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- PDB-8tto: Structure of Hachiman anti-defense 1 (Had1) -

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Basic information

Entry
Database: PDB / ID: 8tto
TitleStructure of Hachiman anti-defense 1 (Had1)
ComponentsHachiman
KeywordsVIRAL PROTEIN / immune evasion / anti-defense / phage
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRagucci, A.E. / Antine, S.P. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Nature / Year: 2024
Title: Phages overcome bacterial immunity via diverse anti-defence proteins.
Authors: Yirmiya, E. / Leavitt, A. / Lu, A. / Ragucci, A.E. / Avraham, C. / Osterman, I. / Garb, J. / Antine, S.P. / Mooney, S.E. / Hobbs, S.J. / Kranzusch, P.J. / Amitai, G. / Sorek, R.
History
DepositionAug 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: 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 1.2Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jun 5, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hachiman
B: Hachiman
C: Hachiman
D: Hachiman


Theoretical massNumber of molelcules
Total (without water)24,8764
Polymers24,8764
Non-polymers00
Water3,099172
1
A: Hachiman
B: Hachiman


Theoretical massNumber of molelcules
Total (without water)12,4382
Polymers12,4382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-9 kcal/mol
Surface area6460 Å2
MethodPISA
2
C: Hachiman
D: Hachiman


Theoretical massNumber of molelcules
Total (without water)12,4382
Polymers12,4382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-9 kcal/mol
Surface area6260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.938, 40.181, 45.291
Angle α, β, γ (deg.)75.220, 89.420, 74.910
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Hachiman


Mass: 6219.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: prophage sequence isolated after integration into Bacillus toyonensis AFS058541 genome
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 6.2, 30% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00011 Å / Relative weight: 1
ReflectionResolution: 2→37.45 Å / Num. obs: 13372 / % possible obs: 97.3 % / Redundancy: 1.8 % / Biso Wilson estimate: 29.25 Å2 / CC1/2: 0.993 / Net I/σ(I): 4.9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 979 / CC1/2: 0.49

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.45 Å / SU ML: 0.2962 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.0547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 1333 9.99 %
Rwork0.2153 12017 -
obs0.2194 13350 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.07 Å2
Refinement stepCycle: LAST / Resolution: 2→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 172 1533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00141385
X-RAY DIFFRACTIONf_angle_d0.40031865
X-RAY DIFFRACTIONf_chiral_restr0.0407217
X-RAY DIFFRACTIONf_plane_restr0.0022211
X-RAY DIFFRACTIONf_dihedral_angle_d9.9705511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.33581330.32371195X-RAY DIFFRACTION95.47
2.07-2.150.31791300.28921172X-RAY DIFFRACTION96.37
2.15-2.250.34061320.26741191X-RAY DIFFRACTION96.29
2.25-2.370.31311330.25521202X-RAY DIFFRACTION96.88
2.37-2.520.28421350.24741211X-RAY DIFFRACTION97.61
2.52-2.710.27991330.24451199X-RAY DIFFRACTION97.58
2.71-2.990.28341330.23081200X-RAY DIFFRACTION98.01
2.99-3.420.26371360.21371225X-RAY DIFFRACTION97.7
3.42-4.310.21161340.17031206X-RAY DIFFRACTION98.24
4.31-37.450.19521340.1751216X-RAY DIFFRACTION98.18
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)
12.818838959670.3222409093610.8285401441272.219329198780.1215827077870.551782044711-0.0244853913329-0.1994228376230.1611071273990.1320397425090.0396084679391-0.08760615412790.0392019540717-0.2329804914470.0001662251678360.2491037509480.01545809016440.002816633536170.283363146594-0.05097174123730.2467440029848.6688870701243.51314647940.437422000126
21.124361063550.9194304849360.530661133830.8803827720720.0793335943941.245448695170.3806747487290.475334622708-0.0564232415685-0.516910270363-0.0964362423530.0794355600132-0.0924337313096-0.0518960660417-8.88079983159E-50.3597182016340.00269166246791-0.008354509056190.3528933094-0.01689727273420.33714044772510.556740738557.44779730767.28898123306
31.209175420351.51111156407-0.2944648173811.89976578243-0.1224952663810.5674590699550.14936806483-0.159321622325-0.07193469599890.186027648804-0.346175060532-0.8732038672690.10954975228-0.174100657733-0.02149700096370.3755125196550.00266422887382-0.004113469830180.2165742300270.002946124964180.26611753521411.98540000638.8925667938-4.11308315578
40.866007082352-0.22718218454-0.506133826060.2729206640350.2058131940860.3182152129360.206077487222-0.3537221726660.322435504179-0.486807825229-0.06003779325210.309583310854-0.3112439559060.270509213661-0.00147989352960.289253288101-0.01648926942660.06246156123870.2476866116990.03494327398710.31328291022815.732125175936.4041303652-0.281921232719
50.5281153320690.1312723237660.4335968372250.68153221281-0.3504238882670.5361521039890.0862998128892-0.078651833272-0.1340505145420.508067649960.01383429222620.130442092789-0.164971187329-0.22063294433-9.8437253207E-50.283218100143-0.0596791489542-0.01386186838360.3824654347170.02769568328580.26682381062910.602225540732.96573933665.71803977527
60.16369785485-0.2301280918720.2150082386491.3488925998-0.5075991370750.316100313224-0.0532662112357-0.261602032987-1.339259709340.6119656074890.0602651021985-0.1331393800380.0560962716131-0.5740546226980.05515324704850.293609461748-0.0123374692037-0.04667987196380.342546408136-0.007268623078930.33283994975310.761068502819.585218478813.1633110274
71.114964099680.266157215657-0.0390826791050.1798465079670.2049821191680.3909373686020.07461269549180.649372273762-0.07100259655730.3264654381480.0964838916878-0.218175718577-0.1405031470340.370667909867-0.001740359528720.302200083706-0.03536021452060.01952755461560.2878084381720.04415953414630.2526249410743.4097936886424.40995211096.63450249889
82.710580605280.475056598144-0.02146066518540.3636921776660.4652870461022.529834478550.350262925282-0.02376536929230.240938692053-0.306831908028-0.3841964685410.0299325683033-0.04330431424020.344219825052-0.0051823634890.292057646606-0.05212673347540.01944514382960.238763507442-0.01656813075310.31051594031613.933504041738.8648212737-3.61165940052
92.905670810480.6745369951781.428047205721.63555468908-0.6755535537621.3951218209-0.0512474886842-0.3178440570150.1053845335860.2446094152390.137248172131-0.05003002531580.0325617963391-0.04698293361357.35219131466E-50.3118201331820.0786898636746-0.00271026045360.304059657365-0.004039822436090.30347345061818.852841978330.358669557522.6338201411
100.481725263427-0.00675800783813-0.5241258932313.924818368630.7223657521990.721117048869-0.2120273508780.4765351602840.166571986287-1.56037419173-0.2518391020061.54947329519-0.66623960928-0.408125887245-0.01580604322540.3372114401770.0089610924672-0.02251659670940.324936470537-0.08388994899060.35045993573214.151249611147.756274187327.9873234549
11-0.01011511003070.005580179733270.00529434044391.346544719630.2726857646640.3612582755160.3697296064470.2921935252680.1202129915380.450949626071-0.600960556799-0.3935081888540.3741926074620.207688927459-0.003605568757070.251287792740.02019440179960.02897737330340.338860604190.004590542412810.30759503868423.925708709342.298593467830.2650482046
120.879322826775-0.336367279328-1.116617655160.2735139518390.7632516936892.166806568840.4146834105150.258353278923-0.156854945294-0.205029158279-0.579711460046-0.141682592305-0.402553790621-0.591829738496-0.1853150663080.3269393996210.0592273635554-0.02549578693780.2053735665910.02931525130960.30987031763322.276981033427.445479985218.2083319808
131.067308781620.2758541959430.2903646605680.344873063484-0.09193073099560.175023214584-0.200296538278-0.7233950449230.404861287626-0.0341180706462-0.0643367689073-0.0793814502429-0.02413948764530.141135120794-0.01788672827960.3458247988330.02396931499060.04010245453590.2697719382860.01823316444670.31090691205926.470668010424.665927867622.4013185152
140.439087902260.1872020116360.39077309081.90748273684-0.05737129661510.361557121987-0.0512884864101-0.3916706200880.0498804847760.7931033568880.1705346054190.33967782786-0.0447169243604-0.2623532791810.0003673589239930.386434073145-0.0288559911240.004606272455620.3252837735680.04700990555720.27159820409619.875845807319.775270020128.0031662906
150.127901349107-0.05317921959410.1488006761070.8902511264410.9481770223761.34817613663-0.531480762228-0.115377165017-0.547999053048-0.2018157054880.1192615478620.140328579436-0.321591654055-0.254583797116-0.03550108200870.244113398604-0.0506209402904-0.02641661658940.3531920488840.06151559922640.34732791915920.21015500277.1111187359135.7641320155
160.5937103231471.490388760550.1166984354318.77566484435-4.844156398995.322616270510.2718259096260.192750523374-0.334388283246-1.23886767235-0.309398350599-0.2801033324640.7396885607610.6790499802440.08921313732930.154370925387-0.03303348618980.001513912643240.3166671371990.06113856583240.28059177034613.002345690411.527745663628.5799317247
170.705069666949-0.0410708240007-1.073276738021.12292522717-0.1828647236292.114833744120.332910924492-0.104017456003-0.03072589587550.764240996494-0.578140699927-0.238936086679-0.2879454452760.367501180436-0.04014449793190.2553271686490.00106303147562-0.003448675016470.2105582137520.01020739173570.23201821642624.594154083423.939986983719.6836277492
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 23 )AA3 - 231 - 21
22chain 'A' and (resid 24 through 34 )AA24 - 3422 - 32
33chain 'A' and (resid 35 through 44 )AA35 - 4433 - 42
44chain 'B' and (resid 4 through 11 )BB4 - 111 - 8
55chain 'B' and (resid 12 through 23 )BB12 - 239 - 20
66chain 'B' and (resid 24 through 28 )BB24 - 2821 - 25
77chain 'B' and (resid 29 through 34 )BB29 - 3426 - 31
88chain 'B' and (resid 35 through 44 )BB35 - 4432 - 41
99chain 'C' and (resid 3 through 23 )CC3 - 231 - 21
1010chain 'C' and (resid 24 through 28 )CC24 - 2822 - 26
1111chain 'C' and (resid 29 through 34 )CC29 - 3427 - 32
1212chain 'C' and (resid 35 through 43 )CC35 - 4333 - 41
1313chain 'D' and (resid 3 through 11 )DD3 - 111 - 9
1414chain 'D' and (resid 12 through 23 )DD12 - 2310 - 21
1515chain 'D' and (resid 24 through 28 )DD24 - 2822 - 26
1616chain 'D' and (resid 29 through 34 )DD29 - 3427 - 32
1717chain 'D' and (resid 35 through 43 )DD35 - 4333 - 41

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