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- PDB-5mvo: FoxE P43212 crystal structure of Rhodopseudomonas ferrooxidans SW... -

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Basic information

Entry
Database: PDB / ID: 5mvo
TitleFoxE P43212 crystal structure of Rhodopseudomonas ferrooxidans SW2 putative iron oxidase
ComponentsFoxE
KeywordsELECTRON TRANSPORT / cytochrome-c / electron transfer / photoferrotrophy
Function / homologyCOPPER (II) ION / HEME C / PHOSPHATE ION / FoxE
Function and homology information
Biological speciesRhodobacter sp. SW2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.668 Å
AuthorsPereira, L. / Saraiva, I.H. / Oliveira, A.S. / Soares, C. / Gomes, R.O. / Frazao, C.
Funding support Portugal, 2items
OrganizationGrant numberCountry
FCTSFRH/BPD/84404/2012(IHS) Portugal
MOSTMICROLisboa-01-0145-FEDER-007660 Portugal
Citation
Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012

Title: Crystallization and preliminary crystallographic studies of FoxE from Rhodobacter ferrooxidans SW2, an Fe(II) oxidoreductase involved in photoferrotrophy.
Authors: Pereira, L. / Saraiva, I.H. / Coelho, R. / Newman, D.K. / Louro, R.O. / Frazao, C.
#1: Journal: J. Biol. Chem. / Year: 2012
Title: Functional characterization of the FoxE iron oxidoreductase from the photoferrotroph Rhodobacter ferrooxidans SW2.
Authors: Saraiva, I.H. / Newman, D.K. / Louro, R.O.
History
DepositionJan 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FoxE
B: FoxE
C: FoxE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,20717
Polymers94,7993
Non-polymers4,40814
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14970 Å2
ΔGint-238 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.850, 116.850, 191.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FoxE


Mass: 31599.607 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sp. SW2 (bacteria) / Gene: foxE / Plasmid: pUX19 / Production host: Escherichia coli (E. coli) / Variant (production host): JCB7123 / References: UniProt: A3DTD8
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.4 % / Description: Polyhedral
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Vapor diffusion at 277 K in siting drops of 1 micro-l of protein solution (15 mg/ml of FoxE in 5 mM potassium phosphate buffer pH 7.0) plus 1 micro-l of precipitant solution (1.3 M ...Details: Vapor diffusion at 277 K in siting drops of 1 micro-l of protein solution (15 mg/ml of FoxE in 5 mM potassium phosphate buffer pH 7.0) plus 1 micro-l of precipitant solution (1.3 M sodium/potassium phosphate pH 7.5, 50 mM copper chloride) equilibrated against 500 ml of precipitant solution in the well.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.67→48.85 Å / Num. obs: 38130 / % possible obs: 99.2 % / Redundancy: 11.4 % / Biso Wilson estimate: 67 Å2 / CC1/2: 0.999 / Rsym value: 0.08 / Net I/σ(I): 19.1
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 2.78 / CC1/2: 0.858 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MAB
Resolution: 2.668→49.847 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.67 / Phase error: 17.58 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.1738 38129 100 %
Rwork0.1738 --
obs0.1738 38129 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.668→49.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 290 44 6219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126437
X-RAY DIFFRACTIONf_angle_d1.4148814
X-RAY DIFFRACTIONf_dihedral_angle_d15.3912294
X-RAY DIFFRACTIONf_chiral_restr0.056921
X-RAY DIFFRACTIONf_plane_restr0.011154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6681-2.69840.326211390.32621139X-RAY DIFFRACTION91
2.6984-2.73020.319112310.31911231X-RAY DIFFRACTION100
2.7302-2.76340.323812610.32381261X-RAY DIFFRACTION100
2.7634-2.79840.295912650.29591265X-RAY DIFFRACTION100
2.7984-2.83520.284212580.28421258X-RAY DIFFRACTION100
2.8352-2.87410.281912660.28191266X-RAY DIFFRACTION100
2.8741-2.91510.283912550.28391255X-RAY DIFFRACTION100
2.9151-2.95860.271612450.27161245X-RAY DIFFRACTION100
2.9586-3.00490.267412750.26741275X-RAY DIFFRACTION100
3.0049-3.05410.272912550.27291255X-RAY DIFFRACTION100
3.0541-3.10680.263812700.26381270X-RAY DIFFRACTION100
3.1068-3.16330.263212520.26321252X-RAY DIFFRACTION100
3.1633-3.22410.259212470.25921247X-RAY DIFFRACTION100
3.2241-3.28990.231712720.23171272X-RAY DIFFRACTION100
3.2899-3.36140.233712750.23371275X-RAY DIFFRACTION100
3.3614-3.43960.21612860.2161286X-RAY DIFFRACTION100
3.4396-3.52560.210712500.21071250X-RAY DIFFRACTION100
3.5256-3.62090.19612770.1961277X-RAY DIFFRACTION100
3.6209-3.72740.174812780.17481278X-RAY DIFFRACTION100
3.7274-3.84770.176612720.17661272X-RAY DIFFRACTION100
3.8477-3.98510.174912600.17491260X-RAY DIFFRACTION100
3.9851-4.14460.147413000.14741300X-RAY DIFFRACTION100
4.1446-4.33310.126412740.12641274X-RAY DIFFRACTION99
4.3331-4.56140.125212800.12521280X-RAY DIFFRACTION100
4.5614-4.8470.128412930.12841293X-RAY DIFFRACTION100
4.847-5.22090.129712950.12971295X-RAY DIFFRACTION100
5.2209-5.74560.12713050.1271305X-RAY DIFFRACTION100
5.7456-6.57540.123513220.12351322X-RAY DIFFRACTION99
6.5754-8.27810.110413410.11041341X-RAY DIFFRACTION99
8.2781-49.85610.125413300.12541330X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0639-0.0727-0.10050.9748-0.05280.26620.10060.0119-0.638-0.8391-0.08020.32280.0903-1.14870.01390.43940.042-0.13190.7814-0.00940.7131.3553-13.12631.1122
20.0896-0.1123-0.06970.17630.15160.1479-0.03560.4472-0.1214-0.2385-0.11660.2703-0.0064-0.4797-0.00030.40290.00970.01470.6682-0.0780.381813.8592-14.2447-6.4768
30.0025-0.0039-0.0070.00910.00650.013-0.0986-0.2056-0.35640.20460.15260.2615-0.4499-0.1866-0.00040.44610.0155-0.02310.54380.0020.395530.5552-17.0677-10.8023
40.18560.43470.14391.15330.34060.10930.0940.75140.0856-0.50170.226-0.2664-0.3449-0.27890.04450.5581-0.0340.09790.9290.01920.350232.2742-13.3222-24.345
50.1463-0.0892-0.27820.1599-0.09741.1707-0.38060.9684-0.9923-0.71690.21050.17420.4462-0.7920.37160.7374-0.28140.11230.8554-0.51520.898525.6872-33.7882-26.5285
60.15620.0683-0.43240.0418-0.16541.1298-0.17790.3797-0.5809-0.03820.21940.24340.9566-0.790.15211.3484-0.54320.27520.8599-0.56461.885216.7706-44.2904-19.3308
70.024-0.0040.08490.8190.20140.619-0.36450.612-1.1502-0.18540.11150.56950.3274-0.5112-0.37140.626-0.15250.0310.8088-0.38570.824524.2218-30.3483-19.3999
80.10730.01910.00040.03550.01560.0372-0.11330.27970.0824-0.12820.05570.0675-0.2426-0.32050.00120.40760.0367-0.05720.87650.04830.43716.6606-12.6014-15.8727
90.0134-0.0276-0.01620.05990.04090.03840.07840.0239-0.2193-0.09910.19040.18870.16090.21640.00020.4529-0.08770.11740.7633-0.20660.54632.0723-22.3313-21.497
100.14770.1034-0.30440.1034-0.31920.9947-0.42640.10770.1577-0.1722-0.2845-0.22850.1847-0.1924-0.04841.3097-0.52030.26981.1614-0.57071.48321.884-39.3623-17.0309
110.2787-0.02390.32540.02280.09441.0641-0.09440.5292-0.0322-0.21620.645-0.58330.3040.00330.36860.6377-0.05880.25811.0779-0.32470.717743.5884-25.9916-28.8834
120.42220.14480.26340.07880.13530.1980.18470.63010.00180.0462-0.2503-0.061-0.0658-0.0243-0.00020.33190.0708-0.02050.5702-0.06230.425943.049-18.5494-14.816
130.6374-0.55970.20970.4616-0.08490.3099-0.15870.33470.3456-0.04240.0804-0.1682-0.2117-0.3030.00020.3936-0.039-0.03990.39530.04120.540845.3212-2.78941.0652
140.6244-0.31760.53530.2589-0.2330.4046-0.15840.09390.16570.1492-0.0289-0.3503-0.10790.1463-0.00130.3039-0.0217-0.06270.50360.00510.545959.1233-11.68985.6658
150.493-0.78240.34181.2435-0.70070.55720.172-0.05450.2236-0.0212-0.2104-0.17220.3060.2433-0.00120.38420.0648-0.09440.62970.01430.491768.5863-25.341811.2322
160.0158-0.0433-0.02730.11780.07010.0423-0.14760.23420.3664-0.0568-0.1431-0.1318-0.16270.11-0.09570.83760.4323-0.11791.25190.10510.565369.9972-28.6091-6.9676
170.4106-0.38480.31390.3605-0.46530.82320.01160.0920.026-0.0239-0.1084-0.1170.17560.1868-0.00020.29550.0123-0.01210.43740.05670.465155.3412-15.95580.628
181.01761.12451.03341.24861.13111.06980.01880.17610.18110.02430.1354-0.08370.05910.00710.59290.61490.09660.13950.74390.22680.440947.1054-4.4804-16.8981
190.03760.0074-0.02980.0031-0.00010.03710.2221-0.01880.312-0.1189-0.0865-0.3910.3935-0.0013-0.00090.5419-0.0296-0.03530.4555-0.02230.612949.1476-6.98045.7578
200.04050.01840.03630.00940.0120.02840.2319-0.16320.16070.00530.0146-0.619-0.0750.0905-0.00090.48120.0613-0.07970.5877-0.00380.63359.5833-24.31287.1499
210.0714-0.05350.07890.9734-0.09470.13960.0129-0.78450.38551.07660.2680.346-0.41920.17250.05260.5904-0.027-0.05130.4741-0.24010.608650.3845-0.259818.2768
220.3608-0.1746-0.1920.07540.08230.11860.2932-0.11690.21120.22850.0273-0.0284-0.51430.0712-00.36520.04780.02440.5264-0.08430.434838.1449-4.899212.2739
230.74530.44050.22250.38240.35930.5651-0.05230.02150.2588-0.18710.0754-0.0704-0.1945-0.15020.00020.36630.14850.01140.45650.04640.39117.7869-2.31473.5672
240.51320.38090.0930.521-0.28230.42970.02260.18370.10850.31810.26890.1874-0.1217-0.3014-00.42420.17260.12080.59660.08960.4557.3645-11.052119.2887
250.04930.1933-0.13180.7275-0.52310.38460.1704-0.1026-0.28190.3941-0.16080.20170.0474-0.38340.00070.44830.01880.1140.67110.03050.46046.1227-20.598628.2184
260.96791.32220.00591.8320.00890.00930.5152-0.06790.05720.8776-0.4575-0.0966-0.70490.02760.14870.75210.01340.15270.5612-0.03630.359514.8239-10.88832.1248
270.00520.0173-0.01930.0399-0.0490.05450.2220.3915-0.032-0.0913-0.22920.3555-0.47960.1264-0.00030.55440.16850.16110.55330.04110.445310.3817-8.97521.6556
280.3731-0.05310.24370.1888-0.10290.45180.0676-0.1885-0.01150.1333-0.1628-0.1307-0.1868-0.1219-0.00010.41290.08080.0060.3841-0.04910.431324.572-7.703210.6631
290.06130.0192-0.04580.0375-0.00490.03830.09170.3288-0.58470.0949-0.38430.4456-0.1605-0.00920.00290.43890.095-0.00710.50370.01330.481713.5375-8.20745.2606
300.0475-0.0181-0.0340.00540.01210.0247-0.1550.25750.00490.0036-0.20990.0422-0.2679-0.2078-0.00230.5687-0.0370.03050.50150.03920.424515.0087-17.700323.3921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:21)
2X-RAY DIFFRACTION2(chain A and resid 22:43)
3X-RAY DIFFRACTION3(chain A and resid 44:59)
4X-RAY DIFFRACTION4(chain A and resid 60:86)
5X-RAY DIFFRACTION5(chain A and resid 87:160)
6X-RAY DIFFRACTION6(chain A and resid 161:211)
7X-RAY DIFFRACTION7(chain A and resid 212:244)
8X-RAY DIFFRACTION8(chain A and resid 245:259)
9X-RAY DIFFRACTION9(chain A and resid 301:301)
10X-RAY DIFFRACTION10(chain A and resid 302:302)
11X-RAY DIFFRACTION11(chain B and resid 1:20 or chain E and resseq 1)
12X-RAY DIFFRACTION12(chain B and resid 21:45)
13X-RAY DIFFRACTION13(chain B and resid 46:89)
14X-RAY DIFFRACTION14(chain B and resid 90:139)
15X-RAY DIFFRACTION15(chain B and resid 140:199)
16X-RAY DIFFRACTION16(chain B and resid 200:207)
17X-RAY DIFFRACTION17(chain B and resid 208:253)
18X-RAY DIFFRACTION18(chain B and resid 254:259)
19X-RAY DIFFRACTION19(chain B and resid 301:301)
20X-RAY DIFFRACTION20(chain B and resid 302:302)
21X-RAY DIFFRACTION21(chain C and resid 1:20 or chain E and resseq 2)
22X-RAY DIFFRACTION22(chain C and resid 21:42)
23X-RAY DIFFRACTION23(chain C and resid 43:103)
24X-RAY DIFFRACTION24(chain C and resid 104:145)
25X-RAY DIFFRACTION25(chain C and resid 146:180)
26X-RAY DIFFRACTION26(chain C and resid 181:217)
27X-RAY DIFFRACTION27(chain C and resid 218:225)
28X-RAY DIFFRACTION28(chain C and resid 226:259)
29X-RAY DIFFRACTION29(chain C and resid 301:301)
30X-RAY DIFFRACTION30(chain C and resid 302:302)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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