluorescent protein 2
E: green fluorescent protein 2
F: green fluorescent protein 2


Theoretical massNumber of molelcules
Total (without water)147,9836
Polymers147,9836
Non-polymers00
Water3,855214
1
A: green fluorescent protein 2
B: green fluorescent protein 2


Theoretical massNumber of molelcules
Total (without water)49,3282
Polymers49,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-15 kcal/mol
Surface area16330 Å2
MethodPISA
2
C: green fluorescent protein 2
E: green fluorescent protein 2


Theoretical massNumber of molelcules
Total (without water)49,3282
Polymers49,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: green fluorescent protein 2
F: green fluorescent protein 2


Theoretical massNumber of molelcules
Total (without water)49,3282
Polymers49,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-15 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.954, 145.954, 53.767
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
31E
41F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 2 - 219 / Label seq-ID: 2 - 217

Dom-IDAuth asym-IDLabel asym-ID
1CC
2DD
3EE
4FF

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Components

#1: Protein
green fluorescent protein 2


Mass: 24663.840 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pontellina plumata (crustacean) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WV12
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGLY 57, TYR 58 AND GLY 59 ARE MODIFIED TO MAKE CHROMOPHORE (CR2 57).

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 22% PEG 3350, 0.1M Sodium Acetate, 0.15M Magnesium Sulphate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→35.714 Å / Num. all: 74759 / Num. obs: 74388 / % possible obs: 99.504 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.155 Å / % possible all: 98.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å14.99 Å
Translation3.5 Å14.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.71 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.668 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 3752 5 %RANDOM
Rwork0.23042 ---
all0.233 74759 --
obs0.2325 70636 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9623 0 0 214 9837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229899
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9413417
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40351269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78222.451408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42151312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7391545
X-RAY DIFFRACTIONr_chiral_restr0.110.21435
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027726
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.24399
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.26514
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2547
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3751.56479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.54429940
X-RAY DIFFRACTIONr_scbond_it0.98333922
X-RAY DIFFRACTIONr_scangle_it1.2934.53477
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1541 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Cmedium positional0.220.5
2Dmedium positional0.240.5
3Emedium positional0.210.5
4Fmedium positional0.240.5
1Cmedium thermal0.312
2Dmedium thermal0.352
3Emedium thermal0.292
4Fmedium thermal0.312
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 273 -
Rwork0.288 5189 -
obs-5462 98.47 %
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)
15.07151.40290.8565.8991.27342.7995-0.1003-0.0833-0.37610.4624-0.10380.9660.4155-0.55030.2041-0.1822-0.07330.1507-0.1129-0.16220.007739.924-48.415-1.398
24.7542.44941.1486.16831.76942.99840.03020.0198-0.01780.6465-0.21110.63330.1881-0.15010.1809-0.2083-0.01380.0986-0.2373-0.0802-0.246347.593-39.6682.903
35.20760.88391.08694.98051.44552.1671-0.45050.33391.0368-0.36070.19870.2402-0.5340.20760.2518-0.0891-0.0513-0.2128-0.22230.09110.043465.102-9.4035.001
44.52932.35911.53036.11811.94672.8298-0.46450.50780.595-0.33320.25620.2771-0.19830.17710.2082-0.217-0.0362-0.1168-0.19840.0599-0.212859.983-20.110.505
57.1131-0.19840.81123.7227-1.35853.14840.19260.39610.7329-0.0818-0.2629-0.8513-0.29690.78160.0703-0.0513-0.13350.00290.13650.16570.125922.155-60.01112.577
69.2920.71472.56563.1544-0.03212.95020.13620.43790.6139-0.139-0.2738-0.3403-0.22170.24640.1376-0.0263-0.05110.0370.00180.0951-0.1510.946-61.1177.854
715.06712.9239-2.82383.0787-0.43361.6514-0.2734-0.6981-1.31230.1581-0.0471-0.64180.07310.55260.3206-0.20980.0620.0593-0.11330.12640.065327.057-18.29813.945
815.41292.9555-4.31572.8761-1.01122.8285-0.0818-1.0845-1.42390.1886-0.302-0.5125-0.06820.27580.3838-0.24720.01560.0356-0.12050.1423-0.055916.2-19.88218.051
94.3362.22561.626.4844-2.26962.4054-0.28740.52780.46250.73720.1582-1.1998-0.24180.58830.1293-0.0312-0.1284-0.22470.12730.03640.151431.415-75.0624.481
103.79641.8615-0.21298.129-1.71432.3098-0.05990.02590.03990.8855-0.0253-0.8994-0.06780.28490.08520.0006-0.0452-0.1780.01440.0263-0.116725.773-84.39628.658
1113.92563.5107-3.26333.477-0.24610.893-0.4720.7403-1.0883-0.3370.1621-0.13660.2219-0.47340.3099-0.1781-0.07580.0972-0.0785-0.1223-0.0409-17.671-27.55319.531
1215.74822.9771-4.61262.7868-0.69482.3931-0.54991.3144-1.4317-0.26710.152-0.13610.1258-0.3210.3979-0.2215-0.04710.075-0.0919-0.1386-0.0645-7.052-24.69215.534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 563 - 56
2X-RAY DIFFRACTION2AA60 - 21858 - 216
3X-RAY DIFFRACTION3BB3 - 563 - 56
4X-RAY DIFFRACTION4BB60 - 21958 - 217
5X-RAY DIFFRACTION5CC2 - 562 - 56
6X-RAY DIFFRACTION6CC60 - 21958 - 217
7X-RAY DIFFRACTION7DD2 - 562 - 56
8X-RAY DIFFRACTION8DD60 - 21958 - 217
9X-RAY DIFFRACTION9EE2 - 562 - 56
10X-RAY DIFFRACTION10EE60 - 21958 - 217
11X-RAY DIFFRACTION11FF2 - 562 - 56
12X-RAY DIFFRACTION12FF60 - 21958 - 217

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