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- PDB-4p29: Crystal structure of the LpoA N-terminal domain from Haemophilus ... -

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Basic information

Entry
Database: PDB / ID: 4p29
TitleCrystal structure of the LpoA N-terminal domain from Haemophilus influenzae
ComponentsLpoA
KeywordsPROTEIN BINDING / peptidoglycan synthesis / TPR-like / outer membrane lipoprotein
Function / homology
Function and homology information


periplasmic side of cell outer membrane / enzyme regulator activity / peptidoglycan biosynthetic process / regulation of cell shape
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #650 / Penicillin-binding protein activator LpoA / LppC putative lipoprotein / Periplasmic binding protein-like I / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Penicillin-binding protein activator LpoA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95006475032 Å
AuthorsVijayalakshmi, J. / Saper, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI099984 United States
Philip Morris External Research Program United States
Citation
Journal: J.Biol.Chem. / Year: 2017
Title: Structural analyses of theHaemophilus influenzaepeptidoglycan synthase activator LpoA suggest multiple conformations in solution.
Authors: Sathiyamoorthy, K. / Vijayalakshmi, J. / Tirupati, B. / Fan, L. / Saper, M.A.
#1: Journal: Proteins / Year: 2008
Title: Structure of YraM, a protein essential for growth of Haemophilus influenzae.
Authors: Vijayalakshmi, J. / Akerley, B.J. / Saper, M.A.
History
DepositionMar 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_struct_oper_list / software
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.title / _citation.year / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LpoA
B: LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3068
Polymers52,7982
Non-polymers5086
Water4,378243
1
A: LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6834
Polymers26,3991
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6234
Polymers26,3991
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.030, 51.180, 198.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein LpoA / Activator of bifunctional peptidoglycan synthetase PBP1A / Activator of penicillin-binding protein ...Activator of bifunctional peptidoglycan synthetase PBP1A / Activator of penicillin-binding protein 1A (PBP1A) / Outer membrane lipoprotein LpoA / YraM / HI1655


Mass: 26399.178 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 33-253)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: lpoA, HI_1655 / Plasmid: pETBlue2
Details (production host): T7 promoter and C-terminal His6 tag
Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) pLacI / References: UniProt: P45299
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.31 Å3/Da / Density % sol: 46.82 % / Description: unknown
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Drop contained 2 microliters protein and 2 microliters precipitant, and reservoir contained 1 ml of precipitant. Protein:10 mg/ml SeMet-containing LpoA(33-253) in 20 mM Tris-HCl pH 8.0, 0.1 ...Details: Drop contained 2 microliters protein and 2 microliters precipitant, and reservoir contained 1 ml of precipitant. Protein:10 mg/ml SeMet-containing LpoA(33-253) in 20 mM Tris-HCl pH 8.0, 0.1 % beta-mercaptoethanol, 1 mM EDTA, 0.1 mM benzamidine. Precipitant: 0.1 M MES pH 6.5, 0.2 M ammonium sulfate, 30% polyethylene monomethyl ether 5000. Cryoprotectant: 10% glycerol in precipitant solution

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Data collection

DiffractionMean temperature: 165 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2003
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→43.24 Å / Num. all: 68969 / Num. obs: 68183 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.42 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.71 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
d*TREK9.3Ddata scaling
SOLVE2.05phasing
RESOLVE2.05model building
RefinementMethod to determine structure: MIR / Resolution: 1.95006475032→40.4911951555 Å / SU ML: 0.198001494988 / Cross valid method: FREE R-VALUE / σ(F): 1.40176591844 / Phase error: 22.6687988533 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.218489952193 3468 5.1006000706 %Random
Rwork0.1837457267 64524 --
obs0.185541194582 67992 98.6578057664 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.436614756 Å2
Refinement stepCycle: LAST / Resolution: 1.95006475032→40.4911951555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 28 243 3689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004853343971543516
X-RAY DIFFRACTIONf_angle_d0.7199537164984757
X-RAY DIFFRACTIONf_chiral_restr0.0299184064662542
X-RAY DIFFRACTIONf_plane_restr0.00316959475148622
X-RAY DIFFRACTIONf_dihedral_angle_d14.01871205491335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-1.97680.3251451512441380.3004764229152572X-RAY DIFFRACTION99.5591476855
1.9768-2.0050.3366727196271390.2778588305392673X-RAY DIFFRACTION99.9644507643
2.005-2.03490.3285123741171300.2740546538032554X-RAY DIFFRACTION99.9255398362
2.0349-2.06670.2565508610121450.253949995962657X-RAY DIFFRACTION99.9643239386
2.0667-2.10060.244049333441390.2366676901432578X-RAY DIFFRACTION99.8897058824
2.1006-2.13680.2599164345961510.2222696556962634X-RAY DIFFRACTION99.8565794191
2.1368-2.17570.2331145003291420.2061068382422630X-RAY DIFFRACTION99.7481108312
2.1757-2.21750.205689630061420.2008920607392584X-RAY DIFFRACTION99.7073884418
2.2175-2.26280.2267719836741470.2022780033262640X-RAY DIFFRACTION99.8566821928
2.2628-2.3120.2522287659491530.1891971291432554X-RAY DIFFRACTION99.7420781135
2.312-2.36580.2792082043181490.1819112531112580X-RAY DIFFRACTION99.7441520468
2.3658-2.42490.1944426640811580.1866949649912625X-RAY DIFFRACTION99.5350500715
2.4249-2.49050.2326534430971460.1816960791882557X-RAY DIFFRACTION99.741697417
2.4905-2.56380.2022384183251690.1813787899912610X-RAY DIFFRACTION99.7487437186
2.5638-2.64650.2359918169721120.1759544608912606X-RAY DIFFRACTION99.7431192661
2.6465-2.74110.2311323483831450.1840511573612592X-RAY DIFFRACTION99.4549418605
2.7411-2.85080.2307667350571510.1905503937762634X-RAY DIFFRACTION99.2869875223
2.8508-2.98050.2359534644291310.2035447303642613X-RAY DIFFRACTION99.7818181818
2.9805-3.13760.2432545182121070.2042936887552599X-RAY DIFFRACTION99.0120746432
3.1376-3.33410.203437215941210.1901062359432630X-RAY DIFFRACTION99.0994236311
3.3341-3.59130.2142064413861550.1838661941222531X-RAY DIFFRACTION98.1008035062
3.5913-3.95250.2127976118941310.1535667289672573X-RAY DIFFRACTION96.8481375358
3.9525-4.52380.1866644544441230.1423296997832511X-RAY DIFFRACTION96.1313868613
4.5238-5.69690.1609326961311240.1691304268342589X-RAY DIFFRACTION97.6953546993
5.6969-40.49990.2391236121331200.1919943077352198X-RAY DIFFRACTION84.4752186589
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)
10.7205479831810.132000365706-0.08603553263460.3117711819940.3290427118980.1715018932340.118771515517-0.1301137504360.0616203834978-0.307829734422-0.06248055350230.1594505696080.92283156764-0.5894958173840.007234015897180.823846829916-0.215466420015-0.06064950086170.4446119560080.01760758134060.39206333111810.209124684513.65596865259.59838914119
20.6498583138310.07737351160020.1870877976520.302025161824-0.1705812987330.2684396926670.0786320448711-0.04218726038580.1731412425990.409239691186-0.06547136437980.1277130641020.488512670188-0.1632755284250.006768154461340.528926651862-0.02090517543760.01156024944320.329220535618-0.01491663559360.37438262282914.655274198524.030819258713.06929098
30.400307958212-0.6388139017860.2760432368930.0215579043553-0.5391323539412.109204930990.04010976837860.1476630627060.124756250571-0.0699763401239-0.08501075299690.008698588764990.165423888460.069659360369-3.65384114124E-50.3209857947710.0173488735822-0.01227572456340.3296093972080.00480786892510.39523114081216.284281106332.9709604479-3.00164677848
40.988417225617-0.4473410163850.367186718720.920993941097-0.1798212046551.444441528030.2580035785630.3857869956540.103410375905-0.442367143434-0.283607382037-0.150619572838-0.157295853081-0.0338004573207-0.0002568554442210.3377472291170.0530303909843-0.01445842394710.4154724346760.01653034109420.3586686423069.6074288839539.905184459-20.3887734728
50.6696649198850.205154901296-0.09832627938753.03404051430.09124459057691.04100007517-0.02333067355-0.05227277101670.0112456390830.08005854431520.13468965273-0.0780946298738-0.487574038745-1.239415178630.1820778220170.4010564309250.1870433826870.0317687564980.7877328655390.05881818011210.309472970883-21.76793474511.7441487663560.353496055
60.45013903097-0.05941119442090.02579424447880.271058155912-0.1645708065380.875843302218-0.07129908155750.461271974801-0.3921869729410.1612083826840.214954232105-0.3066465459070.4247614113920.03144214545510.01223846895250.369865816045-0.0239159766365-0.01492806512310.4240951256520.002193530577970.413638394949-8.56351809873-6.6045490656255.1768488519
70.09446761133480.1934627904330.0423745441870.406589947417-0.4999343107330.73917409606-0.07341496957090.04763997540580.236963288011-0.0944896635373-0.0546629470613-0.284118551420.186755200398-0.29896309721-0.0001330566936540.372130987051-0.04439096439480.03961580660550.3942261919820.01623181923370.419025562348-4.48849129685-1.5339985322345.7794065303
81.14599313561.572865200680.2486159912191.60465359523-0.6411548013781.66231246968-0.3401897637280.2544947169010.0278052541263-0.221807387450.1934075577830.04146411879430.0542884141537-0.037536887282-7.46982750987E-50.406411515364-0.0325639821910.03851863517830.307311640108-0.008776304786120.369924911148-0.3678964430727.0625707213232.2700062805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 33:75)
2X-RAY DIFFRACTION2(chain A and resid 76:111)
3X-RAY DIFFRACTION3(chain A and resid 112:187)
4X-RAY DIFFRACTION4(chain A and resid 188:248)
5X-RAY DIFFRACTION5(chain B and resid 33:103)
6X-RAY DIFFRACTION6(chain B and resid 104:133)
7X-RAY DIFFRACTION7(chain B and resid 134:166)
8X-RAY DIFFRACTION8(chain B and resid 167:249)

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