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- PDB-7pv9: Listeria monocytogene InlB (internalin B) residues 36-392 (intern... -

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Basic information

Entry
Database: PDB / ID: 7pv9
TitleListeria monocytogene InlB (internalin B) residues 36-392 (internalin domain and B-repeat)
ComponentsInternalin B
KeywordsCELL INVASION / LEUCINE RICH REPEAT / PROTEIN BINDING / PATHOGENICITY / VIRULENCE FACTOR
Function / homology
Function and homology information


peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal ...GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGeerds, C. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat.
Authors: Geerds, C. / Bleymuller, W.M. / Meyer, T. / Widmann, C. / Niemann, H.H.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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: Internalin B
B: Internalin B
C: Internalin B


Theoretical massNumber of molelcules
Total (without water)121,2653
Polymers121,2653
Non-polymers00
Water0
1
A: Internalin B


Theoretical massNumber of molelcules
Total (without water)40,4221
Polymers40,4221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Internalin B


Theoretical massNumber of molelcules
Total (without water)40,4221
Polymers40,4221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Internalin B


Theoretical massNumber of molelcules
Total (without water)40,4221
Polymers40,4221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.490, 148.410, 220.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 36 through 353 or resid 373 through 391))
d_2ens_1(chain "B" and (resid 36 through 353 or resid 373 through 391))
d_3ens_1chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUGLNA1 - 318
d_12ens_1ASNGLUA338 - 356
d_21ens_1GLUGLNB1 - 318
d_22ens_1ASNGLUB338 - 356
d_31ens_1GLUGLUC1 - 337

NCS oper:
IDCodeMatrixVector
1given(0.999549117063, -0.0268389989223, 0.0134621958238), (0.026269890277, 0.998821714912, 0.0408053266762), (-0.0145415076378, -0.0404332778434, 0.9990764208)-0.474219594221, -46.8573849964, 0.54177715719
2given(-0.998642235565, 0.052049082464, 0.00213971050509), (0.0520916566761, 0.997472976394, 0.048312738156), (0.000380330286203, 0.0483586019033, -0.998829965996)-44.6582297071, -20.0008996878, -111.552683905

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Components

#1: Protein Internalin B / InlB / Invasion protein InlB


Mass: 40421.789 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: inlB, lmo0434 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P0DQD2

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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 Å3/Da / Density % sol: 59.5 % / Description: rod-shaped (roughly 0.01 x 0.01 x 0.08 mm)
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Reservoir solution (Morpheus screen (Molecular Dimensions) condition E6): 0.1 M (HEPES sodium salt / MOPS acid), pH 7.5, 20 % v/v ethylene glycol, 10 % w/v PEG 8,000, 0.03 M diethylene ...Details: Reservoir solution (Morpheus screen (Molecular Dimensions) condition E6): 0.1 M (HEPES sodium salt / MOPS acid), pH 7.5, 20 % v/v ethylene glycol, 10 % w/v PEG 8,000, 0.03 M diethylene glycol, 0.03 M triethylene-glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol; Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl; Drop size: 100 nl + 100 nl (protein + reservoir)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9164 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9164 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 22938 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 56.76 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.34 / Net I/σ(I): 6.49
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 1677 / CC1/2: 0.6 / Rrim(I) all: 1.205 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSVERSION Jan 26, 2018 BUILT=20180307data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180307data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H6T, 2Y5P

1h6t

2y5p


Resolution: 3.3→48.27 Å / SU ML: 0.4463 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Reference model restraints were used with PDB ID 7nms as reference model. NCS restraints were used during refinement. TLS refinement was used with TLS groups automatically determined by phenix.refine.
RfactorNum. reflection% reflection
Rfree0.2723 1112 4.87 %
Rwork0.2303 21712 -
obs0.2324 22824 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.47 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8279 0 0 0 8279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00278431
X-RAY DIFFRACTIONf_angle_d0.631311451
X-RAY DIFFRACTIONf_chiral_restr0.04921357
X-RAY DIFFRACTIONf_plane_restr0.00461460
X-RAY DIFFRACTIONf_dihedral_angle_d11.99563148
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.664562055878
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS2.03515699394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.450.36021260.31352698X-RAY DIFFRACTION99.93
3.45-3.630.34141130.27742656X-RAY DIFFRACTION99.86
3.63-3.860.30711450.24982639X-RAY DIFFRACTION99.71
3.86-4.160.31851220.23252702X-RAY DIFFRACTION99.89
4.16-4.580.26111530.19852693X-RAY DIFFRACTION99.89
4.58-5.240.20581340.1862709X-RAY DIFFRACTION99.79
5.24-6.590.25041530.21962748X-RAY DIFFRACTION99.9
6.6-48.270.24821660.22342867X-RAY DIFFRACTION98.73
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)
10.478725429080.4225271449090.4459913084570.4767627209140.1175736938572.03238327493-0.09196788110650.08821063960950.0268216977835-0.2592650949370.1261663851070.0973529248674-0.361952494862-0.009564372406910.2955254725660.9770273795370.171470306812-0.2880855205730.986702380394-0.1957370072220.363539394456-28.8645388024-33.1391809605-65.0854237001
20.1613887968110.09902600683840.1471771132920.06325076794270.06217268592170.458891199603-0.0457866115776-0.03868169329660.0452844474216-0.203296387583-0.0462555549910.0656010884874-0.0807726448987-0.308838155452-0.445186632950.7356380706420.0325597303902-0.2391830464430.262957421137-0.09476266870420.0173849684701-20.8320280507-30.275396844-56.1050591792
33.064765182150.4475704738020.1266321693395.04972151046-2.760337362742.293913615050.02158564125540.337788846349-0.0632298568172-0.665468496836-0.440255914579-0.132464215626-0.188685597636-0.5915006306190.4307679341340.562999250522-0.0006312766590480.02629568427640.58690976855-0.04766498406490.18485069136-14.375732767-29.8626959445-46.9166663829
43.120394465781.371353855132.516685266454.561283779951.281904291593.16423358313-0.0232853619290.535888330338-0.11391586021-0.527903050089-0.0126525952727-0.227527983340.447061648322-0.527973897595-0.05268711876970.5256373906320.1406384672150.01502690650170.681682126532-0.03836294893170.22645605378-9.77490309935-27.7278014351-38.4149935066
50.72461006893-0.7435334869770.04468505281150.9338381496220.09421691938660.1167603245190.15748242156-0.0410428356581-0.214158715635-0.0632287933183-0.3560004310620.101991393984-0.0268747486190.0243430210709-0.1719233063890.2157128619160.06569505493520.01564241115680.898196566860.04378000031580.255619282763-8.05066048635-20.3306081895-28.9429729967
60.8664275876220.612481893645-0.7166945112840.475478859929-0.1537397849413.20327892753-0.269585231939-0.0699416906152-0.158359923563-0.0654820469655-0.0342481055077-0.0339933843642-0.00113123442255-0.184335765713-0.2952842922560.2214056646030.08374183762280.01730793992290.736077533247-0.06944152742840.273634790577-12.6539455436-26.9446410094-11.1749010334
73.114215442351.0376933607-1.523637848441.96805656976-0.3834552643780.7611307747540.108552130236-0.186363589773-0.07042134716570.089178853445-0.0887421974423-0.0128226802275-0.002756812661010.2861559636790.1679202327390.178271073227-0.05141780468890.03927816475070.5527337007650.05205237909240.243383579565-11.8562717276-22.0024761874-4.65757787718
81.084921311231.37879204118-1.11617884613.02132440616-2.4754418172.575288250290.4132038721810.25600044260.3980332583010.0568409488178-0.07577576962390.80505790565-0.198995505155-0.00799034587574-0.4046279984570.2207573634140.06342370531920.03614600854850.6652525556460.01266483028090.37047936805-13.8100529962-17.8672041034-16.3532366581
92.65924277066-0.3422977312930.424325178660.9338001609660.3158853573340.334865587565-0.258459993250.0287547636798-0.275701471357-0.03104491002340.3195641145640.00340466262265-0.1297187159680.184983696987-0.0395268873040.233118211582-0.04670776180630.00947027711780.816371646799-0.0177320766140.298443207244-8.72458858089-55.97847606639.70856937412
103.18867976595-0.846501356898-1.259054646991.88164170270.865880151571.0648432887-0.2294012473730.169566516509-0.01276174195180.1624309262860.2131624508510.04222465617310.1496078196570.0325204165557-0.1004451548230.2566948215170.1420824506890.02147898322030.770160544457-0.005838992916820.317558456712-12.182290782-57.728570729310.0357333916
113.41715715775-1.792396782311.490505613075.62277909095-2.726554356232.55223465798-0.10921633340.3487830376510.160371295028-0.560482748754-0.159063544156-0.06063688091880.3536066362950.174013696637-0.004869397863240.9177051173520.394447908069-0.06638628200650.9974863055620.2317527168920.579682903575-27.37653040317.4507997483-65.0222710311
122.467636589980.560053032622-0.3030398236552.465767381320.7971750003794.37040511168-0.354785636094-0.0657505230403-0.410226430497-0.742675188632-0.231435025728-0.405021656087-0.401565883232-0.09597703997810.2485455668730.691956522343-0.1142810259240.01869250988550.7531678541940.2652279520510.488907000618-19.053340292219.3089808951-56.0797632376
131.74218481632-0.113944120731-0.8005050903330.3896839946740.01761421610330.37563851791-0.2825741639420.575009838801-0.0921164190862-0.332930555419-0.0632157914544-0.032245381149-0.1678643762330.0309026039488-1.115835199870.559012315143-0.17550309382-0.154710020190.6997636208650.2705544202650.394057464413-8.4065932756123.1089156724-36.7491038916
142.153471617631.0156187586-0.9621091250245.01717950981-1.835677934311.458807296120.0540294638365-0.2221835617940.5358820262110.789945820214-0.2255545286040.571071488638-0.596861756215-0.2883604684350.2099618963890.622393702433-0.13572326116-0.08902884447040.722248817380.06202528189210.457892224848-11.542099344625.3621274057-9.9375969528
150.864456651740.08492293412410.007487538560160.1225135932580.1200832633430.112541838469-0.116087832037-0.0173936477685-0.2132330057790.008335238998420.06294982328190.139189409472-0.03254691368890.199473696494-1.022777811310.06885074700360.0790603463265-0.03640773924550.977933577940.01008847814260.332723106239-9.60884773716-9.605990948598.92191397755
161.99518857607-1.360372553482.259849775643.15724473888-0.2909355922465.17990610101-0.247701800762-0.0479979201289-0.2180950062960.1740192295630.1628893582790.239723620705-0.08553594534630.005908710871670.05361511557130.3682666542330.0507661034826-0.0342657119770.8037483630230.02498550790250.319195900642-21.8500606637-6.20042517221-51.3259496602
175.64331321830.7088999307071.692062170214.20914214391-1.674236935812.328827035660.54268180263-0.119030243784-0.2421241068640.374042069747-0.2452558741370.01220212429850.2108960427230.342533414586-0.3626889048360.381157176361-0.022387551938-0.0903203664420.5662696010710.06677597559480.196142049506-30.9922712791-4.34777840538-64.4698298605
180.379191040345-0.2906498509440.1409531209090.26825252692-0.3367821524231.059731092760.024437201189-0.0932901846013-0.1097691741020.116628745150.1348164308690.0263778771131-0.139759102497-0.3274666498820.1926750990030.191476908155-0.0383506941785-0.04171389530860.8677664617990.07170517939370.302326861106-35.46597341522.32578972752-83.718320724
191.127572979920.14067752891-0.7846435897821.05539924123-0.2686461194360.6014770022610.02675352786830.221814767629-0.286184761703-0.168244676576-0.325218715002-0.2581723918870.05013389733740.0120251543322-0.09336629048180.235834210320.05659653048920.04629021191210.8173203297830.01452270540160.316956779938-29.90616860975.45271586401-105.70534662
201.776126654150.2788602855651.318233539851.24224187331.111416967152.654574099720.207704102320.222531639813-0.4789831418470.1620361780080.312881224377-0.360761162190.5720041756820.834060889906-0.6858520691220.456201260496-0.0185266237962-0.1499185645590.7863529064610.1607655902080.458452967704-34.4730126001-12.9281462345-108.03885236
211.77038257636-0.725868008401-1.133238539621.17933744319-1.196649844453.856648810860.477347076274-0.0663007823644-1.293156144970.8666449955040.133234388318-1.743797580670.419318274838-0.600308408936-0.405080609960.59886324493-0.0900870687346-0.2235974224580.510667642139-0.08540146840160.961484066151-36.2390357834-32.2897829784-118.656855841
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 36 through 71 )BB36 - 711 - 36
22chain 'B' and (resid 72 through 123 )BB72 - 12337 - 88
33chain 'B' and (resid 124 through 148 )BB124 - 14889 - 113
44chain 'B' and (resid 149 through 192 )BB149 - 192114 - 157
55chain 'B' and (resid 193 through 233 )BB193 - 233158 - 198
66chain 'B' and (resid 234 through 256 )BB234 - 256199 - 221
77chain 'B' and (resid 257 through 292 )BB257 - 292222 - 257
88chain 'B' and (resid 293 through 318 )BB293 - 318258 - 283
99chain 'B' and (resid 319 through 371 )BB319 - 371284 - 336
1010chain 'B' and (resid 372 through 391 )BB372 - 391337 - 356
1111chain 'A' and (resid 36 through 71 )AA36 - 711 - 36
1212chain 'A' and (resid 72 through 123 )AA72 - 12337 - 88
1313chain 'A' and (resid 124 through 233 )AA124 - 23389 - 198
1414chain 'A' and (resid 234 through 318 )AA234 - 318199 - 283
1515chain 'A' and (resid 319 through 391 )AA319 - 391284 - 356
1616chain 'C' and (resid 36 through 123 )CC36 - 1231 - 88
1717chain 'C' and (resid 124 through 148 )CC124 - 14889 - 113
1818chain 'C' and (resid 149 through 268 )CC149 - 268114 - 233
1919chain 'C' and (resid 269 through 304 )CC269 - 304234 - 269
2020chain 'C' and (resid 305 through 349 )CC305 - 349270 - 314
2121chain 'C' and (resid 350 through 391 )CC350 - 391315 - 337

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