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- PDB-8smu: Integral fusion of the HtaA CR2 domain from Corynebacterium dipht... -

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Basic information

Entry
Database: PDB / ID: 8smu
TitleIntegral fusion of the HtaA CR2 domain from Corynebacterium diphtheriae within EGFP
ComponentsHtaACR2 integral fusion within enhanced green fluorescent protein
KeywordsFLUORESCENT PROTEIN / HEME-BINDING DOMAIN / GREEN FLUORESCENT PROTEIN / INTEGRAL FUSION
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / membrane
Similarity search - Function
Htaa / Htaa / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Green fluorescent protein / Membrane protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Corynebacterium diphtheriae NCTC 13129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMahoney, B.J. / Cascio, D. / Clubb, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI161828 United States
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Development and atomic structure of a new fluorescence-based sensor to probe heme transfer in bacterial pathogens.
Authors: Mahoney, B.J. / Goring, A.K. / Wang, Y. / Dasika, P. / Zhou, A. / Grossbard, E. / Cascio, D. / Loo, J.A. / Clubb, R.T.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HtaACR2 integral fusion within enhanced green fluorescent protein
B: HtaACR2 integral fusion within enhanced green fluorescent protein
C: HtaACR2 integral fusion within enhanced green fluorescent protein
D: HtaACR2 integral fusion within enhanced green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,67139
Polymers175,9924
Non-polymers5,67935
Water1,36976
1
A: HtaACR2 integral fusion within enhanced green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,53311
Polymers43,9981
Non-polymers1,53510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HtaACR2 integral fusion within enhanced green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2578
Polymers43,9981
Non-polymers1,2597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HtaACR2 integral fusion within enhanced green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,53311
Polymers43,9981
Non-polymers1,53510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HtaACR2 integral fusion within enhanced green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3499
Polymers43,9981
Non-polymers1,3518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.826, 272.783, 73.518
Angle α, β, γ (deg.)90, 114.22, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
HtaACR2 integral fusion within enhanced green fluorescent protein


Mass: 43998.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Protein is an integral fusion of the second CR domain from Corynebacterium diphtheriae HtaA within enhanced GFP.
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Gene: GFP, DIP0625 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212, UniProt: Q6NIZ1

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Non-polymers , 5 types, 111 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.9 M ammonium sulfate, 0.1 M sodium cacodylate trihydrate, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.353→49.025 Å / Num. obs: 56878 / % possible obs: 92.2 % / Redundancy: 3.4 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.994 / CC1/2 anomalous: -0.011 / Rmerge(I) obs: 0.1038 / Rpim(I) all: 0.0664 / Rrim(I) all: 0.1235 / AbsDiff over sigma anomalous: 0.799 / Net I/σ(I): 7.26 / Num. measured all: 193381 / % possible anomalous: 88.4 / % possible ellipsoidal: 92.2 / % possible ellipsoidal anomalous: 88.4 / % possible spherical: 60.2 / % possible spherical anomalous: 57.7 / Redundancy anomalous: 1.75
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
7.557-49.0253.30.053517.4393999399284428440.994-0.0440.03410.06360.70694.798.794.798.794.71.7398.7
6.001-7.5573.360.071412.0795569556284428440.9910.0330.04590.08510.72594.199.294.199.294.11.7599.2
5.237-6.0013.490.075812.2499329932284428440.991-0.0310.04770.08980.73396.999.596.999.596.91.7999.5
4.762-5.2373.530.071913.451003710037284428440.992-0.0230.04510.08510.77198.199.698.199.698.11.899.6
4.42-4.7623.550.07613.491008210082284428440.9920.0390.04760.08990.8239999.99999.9991.7999.9
4.158-4.423.140.080411.3289418941284328430.990.0420.05360.0970.81493.799.293.799.293.71.6399.2
3.949-4.1583.120.09769.4588688868284428440.987-0.0920.06530.11790.78391.399.191.399.191.31.6399.1
3.777-3.9493.320.11558.3794299429284428440.9830.0430.07490.13810.80593.999.193.999.193.91.7299.1
3.632-3.7773.360.12747.4595599559284528450.9850.1220.08230.15210.894.999.594.999.594.91.7399.5
3.505-3.6323.420.14766.8297149714284328430.979-0.0340.09410.17550.81994.899.394.899.394.81.7699.3
3.396-3.5053.440.17825.6498019801284628460.972-0.040.1140.21220.81695.699.495.699.495.61.7799.4
3.298-3.3963.470.21884.8498749874284428440.960.010.1380.25930.82195.999.695.999.695.91.7899.6
3.211-3.2983.50.25384.0899539953284428440.9610.0050.16010.30090.79996.299.696.299.696.21.7999.6
3.132-3.2113.530.29423.651002910029284428440.9480.0130.18540.34860.81795.99895.99895.91.7998
3.055-3.1323.550.33423.261011110111284528450.9370.0220.21010.39570.83490.392.690.392.590.31.892.6
2.979-3.0553.550.40312.761008110081284228420.91300.2530.47710.81384.586.784.583.381.41.886.7
2.89-2.9793.420.42682.6197449744284528450.867-0.0320.2720.50750.81776797664.562.31.7579
2.787-2.893.260.47862.2492539253284228420.8160.0850.31450.57460.83366.771.966.748.144.91.6871.9
2.648-2.7873.320.48412.2494189418284128410.8120.010.31340.57860.8268.572.768.530.328.81.772.7
2.353-2.6483.370.6161.896009600284628460.686-0.0210.39850.73630.82670.674.270.610.19.71.7274.2

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Processing

Software
NameVersionClassification
autoPROCdata processing
pointlessdata scaling
Aimlessdata scaling
STARANISOdata scaling
BUSTER2.10.4refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→48.32 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.783 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.63 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 2792 -RANDOM
Rwork0.2087 ---
obs0.2099 56446 67.5 %-
Displacement parametersBiso mean: 62.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.1004 Å20 Å22.0262 Å2
2---0.8811 Å20 Å2
3----2.2194 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.45→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11946 0 378 76 12400
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00712605HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9917031HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4222SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2284HARMONIC5
X-RAY DIFFRACTIONt_it12605HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1566SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance32HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact8836SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion16.06
LS refinement shellResolution: 2.45→2.56 Å
RfactorNum. reflection% reflection
Rfree0.3079 60 -
Rwork0.2766 --
obs0.2782 1129 10.67 %
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)
14.89041.6137-0.58985.5555-0.08012.6417-0.1371-0.2066-0.1353-0.20660.0735-0.0569-0.1353-0.05690.0636-0.11810.05230.0034-0.1986-0.0792-0.0451-53.6891170.72413.1438
24.1899-4.7303-0.26214.52691.94331.7157-0.13970.00180.1840.00180.0309-0.00130.184-0.00130.1088-0.086-0.01420.0763-0.179-0.0019-0.0866-23.9149156.21216.5718
34.9522-0.4464-0.30275.7797-0.00375.58550.2637-0.51350.529-0.5135-0.211-0.18130.529-0.1813-0.05270.10750.0234-0.0723-0.29730.0103-0.3733-22.0794153.95652.1915
43.8285-3.4041-0.948210.26912.42842.4821-0.27050.8574-0.03690.85740.26750.1563-0.03690.15630.003-0.01770.01390.0232-0.1521-0.1165-0.0744-24.0315183.4631.6598
55.43231.3433-0.17494.1146-0.49512.1371-0.0389-0.11330.0942-0.11330.0781-0.04430.0942-0.0443-0.0392-0.13580.04970.1177-0.16910.09060.012827.3545102.21615.6369
63.7445-2.03610.602312.2496-3.34511.72510.0410.1594-0.14760.1594-0.22890.0415-0.14760.04150.188-0.0425-0.02170.0803-0.17110.0429-0.1034-2.6931116.95317.7724
74.9391-0.67971.06164.7493-1.07257.3951-0.0119-0.3964-0.1768-0.3964-0.23670.6832-0.17680.68320.2486-0.0530.04530.1002-0.18170.0672-0.3344-0.9262119.30854.3896
83.5785-3.00050.418713.155-2.52251.9362-0.0911.1988-0.11061.1988-0.0165-0.1541-0.1106-0.15410.10750.0336-0.0992-0.0513-0.1530.135-0.1314-1.911791.119935.1773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|38 A|207 - A|397 }A2 - 38
2X-RAY DIFFRACTION1{ A|2 - A|38 A|207 - A|397 }A207 - 397
3X-RAY DIFFRACTION2{ A|39 - A|206 }A39 - 206
4X-RAY DIFFRACTION3{ B|1 - B|38 B|207 - B|396 }B1 - 38
5X-RAY DIFFRACTION3{ B|1 - B|38 B|207 - B|396 }B207 - 396
6X-RAY DIFFRACTION4{ B|39 - B|206 }B39 - 206
7X-RAY DIFFRACTION5{ C|2 - C|38 C|207 - C|396 }C2 - 38
8X-RAY DIFFRACTION5{ C|2 - C|38 C|207 - C|396 }C207 - 396
9X-RAY DIFFRACTION6{ C|39 - C|206 }C39 - 206
10X-RAY DIFFRACTION7{ D|1 - D|38 D|207 - D|397 }D1 - 38
11X-RAY DIFFRACTION7{ D|1 - D|38 D|207 - D|397 }D207 - 397
12X-RAY DIFFRACTION8{ D|39 - D|206 }D39 - 206

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