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- PDB-7sws: Crystal structure of the chromoprotein amilCP -

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Basic information

Entry
Database: PDB / ID: 7sws
TitleCrystal structure of the chromoprotein amilCP
ComponentsChromoprotein amilCP
KeywordsFLUORESCENT PROTEIN / chromoprotein
Function / homologyBROMIDE ION
Function and homology information
Biological speciesAcropora millepora (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.642 Å
AuthorsCaputo, A.T. / Newman, J. / Scott, C. / Ahmed, H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Over the rainbow: structural characterization of the chromoproteins gfasPurple, amilCP, spisPink and eforRed.
Authors: Ahmed, F.H. / Caputo, A.T. / French, N.G. / Peat, T.S. / Whitfield, J. / Warden, A.C. / Newman, J. / Scott, C.
History
DepositionNov 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / 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 / _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: Chromoprotein amilCP
B: Chromoprotein amilCP
C: Chromoprotein amilCP
D: Chromoprotein amilCP
E: Chromoprotein amilCP
F: Chromoprotein amilCP
G: Chromoprotein amilCP
H: Chromoprotein amilCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,36218
Polymers199,9638
Non-polymers39910
Water20,4651136
1
C: Chromoprotein amilCP
hetero molecules

A: Chromoprotein amilCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1425
Polymers49,9912
Non-polymers1513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area2870 Å2
ΔGint-29 kcal/mol
Surface area17530 Å2
MethodPISA
2
B: Chromoprotein amilCP
D: Chromoprotein amilCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0624
Polymers49,9912
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-29 kcal/mol
Surface area17600 Å2
MethodPISA
3
E: Chromoprotein amilCP
hetero molecules

G: Chromoprotein amilCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0624
Polymers49,9912
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2720 Å2
ΔGint-30 kcal/mol
Surface area17510 Å2
MethodPISA
4
F: Chromoprotein amilCP
H: Chromoprotein amilCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0975
Polymers49,9912
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-41 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.524, 131.742, 93.671
Angle α, β, γ (deg.)90, 100.75, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chromoprotein amilCP


Mass: 24995.426 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Residues 63-65 are autocatalytically converted from the sequence QYG to the chromophore modelled in the structure
Source: (gene. exp.) Acropora millepora (invertebrata) / Plasmid: pETcc2 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% w/v polyethylene glycol 3350, 0.2 M sodium bromide, 0.1 M bis-tris propane chloride (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.642→92.026 Å / Num. obs: 108877 / % possible obs: 87.2 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.045 / Rrim(I) all: 0.121 / Net I/σ(I): 11.6
Reflection shellResolution: 1.642→1.797 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.181 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5444 / CC1/2: 0.659 / Rpim(I) all: 0.467 / Rrim(I) all: 1.271 / % possible all: 98

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SWR

7swr


Resolution: 1.642→92.03 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.226 / SU Rfree Blow DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 5415 -RANDOM
Rwork0.1943 ---
obs0.1954 108876 52.6 %-
Displacement parametersBiso mean: 25.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.2444 Å20 Å2-3.258 Å2
2---0.11 Å20 Å2
3----3.1344 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.642→92.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13992 0 10 1136 15138
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00927982HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0350519HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8008SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4341HARMONIC5
X-RAY DIFFRACTIONt_it14440HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1767SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact20652SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.18
X-RAY DIFFRACTIONt_other_torsion14.91
LS refinement shellResolution: 1.642→1.73 Å
RfactorNum. reflection% reflection
Rfree0.2725 112 -
Rwork0.2582 --
obs--7.66 %
Refinement TLS params.

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)
10.6097-0.06490.37450.6238-0.08531.1352-0.05750.1195-0.11640.1195-0.03050.0893-0.11640.08930.0880.0637-0.0162-0.0769-0.0656-0.0037-0.06782.5145-32.65119.4657
20.55050.05940.2310.44890.06080.9532-0.1441-0.1694-0.1976-0.1694-0.0284-0.1116-0.1976-0.11160.17250.1470.0334-0.1419-0.0647-0.0083-0.0456-3.0777-31.7796-31.9788
31.2642-0.26050.90810.7928-0.12631.55840.1963-0.02190.1771-0.02190.0289-0.00540.1771-0.0054-0.22520.0148-0.0096-0.0858-0.0783-0.0105-0.02674.46092.3644-12.2143
40.8485-0.08440.33520.8803-0.24771.4464-0.0124-0.08080.16-0.08080.0027-0.01150.16-0.01150.00980.08410.0011-0.0195-0.0607-0.0053-0.12321.0568-63.0653-35.15
50.94760.03780.46860.94520.28421.86860.017-0.00470.0274-0.00470.10810.38320.02740.3832-0.1251-0.0688-0.0021-0.0510.0852-0.0657-0.080335.00879.4135-12.8519
60.72190.11740.40070.84170.1481.50370.05540.02950.07010.0295-0.00660.13780.07010.1378-0.04880.02020.0124-0.0476-0.01290.0201-0.082832.2692-58.6346-35.8815
71.39750.08050.28960.5873-0.43772.0481-0.21960.0742-0.71310.07420.047-0.3228-0.7131-0.32280.17260.19890.1657-0.1551-0.0737-0.0515-0.025743.3986-26.12866.8888
80.6216-0.1836-0.11770.94220.3581.2323-0.0207-0.1397-0.232-0.1397-0.00920.1068-0.2320.10680.02990.119-0.0619-0.0567-0.07150.0472-0.095828.0737-27.9579-29.613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 221
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION2{ B|* }B2 - 221
4X-RAY DIFFRACTION2{ B|* }B301
5X-RAY DIFFRACTION3{ C|* }C2 - 221
6X-RAY DIFFRACTION3{ C|* }C301
7X-RAY DIFFRACTION4{ D|* }D2 - 221
8X-RAY DIFFRACTION4{ D|* }D301
9X-RAY DIFFRACTION5{ E|* }E2 - 221
10X-RAY DIFFRACTION5{ E|* }E301
11X-RAY DIFFRACTION6{ F|* }F2 - 221
12X-RAY DIFFRACTION6{ F|* }F301
13X-RAY DIFFRACTION7{ G|* }G2 - 221
14X-RAY DIFFRACTION7{ G|* }G301
15X-RAY DIFFRACTION8{ H|* }H2 - 221
16X-RAY DIFFRACTION8{ H|* }H301

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