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- PDB-7thw: Crystal Structure of the Soluble Domain of the Putative OmpA -Fam... -

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Basic information

Entry
Database: PDB / ID: 7thw
TitleCrystal Structure of the Soluble Domain of the Putative OmpA -Family Membrane Protein YPO0514 from Yersinia pestis
ComponentsPutative OmpA-family membrane protein
KeywordsTRANSPORT PROTEIN / OmpA family protein / Type VI secretion system / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Metal binding protein / UNKNOWN FUNCTION
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
Type IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain
Similarity search - Domain/homology
PHOSPHATE ION / OmpA-family membrane protein
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKim, Y. / Tesar, C. / Chhor, G. / Clancy, S. / 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 Soluble Domain of the Putative OmpA -Family Membrane Protein YPO0514 from Yersinia pestis
Authors: Kim, Y. / Tesar, C. / Chhor, G. / Clancy, S. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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

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Assembly

Deposited unit
A: Putative OmpA-family membrane protein
B: Putative OmpA-family membrane protein
C: Putative OmpA-family membrane protein
D: Putative OmpA-family membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6109
Polymers89,3544
Non-polymers2555
Water59433
1
A: Putative OmpA-family membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3792
Polymers22,3391
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative OmpA-family membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3792
Polymers22,3391
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative OmpA-family membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3792
Polymers22,3391
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative OmpA-family membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4743
Polymers22,3391
Non-polymers1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.861, 123.099, 54.183
Angle α, β, γ (deg.)90.000, 89.965, 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

#1: Protein
Putative OmpA-family membrane protein


Mass: 22338.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: YPO0514 / Plasmid: pMCSG73 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A454Y5W9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 meas: 1.79 Mg/m3 / Density % sol: 31.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.3 M Magnesium Formate 0.1 M Tris:HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 29832 / % possible obs: 93.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 54.74 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 18.5
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 1116 / CC1/2: 0.728 / % possible all: 72.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.59 Å / SU ML: 0.3798 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2688 1468 4.95 %
Rwork0.2263 28216 -
obs0.2285 29684 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 9 33 5021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295102
X-RAY DIFFRACTIONf_angle_d0.54546903
X-RAY DIFFRACTIONf_chiral_restr0.035728
X-RAY DIFFRACTIONf_plane_restr0.0051892
X-RAY DIFFRACTIONf_dihedral_angle_d13.42791875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.40261140.36832181X-RAY DIFFRACTION72.4
2.28-2.370.41751360.34552486X-RAY DIFFRACTION83.48
2.37-2.480.41861260.30042756X-RAY DIFFRACTION90.57
2.48-2.610.31241280.27282961X-RAY DIFFRACTION98.44
2.61-2.770.30051840.25782966X-RAY DIFFRACTION99.12
2.77-2.990.28371590.25672968X-RAY DIFFRACTION97.6
2.99-3.290.29571380.24513010X-RAY DIFFRACTION99.49
3.29-3.760.29581360.22182998X-RAY DIFFRACTION98.46
3.76-4.740.21381640.19412963X-RAY DIFFRACTION97.63
4.74-49.590.25181830.20592927X-RAY DIFFRACTION96.55
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)
13.062565425392.21586540796-0.570605651512.72665919498-1.299726646384.2678125971-0.390979357678-1.57081488873-1.829604277831.200314002170.795117801219-0.7509860011460.710563831007-0.641725591825-0.2796848459840.8999840772550.113678644743-0.1270615737520.7031084110260.2668702671771.070361092045.18528224918-16.0922038723-4.87239135205
22.17986875260.7072529079572.219314906122.159680215443.625229672287.39645923769-0.03774149783150.2834533823930.5596189717620.074090651280.318046536484-0.67849855743-0.5953751198891.38484550362-0.1559671130570.6039536835730.0845484014173-0.1433560883480.4772578078920.1143013649360.81125969146411.4155315712-7.04938112621-2.61510654187
37.160381704631.335400461450.1076478558875.38598979229-1.028637365235.69779446270.451839036951-1.414809593870.6834419750351.62221984716-0.2642721932021.145140814590.976096368554-0.389563045702-0.1880659434430.809427873436-0.1879351201190.1255146595760.725436207631-0.03185558348020.7691297291095.69996940321-0.43477168095510.2323993026
45.281628083530.968626911899-0.8591431368824.242574125580.3988513245477.9538575572-0.0514259221149-1.272837986830.8559725654211.071372932330.801450716549-0.796803200596-0.06900814831412.04050456029-0.02678801616190.750373955696-0.0119300664503-0.1334659304290.6181772766760.07079171499930.68125190129715.34860578113.714799088183.57631833161
57.43954626346-1.37282060884-0.4935658539825.73968778535-0.02411442700685.74188695492-0.370195816711-0.06516860729380.1709009225010.1789920261990.401140858266-0.506167764452-0.07576307337340.5044108619010.07354005799820.440317042208-0.029118347741-0.06131860688970.4127241451610.0560349405130.4083350698849.865180554822.26741177094-6.7011602961
69.202896432210.8473466108950.3984038152775.271060841920.3219702335735.944438171240.454056222-1.91168596952.248992349791.336572951770.067991560225-0.49874672251-0.119212945310.155118525460.1743675193510.826411951576-0.124741767018-0.1423004397970.64885290124-0.007836303005140.7526535736948.8568383728212.48424998310.0925921155052
76.66119049385-0.1337305038181.202262830745.277839878070.8896997067485.88670269128-0.2435297330720.5336399489180.84129230811-0.8220409332470.1528715074650.819523093628-1.05995885688-0.2197525045940.23434161130.635428096255-4.0394468777E-5-0.1388533583270.5029087758710.07535202872180.4705692783461.618433656284.94947967726-13.4921043131
88.94369419911-0.294884645913-0.9333305910986.027990542540.8809223175078.2118528068-0.7673200424020.514402632847-1.49059807214-0.06519920976040.09808803753580.3568015563141.347523435960.06593492436810.03139939167920.550286580415-0.0115756683079-0.006803742374170.51154013749-0.02979985644670.7753111286323.6770793853-6.58860425692-11.1643583488
99.547207806051.049174905781.253276027064.987788120180.501402386345.88233020213-0.375231939646-1.020097885280.5779057216011.04806483022-0.08472708813511.06663277904-0.976217772808-1.901812149910.267386357250.4982327046870.0490812720504-0.0988966598490.658300347245-0.1265425036270.67236750617-8.637599389235.61467876675-5.01356473527
108.63704271102-1.18940420297-0.4660147992266.063137643062.204712061625.034797188690.1649693987951.56029642999-1.42705469011-0.0530299454084-0.5034116929660.8319213746750.84627886065-0.9950643628080.1361650127630.457727822330.00957403932954-0.08471271570160.511977276551-0.1260329671640.578561714179-7.55380106989-6.30129825854-10.5836165494
117.184457042590.131301191938-2.703584565664.641846502280.9219357833194.98599867191-0.2690739375820.730569508032-2.09473816388-0.6811816905871.01982948888-0.01340952159831.60886757063-0.1079651351440.007771163236481.34125114349-0.723139480381-0.1826883831271.297802141820.3398741567671.33078668453-9.37021223886-16.7157518918-9.58428004136
124.11293607420.5605082372980.2008270559481.1007903382-0.6014680225996.589015521580.266453779041.330646670270.966880879513-0.7601559171540.07404450261410.60005587158-0.0524497760163-0.46233457228-0.2157745377060.9638977228670.0880965879764-0.2776168987560.5541597541450.1402025585281.0045338013423.27107215312.7867857558312.4874483628
133.55537599667-2.30510324148-0.1022024116537.477954987640.1880240061119.076845557190.1258045627350.1249860644710.184842961133-0.328090250395-0.03915048663380.119904909432-0.05025119719520.328465621968-0.0956474736470.472073869210.0405622527325-0.01288533243380.4319506300150.04342077959570.46620720961631.7204264154-0.31106810250324.4737887092
147.25437671781-4.07587487768-1.628427801923.75418406045-1.247596054924.277883860760.6119442143711.196199101972.10189175624-1.34474481701-0.389655932455-1.754874131220.32320011783-0.281433858512-0.1546723666391.06067179415-0.104036873429-0.03545936526660.5940986870140.1372183602811.007098100595.20256422937-13.78460451064.80930142469
154.574186792870.316915467635-1.169491573335.142684263143.308519093412.9921305799-0.5198666263680.200422216695-0.171762917747-0.5648532963480.00109682545017-1.604013502990.1451786315681.726605892221.147942247520.499035106206-0.136783683016-0.005441569258680.4638975220220.0091232892760.57646872763711.4750887943-22.86973061212.54761905059
166.483373531021.894437816774.035481375523.04188490501-0.09093847734545.4258129423-0.6180732457882.95063925304-1.20319100281-0.9113275342730.5981962892960.4616631660090.5614624136791.944946771440.351497567510.9132780078050.1215129153440.1288902031010.925495284821-0.1592219303290.735593638815.90746937284-30.3068409667-10.4638734355
177.78822627753-1.565632395050.5867983906767.026746054726.057887068835.15531156847-0.4791254268660.293987589187-0.685338705483-1.540314451280.388268967678-0.480090568509-0.8845680517322.346079650780.4655584954230.801808943603-0.0710164561002-0.1030117825230.5059526540310.1070703166810.69405556878617.284051153-32.1979829467-1.03610042557
184.546272774933.252261170370.3649344872297.15246198574-0.03771174292388.34235582053-0.4843702683430.762357930590.2347073825960.1900617794480.440581039862-0.3960387226910.289953639980.708170035862-0.1164204015510.4258355985890.0804547770658-0.0577811025170.4998165712290.06821505385210.3879222849099.78665916686-32.19107994266.66723550413
199.13370490757-3.083016977230.7051620645542.233798224580.4538185539098.78110239810.1541829628411.61982224332-1.07362991586-1.569823768460.09684088804590.4319045801880.863966393210.780121559885-0.3127336480320.7606993803730.08228787066350.01701246318640.6294609330580.00318860148850.856932387779.11282051416-42.496451060.0375474282412
206.94920496418-0.630212315206-1.702672661246.955504232020.7616943620459.34365949007-0.0291565766786-0.125830809934-0.8435234771720.657370952404-0.0250756983222-0.454531832971.04096882545-0.4513286792560.1331920922860.516302796561-0.0270490318670.07310018241350.4321093092630.07096129264940.4856409078211.61629007956-34.846070307513.4191648594
218.406975029911.526170244881.663570869687.724591151450.1273557318232.62577674657-0.045401370489-0.4696429671490.7695123908470.679677370721-0.07756664165020.192719376622-0.294620768038-0.35311546958-0.1275255661340.62822065322-0.00762211086023-0.09226512163210.61921828349-0.002791692201260.507020424323.66933909301-23.329353995711.0867320937
221.994215122173.497531401812.023908742797.10637769621-1.773202339999.47868281036-2.775504819642.616510952710.00162226611426-1.01991359611.049386382271.70086839221.99861928979-1.752663988381.188044338310.780145879127-0.178602088072-0.04674950441060.645159804509-0.1181982593780.688283556887-8.63614686799-35.60844264734.95709347278
234.394485578274.31562442161-0.663315848414.17024049422-0.4624316492824.306919791690.260088656274-0.3364900438280.9585628426090.819037939670.29425083261.226404821690.7835876934-0.486386648586-0.4893537724670.571678710525-0.06460137028540.007882019113490.605453806677-0.00424301448870.555381010116-8.12707300887-24.340383297810.5572801808
242.910041148863.2497289427-4.491617340873.79981162347-4.127892792241.988676607730.4286713299510.2655894135790.9461168781620.4304558657430.7314266264452.34993502593-3.40471574415-1.81146590795-0.8835653924111.61077345589-0.147399546438-0.533569237144-0.02611495778680.5143830697822.29134667555-7.66564576581-13.68052594659.82334035889
254.08262178341-0.967409618895-5.106834581252.055818054042.584057160387.51840833412-1.043188562662.618900367110.112791811763-0.9782325924580.7482936843271.467619888310.828004340273-0.8200416486660.9057030791211.117578503980.00591365643225-0.07134954071660.8923309058660.1472070761521.4426852922328.999919087-46.5432541416-18.8830476313
262.386956740531.306572542762.292718714131.815228725170.3581975783314.623368042930.0359077200403-0.21801885152-1.567236256941.0610269913-0.0428797325211.50330134233-0.352877984132-0.778555738098-0.4196974355381.18846367544-0.07149213434020.1427541308120.621679909730.1102185391420.88333672811818.5635798371-31.9177372486-15.6285715268
273.70990273782-1.35798568764-2.263054937075.78074308528-0.1635248719156.023948087990.376080252792-2.32838568441-0.5405193761451.73904803346-0.214536434341-0.283346159929-0.3028378018450.799345557418-0.09724160040991.18743330659-0.254786702726-0.1565227111650.7398216900410.1087046608490.76490685467528.5170502099-29.7631088854-7.57960300151
282.34130298977-2.37206601550.2264921864178.64017475992-1.612170830193.28201355925-0.294828125015-0.7543558570510.7934663375351.629602319750.3044797391750.367570899018-0.169849274997-0.580487479815-0.05903080038160.777321316422-0.1678281951810.02467716692940.5745625434640.03647670849930.66328991462329.3280926095-26.2896728726-18.3962866521
299.99163945252-0.395088430435-3.579059928267.780382493730.1301926736042.766195073771.365248094380.001954017901651.067415816380.378881700843-1.12993343105-0.274522708196-2.19386503306-0.376891475154-0.2068849305490.983762915721-0.0735093968062-0.07979687944170.6421950233650.01942018594340.7274669434626.9722023655-17.7689901931-18.9814794643
303.334958212112.31363031255-1.332365292255.350712101731.615413873678.49805775483-0.02121744751-0.013443276191-0.6950656533330.5528129552530.068389076941-0.8863708844140.431572553951.16363300265-0.04107780969170.5925072797650.0401282062448-0.1802044621580.6612422863610.04462452653190.70937469133336.4808993714-33.9901137711-24.4403315809
312.287306830051.10150943589-1.103325297454.263793143310.749624551348.408004326480.7627154356521.214536958330.2127498815980.1747851146430.1675907162750.600076990271-1.19946930799-0.460744846273-0.2194299725890.7538764630090.080713336892-0.07212332935050.7525679889430.04991357534160.65036437961226.3665592696-25.608058481-34.2517508391
322.704297206411.69248832834-0.7648909121186.02164260834-0.8748290418489.082951931330.413638172687-0.271585307952-0.695820572595-0.36634628515-0.191195083431-0.3795317612632.331638120070.751899911612-0.02202279807111.138591007620.0427508981406-0.05281256684050.6770507522920.1915362133120.58936516002532.3471899995-37.8633600963-33.785782222
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 133 through 142 )AA133 - 1421 - 10
22chain 'A' and (resid 143 through 150 )AA143 - 15011 - 18
33chain 'A' and (resid 151 through 162 )AA151 - 16219 - 30
44chain 'A' and (resid 163 through 186 )AA163 - 18631 - 54
55chain 'A' and (resid 187 through 209 )AA187 - 20955 - 77
66chain 'A' and (resid 210 through 227 )AA210 - 22778 - 88
77chain 'A' and (resid 228 through 247 )AA228 - 24789 - 108
88chain 'A' and (resid 248 through 262 )AA248 - 262109 - 123
99chain 'A' and (resid 263 through 274 )AA263 - 274124 - 135
1010chain 'A' and (resid 275 through 291 )AA275 - 291136 - 152
1111chain 'A' and (resid 292 through 297 )AA292 - 297153 - 158
1212chain 'B' and (resid 136 through 186 )BB136 - 1861 - 46
1313chain 'B' and (resid 187 through 292 )BB187 - 29247 - 144
1414chain 'C' and (resid 133 through 142 )CC133 - 1421 - 10
1515chain 'C' and (resid 143 through 150 )CC143 - 15011 - 18
1616chain 'C' and (resid 151 through 167 )CC151 - 16719 - 32
1717chain 'C' and (resid 168 through 186 )CC168 - 18633 - 51
1818chain 'C' and (resid 187 through 209 )CC187 - 20952 - 74
1919chain 'C' and (resid 210 through 227 )CC210 - 22775 - 85
2020chain 'C' and (resid 228 through 247 )CC228 - 24786 - 105
2121chain 'C' and (resid 248 through 262 )CC248 - 262106 - 120
2222chain 'C' and (resid 263 through 274 )CC263 - 274121 - 132
2323chain 'C' and (resid 275 through 290 )CC275 - 290133 - 148
2424chain 'C' and (resid 291 through 297 )CC291 - 297149 - 155
2525chain 'D' and (resid 134 through 142 )DD134 - 1421 - 9
2626chain 'D' and (resid 143 through 169 )DD143 - 16910 - 31
2727chain 'D' and (resid 170 through 190 )DD170 - 19032 - 52
2828chain 'D' and (resid 191 through 209 )DD191 - 20953 - 71
2929chain 'D' and (resid 210 through 234 )DD210 - 23472 - 88
3030chain 'D' and (resid 235 through 262 )DD235 - 26289 - 116
3131chain 'D' and (resid 263 through 274 )DD263 - 274117 - 128
3232chain 'D' and (resid 275 through 292 )DD275 - 292129 - 146

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