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- PDB-7tav: Crystal Structure of the PBP2_YvgL_like protein Lmo1041 from List... -

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Basic information

Entry
Database: PDB / ID: 7tav
TitleCrystal Structure of the PBP2_YvgL_like protein Lmo1041 from Listeria monocytogene
ComponentsMolybdate ABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / Type 2 periplasmic binding protein / substrate binding domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyYvgL-like, substrate binding domain / Molybdate ABC transporter, substrate-binding protein / : / Bacterial extracellular solute-binding protein / molybdate ion transport / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Molybdate ABC transporter substrate-binding protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKim, Y. / Maltseva, N. / Grimshaw, S. / 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 PBP2_YvgL_like protein Lmo1041 from Listeria monocytogenes
Authors: Kim, Y. / Maltseva, N. / Grimshaw, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 19, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdate ABC transporter substrate-binding protein
B: Molybdate ABC transporter substrate-binding protein
C: Molybdate ABC transporter substrate-binding protein
D: Molybdate ABC transporter substrate-binding protein
E: Molybdate ABC transporter substrate-binding protein
F: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,74633
Polymers152,2296
Non-polymers1,51727
Water64936
1
A: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7207
Polymers25,3711
Non-polymers3486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5434
Polymers25,3711
Non-polymers1723
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6286
Polymers25,3711
Non-polymers2565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5484
Polymers25,3711
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6286
Polymers25,3711
Non-polymers2565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6806
Polymers25,3711
Non-polymers3085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.715, 113.715, 114.598
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Molybdate ABC transporter substrate-binding protein / Molybdenum ABC transporter / periplasmic molybdenum-binding protein ModA


Mass: 25371.494 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: modA / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A5D5LL32

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Non-polymers , 5 types, 63 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Calcium Chloride, 20 % (w/v) PEG 3360

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 42691 / % possible obs: 99.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 54.47 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.176 / Net I/σ(I): 9.58
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 2126 / CC1/2: 0.393 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alpha Fold 2

Resolution: 2.75→37.22 Å / SU ML: 0.2977 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.593
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251 2225 5.24 %
Rwork0.2131 40277 -
obs0.2151 42502 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.75 Å2
Refinement stepCycle: LAST / Resolution: 2.75→37.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10358 0 61 36 10455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001410535
X-RAY DIFFRACTIONf_angle_d0.377614216
X-RAY DIFFRACTIONf_chiral_restr0.03911650
X-RAY DIFFRACTIONf_plane_restr0.00251843
X-RAY DIFFRACTIONf_dihedral_angle_d13.34773944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.810.34771040.30812286X-RAY DIFFRACTION88.98
2.81-2.880.30811760.2922474X-RAY DIFFRACTION97.86
2.88-2.950.29531530.27582490X-RAY DIFFRACTION99.14
2.95-3.030.29431200.26212566X-RAY DIFFRACTION99.63
3.03-3.120.30371440.272526X-RAY DIFFRACTION99.74
3.12-3.220.30211270.26852582X-RAY DIFFRACTION99.78
3.22-3.330.3411240.25092533X-RAY DIFFRACTION99.92
3.33-3.470.31731440.23642524X-RAY DIFFRACTION99.85
3.47-3.620.26641880.23192494X-RAY DIFFRACTION99.89
3.62-3.820.24851150.21762585X-RAY DIFFRACTION99.82
3.82-4.050.27181860.19422495X-RAY DIFFRACTION99.89
4.05-4.370.20231480.17692543X-RAY DIFFRACTION99.89
4.37-4.810.2353980.16972570X-RAY DIFFRACTION99.81
4.81-5.50.20491200.19382552X-RAY DIFFRACTION99.96
5.5-6.920.24951240.21492556X-RAY DIFFRACTION99.78
6.93-37.220.18781540.17352501X-RAY DIFFRACTION98.52
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)
12.26270881011-1.666413131751.044445829413.67463004586-1.233525618162.28280309456-0.0892054068791-0.188452338664-0.02307719998380.06902311601570.0155227989339-0.0020947278857-0.05119635473790.04760803039520.07430095006920.280972352739-0.01795196617990.04248062208250.426738364990.04667078307370.481545819741-45.3996369797-3.95030914314-3.82625481351
23.27499435734-0.140830796561-0.2944006222273.214543916450.3631530112852.2741943711-0.00997916496937-0.157955197373-0.01287426521120.1314788166820.00207713166158-0.166898193287-0.112186039940.1302150997870.001101060187630.449436022946-0.0200226830482-0.002816003095380.4096156439520.03215445745880.503609885346-27.485141902411.82831202582.67062951414
35.187075593550.1484070312430.8561065815290.8859036057280.430996531241.411062347740.0255878285282-0.371281726977-0.2148163763140.110130015510.0289456069107-0.05669695210050.158859777541-0.345256884333-0.06921768527510.555363734129-0.01018679510710.00187450207830.4881977571610.08123255074890.566923654235-44.608800041-8.627967799282.3542637109
43.12243476533-0.3221046837851.005339998452.939388331561.221951437882.78663820499-0.09790254777820.027451934013-0.2770218659490.1396790809470.004089503505980.265556624856-0.08545699325950.2250059761570.1307089800070.396079147458-0.01342767911710.0652886618960.4338281736530.04894917344410.432680268457-25.43198680716.91633843693-20.4887672212
54.55699901154-1.720856894111.321407947091.14376542727-0.2920774267693.283894034840.3833292244890.252338568665-0.170738522815-0.093942223302-0.231334410.5376284243810.221077375165-0.338485893513-0.142960536230.476793422868-0.03085132570610.001544604683810.413098174015-0.07209744748110.501288948035-48.1835822086-1.78235231151-30.6442409204
63.202054551770.5101330287560.4235225697091.394094930450.3249449975531.35455415317-0.05733981236230.155066037269-0.131575030771-0.130244949709-0.0129980474491-0.0614486380976-0.117834214780.02939735333390.05323452755080.4731390107160.00473593985680.06765844560710.388814027840.007888741544430.426724182408-36.103290169-0.188609243674-27.2851687788
74.169393830310.1014172688240.1695590839813.760661756120.2547022908051.71577061765-0.1308553961340.0424571002310.17439846135-0.01434473575860.09437805581430.252882515601-0.0121327951092-0.174887925770.04491531009030.3915802630290.000632678476337-0.01621374431650.4027651574750.003073153971390.357787243429-15.069157818639.62761383368.50981430682
83.96689184237-0.591194256948-1.573610188942.120719118030.2106048641613.770357814830.127287173269-0.4764795273410.109542657080.1097156494810.07547929462260.488000860651-0.1150770272980.133494712635-0.16098588840.4150023131730.0483362350526-0.01294181795560.5346961591330.05453870379940.40516967039-30.319451373760.343826936315.2052770565
93.00730247468-0.6533073013041.230156738082.004248675730.1215943965313.74914613010.1419017803080.129058998634-0.250613733903-0.230710683577-0.0255237039136-0.0769013144316-0.265243997625-0.149832136593-0.1354524445650.4577462832990.08738776903210.002501512419020.4952730798170.01695707658090.567711645191-27.359788373459.579892464210.8176027379
102.38388312492-1.17670264633-0.5796902205783.101251616760.2167008702741.58194485854-0.144864553463-0.1796907888470.2231268675720.4442238384130.2861774645960.1368444568660.1454963196540.0336236122392-0.1426616154740.471547106461-0.0312076094589-0.1082318560470.4642663912740.02666596044330.35381464298-20.254892692249.309134299116.1229752133
111.76490236361-0.8360956109130.5596967941728.960325265041.171792946992.924059228120.00641006703949-0.2947773465980.1014161596630.6057147464410.096340571029-0.7224856380330.2962417649760.129754357774-0.006618333183310.477276229633-0.008493785363-0.06302504668420.606775593184-0.01209314892740.45758252941-7.6786756763842.354817813316.2038419225
124.03627468559-1.457607534070.8846487786822.726482832551.371290266824.102016425080.12430739087-0.0497118847338-0.01228068573970.009071511976970.106900905888-0.382309189460.01188166840920.183581716183-0.1959306865990.505447648971-0.0137999611670.001252145707770.415166849660.055576671130.514983814985-20.093802182160.7509499195-6.90792729153
133.87148751436-1.52474217256-1.640656713453.981503393231.944733114173.68521584520.386097210930.231900445022-0.00666048344489-0.869559639205-0.2291018597950.452030817459-0.223301153695-0.446321812417-0.04148729864090.5026042684660.0610505470603-0.1673363729550.480992324131-0.05404923059790.540031576031-34.064056790457.989723789-15.5736784209
140.7653165109330.379993104289-0.3834456201567.07174672439-1.013798228182.31603300549-0.05489355799830.187574191212-0.218227504063-0.8019937008190.2954719059680.6358910516650.1898442840560.0340016647891-0.1912902974430.392339225604-0.0516908851004-0.08029633192440.5514481419210.004041166816690.497575279481-17.867582302836.688432144-16.7009276953
152.16159967465-0.848642353855-0.9406820518853.11692579956-0.7409153880941.419073403440.118006066898-0.09903836605110.04334706918240.199886093721-0.202777884402-0.1380785295410.0927002148264-0.1450475231520.09251166257050.505802548617-0.040523539134-0.02860867540580.453788930092-0.01523804552730.380942751127-20.11490913237.0179258641-13.8831242762
161.71360162534-0.0315952177906-0.5048601739222.285916829861.04082194591.394038352290.08430350279990.09083291804880.0280622860709-0.271321333827-0.1202405375390.174844703899-0.228786078405-0.0989709504096-0.004866435913440.538190896038-0.053728421319-0.04190604273060.5294895672560.1386230413520.405314883198-20.447391016854.8790359224-16.2756869775
174.42525437054-0.994205885377-1.578539389582.32700869488-0.7924669507174.96898158054-0.3683849718060.4907839268331.15970982053-0.7949513398190.245554387122-1.23776021445-1.3662640990.268438100490.0143123100470.834408945995-0.0867913844173-0.01866543137220.5982822992990.02422491102730.666682231191-11.302689807658.2242231588-20.7076613005
183.546850433440.7590981868680.03909177161472.015049094670.6629776990031.633455442110.1459125439520.184518261364-0.349547385710.0798561873415-0.0324091240317-0.2680501008380.04194756132810.0749592635519-0.08311616570340.51715303429-0.004769954525020.02862905657770.5039481646030.04641917758680.607564744162-8.4362126020828.931837254142.5441561774
190.669022366302-0.3091771556970.4200138888082.948426864761.519580549031.64393319489-0.0232292776050.173339971437-0.2018680813-0.0648036329938-0.2163044290760.2337974389410.0292343203854-0.07514204153540.2347471230.4375044982010.01897180285740.08022736178450.4527235157640.05923885858550.637527722708-21.492418453429.326289253738.806958386
203.79183506398-0.6930658335571.166751289833.60719026754-0.463966847283.16945878201-0.06105110463460.2626898165540.048261834073-0.2238967941380.164152072182-0.08708637870830.138325119168-0.0861985959566-0.07742223269180.454163115734-0.03189577221470.08824418173560.475122175924-0.004305466739990.571711570037-28.38234175129.1960028461835.6955592734
210.8973289633131.501235065580.4379644611293.421226986961.587881138932.12808852725-0.1157526876450.2317422842290.125157714765-0.3581559733060.131632489610.0281709253489-0.354848102183-0.00262427070663-0.01495605285880.4971172151820.06951676891590.1138107682450.4815003940910.02950845211610.545602757233-15.39677390425.191827943832.7179759314
222.91968789956-0.08455729734170.1224058446793.042468227390.785652687342.129240085010.05155175258510.2933586086160.302547714242-0.0844761692098-0.0325877994137-0.469405340173-0.01910953978930.155514392891-0.03328416489820.38677097925-0.0403634307625-0.01304876742340.4011252899790.07426801445070.511946773846-20.65534174819.4441992782956.6394236345
234.583948969470.3230801592571.22699913311.77165524066-1.372087900652.757537454060.176646221132-0.896553004961-0.3146956303590.621381937367-0.277705772062-0.01733181606330.663250555067-0.2113473953210.1213995602460.6739228098-0.04968439099780.00148312663660.4812661125860.03047264359180.584012126812-25.4240617899.1126680519166.3034086938
243.85612541564-1.84154477286-0.1693333601923.822518901890.6996890728013.757991403430.137661316064-0.07074098736650.1997594408310.008625775084950.0124886474027-0.482679899461-0.1689816832370.118652403893-0.1165670235680.437679682801-0.004339423356730.005173149548860.3829523233140.05198057927150.516137250325-21.009844577733.842442689963.7804712881
251.40408911665-0.216098570041-0.2230003828934.580612796671.562327346152.285582091490.0859993708419-0.142056667109-0.2258544283020.414384012766-0.0123567205386-0.4086898085220.354443589788-0.0280276968909-0.08413262962050.495859029412-0.00956817274889-0.04860281778780.5137587542640.07310840631430.57809721557-17.001330107113.322366657565.9448234421
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 83 )AA1 - 831 - 83
22chain 'A' and (resid 84 through 189 )AA84 - 18984 - 184
33chain 'A' and (resid 190 through 230 )AA190 - 230185 - 225
44chain 'B' and (resid 1 through 76 )BC1 - 761 - 76
55chain 'B' and (resid 77 through 131 )BC77 - 13177 - 131
66chain 'B' and (resid 132 through 229 )BC132 - 229132 - 229
77chain 'C' and (resid 1 through 83 )CD1 - 831 - 83
88chain 'C' and (resid 84 through 130 )CD84 - 13084 - 124
99chain 'C' and (resid 131 through 171 )CD131 - 171125 - 165
1010chain 'C' and (resid 172 through 201 )CD172 - 201166 - 195
1111chain 'C' and (resid 202 through 230 )CD202 - 230196 - 224
1212chain 'D' and (resid 1 through 60 )DE1 - 601 - 60
1313chain 'D' and (resid 61 through 76 )DE61 - 7661 - 76
1414chain 'D' and (resid 77 through 118 )DE77 - 11877 - 112
1515chain 'D' and (resid 119 through 171 )DE119 - 171113 - 165
1616chain 'D' and (resid 172 through 213 )DE172 - 213166 - 207
1717chain 'D' and (resid 214 through 230 )DE214 - 230208 - 224
1818chain 'E' and (resid 1 through 27 )EF1 - 271 - 27
1919chain 'E' and (resid 28 through 89 )EF28 - 8928 - 89
2020chain 'E' and (resid 90 through 171 )EF90 - 17190 - 165
2121chain 'E' and (resid 172 through 229 )EF172 - 229166 - 223
2222chain 'F' and (resid 2 through 69 )FG2 - 691 - 68
2323chain 'F' and (resid 70 through 83 )FG70 - 8369 - 82
2424chain 'F' and (resid 84 through 171 )FG84 - 17183 - 167
2525chain 'F' and (resid 172 through 230 )FG172 - 230168 - 226

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