[English] 日本語
Yorodumi
- PDB-3ckm: LpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ckm
TitleLpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A
ComponentsYRAM (HI1655)
KeywordsBIOSYNTHETIC PROTEIN / YraM / periplasmic-binding protein / lipoprotein / unliganded / PBP1A / TRANSPEPTIDASE / PEPTIDOGLYCAN
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
Penicillin-binding protein activator LpoA / LppC putative lipoprotein / Response regulator / Periplasmic binding protein-like I / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Penicillin-binding protein activator LpoA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsVijayalakshmi, J. / Saper, M.A.
Citation
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.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution.
Authors: Sathiyamoorthy, K. / Vijayalakshmi, J. / Tirupati, B. / Fan, L. / Saper, M.A.
History
DepositionMar 16, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionMay 13, 2008ID: 2H4A
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_related / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct / struct_keywords
Item: _struct.title / _struct_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YRAM (HI1655)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3993
Polymers36,2251
Non-polymers1742
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.907, 50.644, 63.676
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-917-

HOH

-
Components

#1: Protein YRAM (HI1655) / LpoA


Mass: 36225.055 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 256-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: YraM / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) pLacI / References: UniProt: P45299
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CHEMICAL IDENTITY OF BME A 583 IS UNKNOWN BUT MODELED AS BETA-MERCAPTOETHANOL

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.49 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0M Li sulfate monohydrate, 2% W/V PEG 8000 and 0.05% BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 165 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97857,0.97843,0.96321
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 28, 2004 / Details: Si(111)Monochromator
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978571
20.978431
30.963211
ReflectionRedundancy: 5.58 % / Av σ(I) over netI: 10.8 / Number: 596801 / Rmerge(I) obs: 0.095 / Χ2: 1.51 / D res high: 1.09 Å / D res low: 47.1 Å / Num. obs: 106384 / % possible obs: 76.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
2.3547.198.70.0713.666.121377
1.872.351000.0991.86.22929
1.631.8799.90.1721.156.16667
1.481.6399.70.2910.986.13284
1.381.4899.30.4590.946.15107
1.291.3897.70.5840.955.7252
1.231.2977.90.6320.934.2117
1.181.23530.6740.963.6410
1.131.1829.90.7050.983.347
1.091.1310.10.7170.982.872
ReflectionResolution: 1.35→47.1 Å / Num. all: 144362 / Num. obs: 143557 / % possible obs: 99.4 % / Redundancy: 3.14 % / Biso Wilson estimate: 14.73 Å2 / Rmerge(I) obs: 0.044 / Χ2: 0.96 / Net I/σ(I): 12.2 / Scaling rejects: 3409
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsΧ2% possible all
1.35-1.43.10.4282.8446484455414456143501.0599.3
1.4-1.453.110.3613.2447124463514402143321.0399.5
1.45-1.523.110.2763.944741446191440814354199.6
1.52-1.63.10.2034.9449334477414452144250.9799.8
1.6-1.73.130.1526.1453204516414439144250.9299.9
1.7-1.833.160.1038.3459604572014481144660.8699.9
1.83-2.023.180.0711.7460584576614418143980.8199.9
2.02-2.313.190.04818.4462794586414399143710.8999.8
2.31-2.913.220.03824470654651314466144410.9799.8
2.91-47.13.10.02538.7447444344214441139951.1396.9

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97863.39-10.06
13 wavelength20.97845.05-8.13
13 wavelength30.96323.72-3.11
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se21.0540.190.0020.1340.623
2Se17.010.8570.3990.2780.533
3Se18.7740.7540.2340.1910.776
4Se16.2390.4320.0370.2330.524
5Se16.5210.3460.2090.3060.519
6Se25.490.7020.3940.0340.537
7Se18.8360.7870.30.0630.628
8Se28.330.1140.460.2490.631
9Se30.6410.540.3080.1320.328

-
Processing

Software
NameVersionClassificationNB
d*TREK9.3Ddata scaling
SOLVE2.06phasing
REFMACrefmac_5.4.0034refinement
PDB_EXTRACT3.004data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.35→38.95 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.159 / SU B: 1.766 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FRIEDEL PAIRS WERE AVERAGED FOR REFINEMENT. RESIDUES 346-359, 428 (SIDE CHAIN), 429, 430 HAVE NO INTERPRETABLE ELECTRON DENSITY. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FRIEDEL PAIRS WERE AVERAGED FOR REFINEMENT. RESIDUES 346-359, 428 (SIDE CHAIN), 429, 430 HAVE NO INTERPRETABLE ELECTRON DENSITY. COORDINATES REPRESENT A HYPOTHETICAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 7201 9.8 %RANDOM
Rwork0.157 ---
obs0.16 73215 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.197 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.35→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 9 353 2795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222503
X-RAY DIFFRACTIONr_bond_other_d0.0010.021609
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9583421
X-RAY DIFFRACTIONr_angle_other_deg1.63633960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.315326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77926.05119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4551510
X-RAY DIFFRACTIONr_chiral_restr0.0070.02386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022866
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02468
X-RAY DIFFRACTIONr_mcbond_it1.6161.51590
X-RAY DIFFRACTIONr_mcbond_other0.8981.5645
X-RAY DIFFRACTIONr_mcangle_it2.45622564
X-RAY DIFFRACTIONr_scbond_it3.533913
X-RAY DIFFRACTIONr_scangle_it5.0184.5853
X-RAY DIFFRACTIONr_rigid_bond_restr1.59834112
X-RAY DIFFRACTIONr_sphericity_free7.7313354
X-RAY DIFFRACTIONr_sphericity_bonded5.23834061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.35-1.3850.2555130.2248155438481597.977
1.385-1.4230.2465030.20647275269472799.26
1.423-1.4640.2574830.18646145127461499.415
1.464-1.5090.2175040.16944775004447799.54
1.509-1.5590.1944390.15943584815435899.626
1.559-1.6130.1764890.14141694669416999.764
1.613-1.6740.1944510.1440894546408999.868
1.674-1.7420.1894110.13439054320390599.907
1.742-1.820.1644300.132377542053775100
1.82-1.9080.1823780.13235983978359899.95
1.908-2.0110.1663910.133340737983407100
2.011-2.1330.1753530.12732503606325099.917
2.133-2.2790.1823260.13830603388306099.941
2.279-2.4610.1823210.142283631572836100
2.461-2.6950.1872940.151261829122618100
2.695-3.0120.2082800.16423772658237799.962
3.012-3.4740.22230.172210823312108100
3.474-4.2460.1722020.15917822001178299.15
4.246-5.970.2041300.17213731550137396.968
5.97-38.9540.288800.24367689467684.564

+
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