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- PDB-1mou: Crystal structure of Coral pigment -

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Basic information

Entry
Database: PDB / ID: 1mou
TitleCrystal structure of Coral pigment
ComponentsGFP-like non-fluorescent chromoprotein
KeywordsLUMINESCENT PROTEIN / blue coral pigment / chromophore / beta can fold / similar to Green fluorescent protein and DsRed
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / GFP-like non-fluorescent chromoprotein
Similarity search - Component
Biological speciesMontipora efflorescens (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPrescott, M. / Ling, M. / Beddoe, T. / Oakley, A.J. / Dove, S. / Hoegh-Guldberg, O. / Devenish, R.J. / Rossjohn, J.
CitationJournal: Structure / Year: 2003
Title: The 2.2 a crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation.
Authors: Prescott, M. / Ling, M. / Beddoe, T. / Oakley, A.J. / Dove, S. / Hoegh-Guldberg, O. / Devenish, R.J. / Rossjohn, J.
History
DepositionSep 10, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 18, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value ..._pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4506
Polymers24,8151
Non-polymers6355
Water3,963220
1
A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules

A: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,79924
Polymers99,2604
Non-polymers2,53820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area11180 Å2
ΔGint-44 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.7, 131.7, 150.5
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

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Components

#1: Protein GFP-like non-fluorescent chromoprotein / Rtms 5 / Non-fluorescent pocilloporin


Mass: 24815.123 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Montipora efflorescens (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: P83690
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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 / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG, Tris buffer, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlprotein1drop
210-15 %PEG33501reservoir
30.1 MTris-HCl1reservoirpH8.2
40.2 Mpotassium iodide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2002 / Details: osmic mirrors
RadiationMonochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 32494 / Num. obs: 32494 / % possible obs: 96.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.247 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 109869
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ggx

1ggx


Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1016 -random
Rwork0.224 ---
all0.224 32494 --
obs0.224 31636 96.1 %-
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 5 220 1971
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.374
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg26.47
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.83

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