[English] 日本語
Yorodumi
- PDB-4p29: Crystal structure of the LpoA N-terminal domain from Haemophilus ... -

+
Open data


ID or keywords:

Loading...

-
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 / peptidoglycan biosynthetic process / enzyme regulator activity / 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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


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


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

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)
10.7205479831810.132000365706-0.08603553263460.3117711819940.3290427118980.1715018932340.118771515517-0.1301137504360.0616203834978-0.307829734422-0.06248055350230.1594505696080.92283156764-0.5894958173840.007234015897180.823846829916-0.215466420015-0.06064950086170.4446119560080.01760758134060.39206333111810.209124684513.65596865259.59838914119
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more