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- PDB-6vjv: Crystal structure of the Prochlorococcus phage (myovirus P-SSM2) ... -

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Basic information

Entry
Database: PDB / ID: 6vjv
TitleCrystal structure of the Prochlorococcus phage (myovirus P-SSM2) ferredoxin at 1.6 Angstroms
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / Iron Sulfur Cluster Binding / myovirus P-SSM2 / Prochlorococcus phage / ferredoxin / 2 Iron 2 Sulfur
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
ACETATE ION / FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesProchlorococcus phage P-SSM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsOlmos Jr., J.L. / Campbell, I.J. / Miller, M.D. / Xu, W. / Kahanda, D. / Atkinson, J.T. / Sparks, N. / Bennett, G.N. / Silberg, J.J. / Phillips Jr., G.N.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0014462 United States
National Science Foundation (NSF, United States)1231306 United States
National Aeronautic Space Administration (NASA, United States)80NSSC18M0093 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Prochlorococcusphage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases.
Authors: Campbell, I.J. / Olmos Jr., J.L. / Xu, W. / Kahanda, D. / Atkinson, J.T. / Sparks, O.N. / Miller, M.D. / Phillips Jr., G.N. / Bennett, G.N. / Silberg, J.J.
History
DepositionJan 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 12, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,26622
Polymers20,7632
Non-polymers1,50420
Water3,783210
1
A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,13311
Polymers10,3811
Non-polymers75210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,13311
Polymers10,3811
Non-polymers75210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.619, 31.446, 61.288
Angle α, β, γ (deg.)90.000, 92.480, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ferredoxin /


Mass: 10381.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus phage P-SSM2 (virus) / Gene: PCMG_00283, PSSM2_281 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58M74
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 10% (w/v) PEG 3000, 200 mM zinc acetate, and 100 mM sodium acetate/acetic acid pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo-stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2019 / Details: Adjustable focus K-B pair
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.589→52.57 Å / Num. obs: 27020 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Rrim(I) all: 0.131 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.589-1.6175.11.881111780.3190.9142.10786.1
4.314-52.576.30.06321.514570.9950.0270.06999.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSJan 26, 2018data reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H57

5h57


Resolution: 1.59→39.06 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.12
Details: In chain B, the iron-sulfur cluster site was disrupted. The density surrounding the cluster in chain B is consistent with a mixture of zinc bound and an intact 2Fe-2S cluster. To account for ...Details: In chain B, the iron-sulfur cluster site was disrupted. The density surrounding the cluster in chain B is consistent with a mixture of zinc bound and an intact 2Fe-2S cluster. To account for the poor density and the anomalous data, chain B has been modeled as a grouped occupancy, where the model is partially comprised of intact cysteine-coordinated iron-sulfur cluster, and a zinc ion with a hydration shell.
RfactorNum. reflection% reflection
Rfree0.2134 1244 4.61 %
Rwork0.1783 --
obs0.1799 26984 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.9 Å2 / Biso mean: 33.7873 Å2 / Biso min: 11.18 Å2
Refinement stepCycle: final / Resolution: 1.59→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 51 212 1703
Biso mean--39.87 40.94 -
Num. residues----192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.650.32961330.2882592272590
1.65-1.730.23661160.24192829294599
1.73-1.820.26491360.20342866300299
1.82-1.930.22981460.18012848299499
1.93-2.080.21711720.17472858303099
2.08-2.290.19721270.156128923019100
2.29-2.620.22211290.162629233052100
2.62-3.310.19381580.171628973055100
3.31-39.060.20261270.175230353162100
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)
15.92671.2087-4.32394.2066-2.13945.45580.049-0.31240.1666-0.01110.1754-0.3702-0.03460.4697-0.16920.1272-0.0092-0.00430.1223-0.04990.14822.48811.26535.0069
26.7668-3.808-6.42912.04343.56997.43-0.4503-0.3007-0.39620.1210.2034-0.04170.60140.17530.28160.14790.0065-0.00310.12070.02930.132418.20917.62939.8792
35.7348-1.61150.40834.6415-0.18884.9729-0.0171-0.0087-0.1723-0.03320.08870.0059-0.1481-0.0604-0.02250.19730.00050.00780.105-0.00970.178219.38894.221-1.3942
46.2882.97541.11886.80853.95616.53250.00210.2879-0.1798-0.0038-0.17170.22180.1193-0.38190.14880.16110.02030.00730.13080.01570.14169.03289.8916-0.9273
56.0046-0.59610.71252.67740.23113.52920.2950.75220.1119-0.2863-0.2744-0.155-0.1205-0.1205-0.04950.22590.04790.02920.17640.04910.145112.679116.0485-7.1379
66.3513-0.10792.86617.5818-0.71456.70410.00480.02630.77440.07030.0146-0.0698-0.6348-0.19490.00180.20530.02710.0460.17440.04830.24158.896520.5213-2.3519
75.7689-0.5293-0.25931.0790.14392.0321-0.001-0.02420.1634-0.06810.0016-0.0944-0.0817-0.0202-0.0090.18180.00560.01510.0840.00740.156616.707912.48621.1712
83.425-4.14090.78255.0716-1.03592.50860.05880.198-0.115-0.2629-0.22750.4514-0.1983-0.87470.32450.20620.0523-0.00130.2278-0.0210.25191.559216.3733.5851
93.25971.95693.70483.38772.73826.39770.2848-0.89470.09540.4854-0.36350.27190.3578-1.3339-0.04410.3168-0.06510.02320.48830.0220.19912.459714.544329.4778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 8 )A2 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 19 )A9 - 19
3X-RAY DIFFRACTION3chain 'A' and (resid 20 through 36 )A20 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 54 )A37 - 54
5X-RAY DIFFRACTION5chain 'A' and (resid 55 through 66 )A55 - 66
6X-RAY DIFFRACTION6chain 'A' and (resid 67 through 76 )A67 - 76
7X-RAY DIFFRACTION7chain 'A' and (resid 77 through 92 )A77 - 92
8X-RAY DIFFRACTION8chain 'A' and (resid 93 through 97 )A93 - 97
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 97 )B2 - 97

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