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- PDB-7tmu: Crystal Structure of the Protein of Unknown Function YPO0625 from... -

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Basic information

Entry
Database: PDB / ID: 7tmu
TitleCrystal Structure of the Protein of Unknown Function YPO0625 from Yersinia pestis
ComponentsSRPBCC family protein
KeywordsUNKNOWN FUNCTION / Uncharacterized protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily / : / DI(HYDROXYETHYL)ETHER / SRPBCC family protein
Function and homology information
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Protein of Unknown Function YPO0625 from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SRPBCC family protein
B: SRPBCC family protein
C: SRPBCC family protein
D: SRPBCC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,43422
Polymers68,3184
Non-polymers1,11618
Water50428
1
A: SRPBCC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2604
Polymers17,0801
Non-polymers1813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SRPBCC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3586
Polymers17,0801
Non-polymers2785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SRPBCC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3886
Polymers17,0801
Non-polymers3085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SRPBCC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4286
Polymers17,0801
Non-polymers3495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.872, 92.935, 82.991
Angle α, β, γ (deg.)90.000, 92.053, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SRPBCC family protein


Mass: 17079.598 Da / Num. of mol.: 4 / Mutation: The N-terminus residue Met is deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: y3553, YP_2942, EGX46_19825 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A3G5LAW0

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Non-polymers , 6 types, 46 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 10 %(w/v) PEG 8000,10 %(w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 29739 / % possible obs: 96.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 62.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.049 / Rrim(I) all: 0.095 / Net I/σ(I): 20.4
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 1078 / CC1/2: 0.665 / Rpim(I) all: 0.451 / Rrim(I) all: 0.838 / % possible all: 69.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
SHELXDEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.55→37.87 Å / SU ML: 0.317 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.3185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2342 1466 4.95 %
Rwork0.1933 28173 -
obs0.1953 29639 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.06 Å2
Refinement stepCycle: LAST / Resolution: 2.55→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4626 0 59 28 4713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00144775
X-RAY DIFFRACTIONf_angle_d0.41846474
X-RAY DIFFRACTIONf_chiral_restr0.0445720
X-RAY DIFFRACTIONf_plane_restr0.0027834
X-RAY DIFFRACTIONf_dihedral_angle_d12.84021725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.640.35211140.29422174X-RAY DIFFRACTION74.92
2.64-2.750.33441740.28462733X-RAY DIFFRACTION94.72
2.75-2.870.33651470.28022894X-RAY DIFFRACTION99.74
2.87-3.020.3271250.26272914X-RAY DIFFRACTION99.74
3.02-3.210.28141420.23912922X-RAY DIFFRACTION99.8
3.21-3.460.28581780.20782901X-RAY DIFFRACTION99.87
3.46-3.810.26071400.19662910X-RAY DIFFRACTION99.74
3.81-4.360.18421450.16352925X-RAY DIFFRACTION99.77
4.36-5.490.19231490.14692930X-RAY DIFFRACTION99.74
5.49-37.870.19391520.1842870X-RAY DIFFRACTION96.18
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)
13.67181683515-4.168378407371.741482604614.65561595755-2.16832454758.06980173888-0.857478542563-0.2928923758130.04236660921841.038264177011.239979509510.553585624936-0.115973116773-0.737829674823-0.172692388010.645256801113-0.0997447317606-0.08732073723040.5504310706180.09753855932460.86112096406617.61087690613.228789986568.4367369289
23.759382818831.32655199825-0.1599392283962.39966645699-2.212501312.5517752181-0.06220437467570.246331835503-0.0776179730736-1.14070323587-0.168819594684-0.4535115303340.6235371598080.2129413859470.2049616206570.7225920818080.0212728339448-0.05258180677350.787533959419-0.1683147195010.50392740924737.34073198367.3852459800860.9568274836
32.38820467207-1.21158258082.322097734787.783992036541.875375344888.497110361860.9810469833081.60340145985-0.898360637571-2.56796707388-0.1924415639270.03919052778481.513195766230.284563941735-0.720419636671.00220673391-0.0149270798767-0.1262308468060.829384451887-0.07210975513710.56140374108529.892913439616.479414530951.7603385764
49.41160612537-0.6293453249141.140801970388.374627955140.8481816509148.47986839067-0.1286490385880.8064852494910.589338151925-1.114429293280.1173108996070.153051477621-0.171352199022-0.0539381939483-0.1955472237230.57268259192-0.0793393974487-0.04187674829540.573314835853-0.02654902885650.33868728764329.318686092624.116071144456.0135434543
53.739824382330.263421698512.576682005170.1002400117050.07070884138952.19108069278-0.301432371015-0.2569154961320.3625184292931.60194751410.389136364282-0.94768773599-0.5739535208951.20939617588-0.09906426245970.6317453561420.0327317867215-0.1012708591430.653705864787-0.03748282649080.5396822681337.252499402816.186507406869.8686418127
63.20489214063-3.98700362652-0.8696989827948.74668096175-3.121461321283.589014129760.4028860604350.405877102736-0.554047110756-0.57257213356-0.07302021380881.015097169380.235999492002-0.210389910583-0.3855773050950.526773799255-0.0558152083689-0.2199723853330.494830053551-0.1306440304830.49988505285926.698836487315.395974934664.6979056848
76.659574585410.3836905604980.9146442338881.84118278210.01550329434724.267479099510.542236044208-0.0785522174146-0.263193090688-1.132016187890.02905287220981.264009337940.809572764552-0.690522123588-0.4311745152480.607131135552-0.0659766307469-0.2075345825360.56290756636-0.005775067555190.64889837580519.482080842713.834828601765.1984971034
82.55715165262-4.0998564512-0.1748300043189.076059945611.919984134381.443930489260.1550132699340.625504089830.661639071325-0.861620060060.0909267402071-0.2109334617580.504458516511-0.365581150291-0.08959029156751.02515278515-0.242695640956-0.545109698560.7727428142050.05802338548160.89860516211611.874511865712.74857312860.6019231258
92.596238881220.652092958437-1.669061416082.20785889018-1.841474376711.99175339190.1321235732711.71234608913-1.70936628912-1.830111413930.08082375401920.3575165409370.919186268839-0.0436760420567-0.3949678767591.11944526298-0.0307711616034-0.3753660102930.74333989909-0.2256484351680.77641637999227.22182069155.1058224362656.0884700808
105.027768788180.913579704974.841929128187.63817342605-0.1300721106045.278229608760.298714704449-0.01535742849420.6855223826120.0294104335621-0.392354472438-0.5170063009050.409480916559-0.157190285040.2865431100370.569668491429-0.002034946797440.09698554823560.564641267567-0.02872325476720.51495618754613.582813104443.785379830585.7349928119
115.5520019235-1.824279806524.899475990555.60037438302-2.8565699024.562145231250.2825691737570.464285167731-0.473409440042-0.3410555317020.73437075505-1.494797900920.6694104888081.15245262433-0.4901974260910.3235909208040.15786734684-0.1864305516520.626693650606-0.06459257540341.117677257734.995978140240.580690844285.0889657219
125.188861312321.335154432953.251435779525.177507347962.511601597772.752740192190.881136950656-0.366525461312-1.150112161060.566601185897-0.0475829683481-1.694243316951.83713135961.02614981359-0.8700657167850.8151201084010.0866544514435-0.2910452529830.615193421033-0.20870744961.1202860988327.522634885230.922486893176.4201657985
133.312045899353.065029265710.3964190064717.37414580232-2.654371499956.55849723831.313745927930.3105519802580.662909441469-0.168045321381-0.898666686974-2.269726633420.216635778020.759179326516-0.3215295210050.429995213084-0.005230028990190.245129142080.818798759117-0.1883253869391.1751127485830.504039304241.985415839166.5989895319
149.466696114414.60126287882-0.5915942817763.43607046224-3.05984611236.9503980391-0.5693064013420.687372489109-1.39200329288-0.7499018647520.875133322891-0.3584735293191.09734374706-0.272191416328-0.3339129994810.5419682296170.07089824588260.02778624115630.539355579044-0.08842530310340.75507620900520.3962159932.291018518671.9155985446
155.20974569057-4.481804766864.304784443184.16072763196-4.349348605685.04493849119-0.1509394432781.40201163215-0.05682580187950.1792964071720.114007417837-1.61403515688-2.124945992120.784604514406-0.1243437723770.489775998916-0.100258309391-0.03948648029980.592811120293-0.1698538616740.83505904495130.525865438350.190720150978.2559615928
160.8271450241071.324669623212.216965926994.881546367123.060392169665.602303941310.2951296573590.18320048042-0.624541155242-0.1947067398340.139103908921-0.6058412597130.3620424700410.156501434175-0.4333418280590.3078852487910.0319047350114-0.05522780325570.477001603269-0.004748080156590.58987042118120.171650881442.134272625978.2325812558
175.810154556783.049356915676.044246918252.991021482743.86418205025.164528028031.15425988165-0.87793883978-0.5170803913181.13493096996-0.145000532943-1.028038969951.50316005386-0.328185626198-0.9898237875930.7238982325610.0364900131878-0.2207607994230.5315040960990.0864144630180.79827315020725.367360126943.701207412389.3865694085
183.9573284828-0.3627383320114.673770223834.35822265915-1.394368602155.634694696190.639355897116-0.228958710723-0.8427020156930.152214682398-0.2040243178820.5261528383711.54269081461-0.831098545459-0.5242188239980.604959614105-0.1508090079770.02761682817750.6010972302640.08021128123880.7027982623437.8942468124434.683451850982.8674047039
198.28836609325-3.85653791964-4.187464447812.271137726870.4408882313495.728202549580.944496504327-1.41920788264-1.552544928520.775146676237-0.0197587265765-1.422455192481.295346167360.935622194485-0.5048871812840.7927189770340.103697571101-0.4009352067810.6043149534950.06642294681431.2188437379228.521664210632.530656382288.8876422214
201.853237592741.637343184130.6622724791543.845661827120.9085775620643.40591477841-0.3084018746040.191810304590.0109568435463-0.335457329410.189363784551-0.213135099248-0.02146491397520.2543076483270.09462914199980.5864150317820.05528263931730.01480117004660.419430394718-0.009987718249050.446770848564-1.9680200033837.349147040944.3975490251
212.749465163940.5791950052690.674003356583.460155182144.192608533294.03334977236-0.108183883069-0.2533669125480.0380540597292-0.1482750731150.04786480690880.2194584005090.321659399561-0.127309228660.07338653771880.6084394341020.0279174548695-0.005934292258960.4047651666490.04923369580540.447673957379-7.2458610767436.395883880645.1524728069
222.49286448606-1.016252232310.9582193215526.04137707297-0.886261771123.6613772308-0.380437293999-0.06278450830050.1423279525540.3019304727720.0718784981957-0.542480080902-0.5443993855530.3333398835120.305612340820.5540911847990.0241030929404-0.01998622174080.468109751957-0.04566002465480.40833037912411.82039490660.307001619961.7500242984
232.21809950601-4.627561724622.50577865299.98304241273-5.440747348873.054271184060.1187529442181.013201948980.1510214482870.0127059123432-0.3080413267750.127333064706-0.05746471027772.03681942309-0.0004574473847710.503991866790.09452493494040.02216768756020.874113962825-0.07889359455510.72084160110918.916464904548.945295385753.5277809799
246.828172020523.41536740169-1.721379011767.380883930710.906773090836.62414991739-1.90478912617-1.69711958930.506871687921.176876129290.03900020043771.48674205874-0.8395627777321.978850661520.5553507256940.4485649344720.2931223146220.08711676242970.723306338287-0.03299862202980.57107754402911.097031290451.274682231970.4753974192
254.16357775771-0.9797550898730.551762018572.55099046831-1.784984826663.46234202640.0350191727679-0.08323827939730.04031609996840.1487637095740.2847838786980.0254288196633-0.2322939826150.149393321728-0.3945583545020.638642843320.04465841901820.03283839989550.486166147108-0.03472729542270.4728188021017.7830325167852.569090582958.6419255104
263.875945624982.23648632424-1.635719260813.80202794897-3.721690507154.864275539760.00260770941406-0.1575970641780.6097339343850.3923487956470.005633938508160.302147889534-0.4820408748560.120003861842-0.1221076900850.6905210146740.0394223294552-0.04536295718530.493453218944-0.01389032865590.4541793203998.013098891867.462134935454.6429488571
274.498887262923.582725874-1.072235089338.68525611625-1.660128195264.711769988730.0576920564282-0.8927900799030.4598893647640.17188922336-0.2846900394590.762471382209-0.356125347701-0.692805887794-0.07714928281410.8288592166760.2951367726820.1516320069070.7579232093090.003405295167250.531874440343-5.2719522252257.837870713969.3061447385
286.695149461421.87487252727-3.860913171683.75715301213-1.812991980134.623163625890.381890042691-1.079201244110.3453706466181.45972710925-0.311945272292-0.620558417218-0.2779809261390.491935091693-0.03317277170080.8606226715640.0144260799422-0.1061256114910.561636753046-0.0590421590170.54005114707212.197837400468.354803050365.9344801238
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 13 )AA2 - 131 - 12
22chain 'A' and (resid 14 through 25 )AA14 - 2513 - 24
33chain 'A' and (resid 26 through 42 )AA26 - 4225 - 41
44chain 'A' and (resid 43 through 67 )AA43 - 6742 - 66
55chain 'A' and (resid 68 through 75 )AA68 - 7567 - 74
66chain 'A' and (resid 76 through 104 )AA76 - 10475 - 103
77chain 'A' and (resid 105 through 120 )AA105 - 120104 - 119
88chain 'A' and (resid 121 through 131 )AA121 - 131120 - 130
99chain 'A' and (resid 132 through 145 )AA132 - 145131 - 144
1010chain 'B' and (resid 2 through 13 )BC2 - 131 - 12
1111chain 'B' and (resid 14 through 25 )BC14 - 2513 - 24
1212chain 'B' and (resid 26 through 42 )BC26 - 4225 - 41
1313chain 'B' and (resid 43 through 52 )BC43 - 5242 - 51
1414chain 'B' and (resid 53 through 67 )BC53 - 6752 - 66
1515chain 'B' and (resid 68 through 75 )BC68 - 7567 - 74
1616chain 'B' and (resid 76 through 101 )BC76 - 10175 - 100
1717chain 'B' and (resid 102 through 114 )BC102 - 114101 - 113
1818chain 'B' and (resid 115 through 132 )BC115 - 132114 - 131
1919chain 'B' and (resid 133 through 146 )BC133 - 146132 - 145
2020chain 'C' and (resid 0 through 52 )CF0 - 521 - 53
2121chain 'C' and (resid 53 through 145 )CF53 - 14554 - 146
2222chain 'D' and (resid 2 through 44 )DI2 - 441 - 43
2323chain 'D' and (resid 45 through 52 )DI45 - 5244 - 51
2424chain 'D' and (resid 53 through 61 )DI53 - 6152 - 60
2525chain 'D' and (resid 62 through 91 )DI62 - 9161 - 90
2626chain 'D' and (resid 92 through 114 )DI92 - 11491 - 113
2727chain 'D' and (resid 115 through 131 )DI115 - 131114 - 130
2828chain 'D' and (resid 132 through 145 )DI132 - 145131 - 144

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