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- PDB-5cea: Bd3460 Immunity Protein from Bdellovibrio bacteriovorus -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5cea
TitleBd3460 Immunity Protein from Bdellovibrio bacteriovorus
ComponentsBd3460
KeywordsPROTEIN BINDING / ankyrin repeat
Function / homology
Function and homology information


Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 Å
AuthorsLovering, A.L. / Cadby, I.T. / Lambert, C. / Sockett, R.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J015229/1 United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus.
Authors: Lambert, C. / Cadby, I.T. / Till, R. / Bui, N.K. / Lerner, T.R. / Hughes, W.S. / Lee, D.J. / Alderwick, L.J. / Vollmer, W. / Sockett, E.R. / Lovering, A.L.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bd3460
D: Bd3460
C: Bd3460
B: Bd3460
E: Bd3460


Theoretical massNumber of molelcules
Total (without water)123,7775
Polymers123,7775
Non-polymers00
Water11,007611
1
A: Bd3460


Theoretical massNumber of molelcules
Total (without water)24,7551
Polymers24,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Bd3460


Theoretical massNumber of molelcules
Total (without water)24,7551
Polymers24,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bd3460


Theoretical massNumber of molelcules
Total (without water)24,7551
Polymers24,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Bd3460


Theoretical massNumber of molelcules
Total (without water)24,7551
Polymers24,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bd3460


Theoretical massNumber of molelcules
Total (without water)24,7551
Polymers24,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.430, 99.640, 173.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22C
13A
23B
14A
24E
15D
25C
16D
26B
17D
27E
18C
28B
19C
29E
110B
210E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA26 - 21826 - 218
21SERSERLYSLYSDB26 - 21826 - 218
12SERSERSERSERAA26 - 21726 - 217
22SERSERSERSERCC26 - 21726 - 217
13SERSERSERSERAA26 - 21726 - 217
23SERSERSERSERBD26 - 21726 - 217
14LYSLYSLEULEUAA28 - 21628 - 216
24LYSLYSLEULEUEE28 - 21628 - 216
15SERSERSERSERDB26 - 21726 - 217
25SERSERSERSERCC26 - 21726 - 217
16SERSERSERSERDB26 - 21726 - 217
26SERSERSERSERBD26 - 21726 - 217
17LYSLYSLEULEUDB28 - 21628 - 216
27LYSLYSLEULEUEE28 - 21628 - 216
18SERSERLYSLYSCC26 - 21926 - 219
28SERSERLYSLYSBD26 - 21926 - 219
19LYSLYSLEULEUCC28 - 21628 - 216
29LYSLYSLEULEUEE28 - 21628 - 216
110LYSLYSLEULEUBD28 - 21628 - 216
210LYSLYSLEULEUEE28 - 21628 - 216

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Bd3460


Mass: 24755.465 Da / Num. of mol.: 5 / Fragment: Bd3460 / Mutation: A25M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Gene: Bd3460 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6MHS9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 40% v/v glycerol ethoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 80551 / % possible obs: 99 % / Redundancy: 3.8 % / Rsym value: 0.07 / Net I/σ(I): 10
Reflection shellRsym value: 0.493

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
SHELXphasing
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.85→86.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.802 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 4252 5 %RANDOM
Rwork0.1765 ---
obs0.1782 80551 98.69 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 130.61 Å2 / Biso mean: 38.045 Å2 / Biso min: 12.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.49 Å2-0 Å2
3----0.86 Å2
Refinement stepCycle: final / Resolution: 1.85→86.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7175 0 0 611 7786
Biso mean---34.54 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.027232
X-RAY DIFFRACTIONr_bond_other_d0.0140.027378
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9839713
X-RAY DIFFRACTIONr_angle_other_deg2.109317027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3435968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25128.11291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.414151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.4661510
X-RAY DIFFRACTIONr_chiral_restr0.0990.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028296
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021402
X-RAY DIFFRACTIONr_mcbond_it3.271.5593869
X-RAY DIFFRACTIONr_mcbond_other3.2641.5583868
X-RAY DIFFRACTIONr_mcangle_it3.9642.314829
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A232800.09
12D232800.09
21A227540.11
22C227540.11
31A223760.11
32B223760.11
41A225740.1
42E225740.1
51D228800.11
52C228800.11
61D223080.12
62B223080.12
71D225480.11
72E225480.11
81C227040.12
82B227040.12
91C223920.12
92E223920.12
101B219120.13
102E219120.13
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 303 -
Rwork0.299 5941 -
all-6244 -
obs--99.89 %
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)
15.8623-2.4990.84384.5948-0.65568.4304-0.17830.0369-0.24240.08330.10870.31630.2597-0.78280.06960.0562-0.0728-0.00360.15470.00320.090758.39654.457123.64
24.1415-1.8842-0.14764.7945-0.81455.6966-0.08960.1461-0.00740.02840.01040.12440.1935-0.49790.07930.0379-0.037-0.01960.0842-0.00390.049265.77956.715117.889
35.00682.14920.044212.66056.66467.8136-0.03820.3015-0.2926-0.0964-0.1395-0.03880.260.10790.17770.1184-0.0138-0.03160.05230.00250.047274.6250.86115.249
45.51940.3270.47036.536-1.06055.92810.03080.40760.0172-0.2824-0.08080.3109-0.0105-0.4620.05010.0368-0.0017-0.02860.10770.00270.039870.02759.236107.308
53.807-2.3966-2.28169.75345.33997.9411-0.07640.2097-0.2748-0.079-0.25230.40150.5387-0.32150.32870.111-0.0567-0.03540.0870.01850.07277.78855.543106.435
65.7212-0.49841.49626.92761.70537.50770.00110.46790.1249-0.3242-0.01270.3136-0.205-0.33760.01170.06570.0032-0.02330.08550.01850.02277.80762.055100.145
71.7317-0.40390.58222.89271.92588.07510.03110.166-0.064-0.22340.0696-0.047-0.17440.3545-0.10070.1129-0.0013-0.03150.1386-0.01650.057985.5557.04387.53
88.5612-0.551-0.86115.9766-1.56636.0909-0.0495-0.5292-0.38090.0172-0.168-0.09630.3420.12240.21750.1917-0.00680.03630.12030.07870.067281.00251.302139.583
93.8743-0.1502-0.93983.6988-1.23443.5741-0.1129-0.134-0.15970.005-0.0499-0.22440.31230.0810.16280.078-0.04030.02170.06880.0230.073683.09557.372130.332
103.02180.4917-1.50453.1258-0.23754.2596-0.0042-0.352-0.15760.2879-0.1254-0.22620.0890.19390.12960.067-0.0383-0.02490.07190.02660.038592.18565.042121.876
119.7417-2.60854.519511.0853-0.61877.26750.01450.3847-0.5027-0.1943-0.2014-0.14660.75080.31990.18690.11780.02010.06190.0469-0.00470.086394.65461.779112.492
126.7070.53940.79721.83580.47072.2209-0.0828-0.22830.02530.17270.00250.03980.09580.03050.08030.0379-0.0102-0.0080.02770.02110.038398.22177.096113.482
132.9028-0.4225-0.02187.72151.03472.6656-0.05440.2106-0.0486-0.2227-0.03930.1142-0.00360.07660.09370.0337-0.0236-0.0060.05260.01360.0124100.28678.722107.96
147.6487-2.54370.486810.00775.063714.3711-0.05450.35130.3398-0.11710.1216-1.1596-0.20591.2935-0.06710.0409-0.0484-0.00740.17090.06040.1711110.57182.062110.9
159.87330.00451.02555.87530.69187.6180.0397-0.54560.4570.2036-0.2740.1513-0.3586-0.21430.23420.14910.0242-0.02210.1913-0.10280.060661.0631.16135.436
163.71190.77941.20463.28151.6473.724-0.0757-0.39970.16110.0089-0.10140.1095-0.1592-0.30390.17710.0516-0.002-0.0150.0809-0.03190.037659.5825.184126.119
172.7615-0.17010.19568.4683-0.06164.8561-0.00960.0040.2032-0.1603-0.06070.0313-0.0795-0.14260.07030.0494-0.0411-0.01340.0773-0.01320.035955.88418.66116.421
184.0305-0.71750.0845.7468-0.30896.2393-0.1554-0.00930.1916-0.07250.12110.254-0.1871-0.46530.03440.0465-0.0178-0.01870.0676-0.00320.049849.24116.684111.489
194.76920.3753-0.6422.8528-0.40851.7860.02-0.05670.0420.1935-0.05970.0026-0.16820.03340.03970.0802-0.0371-0.00780.0284-0.00840.015946.8644.703110.869
209.4306-0.8772-3.2377.9253-1.00667.21020.08320.43610.4069-0.03550.06150.42-0.423-0.2867-0.14470.1363-0.0265-0.04340.08920.0150.070142.2039.956103.42
218.5702-0.9139-2.38684.52930.25613.6681-0.00550.6264-0.1654-0.2064-0.16330.2127-0.0961-0.34480.16890.0959-0.0255-0.01220.075-0.030.032641.868-2.019106.328
227.906-1.9973-0.32933.9395-0.18196.7608-0.12060.28690.6673-0.0483-0.0648-0.355-0.27730.52110.18540.0757-0.0371-0.05490.13130.080.148286.71228.921119.188
233.9717-1.33841.99033.0196-0.26454.4976-0.0510.18360.06940.0079-0.001-0.17610.00410.31120.05190.06680.0097-0.00080.03750.02910.067280.3825.835118.053
242.9646-0.53110.6693.50741.10056.62450.00270.36830.0882-0.21840.0098-0.1194-0.1370.2677-0.01240.0662-0.02380.00010.10270.02110.050673.81526.43107.768
256.6399-1.16973.38183.67930.33297.1534-0.31540.23990.20340.11370.12260.0575-0.25710.22510.19280.0893-0.06730.01770.09120.00670.059868.62224.778104.137
269.31330.7551-0.59444.2805-0.25646.7285-0.22010.7369-0.3219-0.22760.2121-0.20720.54540.4470.00810.1368-0.00070.02070.1851-0.04230.038568.49318.50497.364
272.5788-1.19771.4633.8197-0.74078.4425-0.08780.56740.2725-0.5049-0.1498-0.13950.05510.12650.23750.2423-0.1191-0.04620.3110.06020.185560.7925.2287.189
2811.48480.4982-2.501914.2198-4.68779.6327-0.14890.8844-0.3834-0.9611-0.3267-0.71520.30180.37770.47560.5342-0.0288-0.02470.64420.13120.180362.72824.24475.252
294.74760.4652-0.205310.2399-1.315711.25740.09730.58480.5405-0.68940.23170.5561-0.0194-0.3371-0.3290.1443-0.0454-0.07630.3340.0440.352439.27564.27753.618
304.13920.2329-0.25875.63820.15137.75960.24330.15850.36830.06770.20970.2647-0.16530.309-0.4530.109-0.02580.05590.1697-0.0470.205645.9265.02462.781
312.6481-0.7389-0.15314.91232.682711.68960.0489-0.21620.02020.63130.4183-0.00460.58840.5432-0.46710.21210.05860.00630.2965-0.11150.143648.8459.93674.476
320.89670.7809-2.51490.7128-2.238110.34690.2099-0.0067-0.1030.05230.1135-0.09030.88961.1998-0.32340.77120.2712-0.21380.6924-0.27470.291551.86856.86484.929
3311.40951.4293-4.61326.27274.15379.72960.0033-0.3868-1.2534-1.3084-0.1638-0.00551.32441.13750.16041.67330.6397-0.45580.8729-0.18250.517852.80750.77692.536
348.81632.1406-1.431915.99953.89482.47380.6579-0.4154-0.244-0.1144-0.11260.0780.16770.5262-0.54530.32530.0291-0.18060.3977-0.22110.378448.76661.304100.761
3515.833-2.1139-3.530613.0934-5.0243.1692-0.0342-0.5646-1.31010.0726-0.14490.41680.07860.15250.17910.7141-0.0168-0.25720.4342-0.07740.582443.97150.221101.093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 55
2X-RAY DIFFRACTION2A56 - 87
3X-RAY DIFFRACTION3A88 - 97
4X-RAY DIFFRACTION4A98 - 116
5X-RAY DIFFRACTION5A117 - 131
6X-RAY DIFFRACTION6A132 - 154
7X-RAY DIFFRACTION7A155 - 217
8X-RAY DIFFRACTION8B26 - 54
9X-RAY DIFFRACTION9B55 - 97
10X-RAY DIFFRACTION10B98 - 143
11X-RAY DIFFRACTION11B144 - 156
12X-RAY DIFFRACTION12B157 - 178
13X-RAY DIFFRACTION13B179 - 206
14X-RAY DIFFRACTION14B207 - 216
15X-RAY DIFFRACTION15C26 - 50
16X-RAY DIFFRACTION16C51 - 112
17X-RAY DIFFRACTION17C113 - 131
18X-RAY DIFFRACTION18C132 - 156
19X-RAY DIFFRACTION19C157 - 178
20X-RAY DIFFRACTION20C179 - 190
21X-RAY DIFFRACTION21C191 - 220
22X-RAY DIFFRACTION22D26 - 48
23X-RAY DIFFRACTION23D49 - 86
24X-RAY DIFFRACTION24D87 - 113
25X-RAY DIFFRACTION25D114 - 134
26X-RAY DIFFRACTION26D135 - 154
27X-RAY DIFFRACTION27D155 - 204
28X-RAY DIFFRACTION28D205 - 218
29X-RAY DIFFRACTION29E28 - 53
30X-RAY DIFFRACTION30E54 - 97
31X-RAY DIFFRACTION31E98 - 135
32X-RAY DIFFRACTION32E136 - 173
33X-RAY DIFFRACTION33E174 - 192
34X-RAY DIFFRACTION34E193 - 205
35X-RAY DIFFRACTION35E206 - 216

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