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- PDB-2arl: The 2.0 angstroms crystal structure of a pocilloporin at pH 3.5: ... -

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Basic information

Entry
Database: PDB / ID: 2arl
TitleThe 2.0 angstroms crystal structure of a pocilloporin at pH 3.5: the structural basis for the linkage between color transition and halide binding
ComponentsGFP-like non-fluorescent chromoprotein
KeywordsLUMINESCENT PROTEIN / Chromophore / Luminescence
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
ACETIC ACID / IODIDE ION / GFP-like non-fluorescent chromoprotein
Similarity search - Component
Biological speciesMontipora efflorescens (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWilmann, P.G. / Battad, J. / Beddoe, T. / Olsen, S. / Smith, S.C. / Dove, S. / Devenish, R.J. / Rossjohn, J. / Prescott, M.
CitationJournal: Photochem.Photobiol. / Year: 2006
Title: The 2.0 angstroms crystal structure of a pocilloporin at pH 3.5: the structural basis for the linkage between color transition and halide binding
Authors: Wilmann, P.G. / Battad, J. / Beddoe, T. / Olsen, S. / Smith, S.C. / Dove, S. / Devenish, R.J. / Rossjohn, J. / Prescott, M.
History
DepositionAug 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,64512
Polymers24,7661
Non-polymers87911
Water2,774154
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)102,57948
Polymers99,0644
Non-polymers3,51544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area11980 Å2
ΔGint-116 kcal/mol
Surface area31080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.770, 92.770, 75.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-504-

IOD

21A-638-

HOH

31A-645-

HOH

41A-671-

HOH

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Components

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


Mass: 24766.066 Da / Num. of mol.: 1 / Mutation: H146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Montipora efflorescens (invertebrata) / Plasmid: pRSETBN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83690
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS BELIEVE THAT LYS36 IS CORRECT AND UNIPROT IS INCORRECT AT THIS POSITION. RESIDUES ...THE DEPOSITORS BELIEVE THAT LYS36 IS CORRECT AND UNIPROT IS INCORRECT AT THIS POSITION. RESIDUES GLN 62, TYR 63 AND GLY 64 AUTOCATALYTICALLY FORM THE CHROMOPHORE CRQ LABELLED AS RESIDUE 66 IN THE COORDINATES.

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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: 3.26 Å3/Da / Density % sol: 62.23 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22733 / % possible obs: 98.9 % / Observed criterion σ(F): 6.3 / Observed criterion σ(I): 6.3
Reflection shellResolution: 2→2.07 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / σ(F): 5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2533 1154 RANDOM
Rwork0.2367 --
obs-22586 -
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 26 154 1922

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