[English] 日本語
Yorodumi
- PDB-4eg0: Crystal Structure of D-alanine--D-alanine ligase from Burkholderi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eg0
TitleCrystal Structure of D-alanine--D-alanine ligase from Burkholderia ambifaria
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7657
Polymers67,4542
Non-polymers3105
Water6,972387
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-6 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.380, 118.110, 56.930
Angle α, β, γ (deg.)90.000, 91.560, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

-
Components

#1: Protein D-alanine--D-alanine ligase / D-Ala-D-Ala ligase / D-alanylalanine synthetase


Mass: 33727.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: ddl, BamMC406_0490 / Production host: Escherichia coli (E. coli) / References: UniProt: B1YSS6, D-alanine-D-alanine ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus condition A12: 0.06 M magnesium chloride, 0.06 M calcium chloride, 0.1 M TRIS-Bicine, 37.5% MPD/PEG1000/PEG3350, 20.26 mg/ml BuamA.00119.a.A1 PS01236, pH 8.5, VAPOR DIFFUSION, ...Details: Morpheus condition A12: 0.06 M magnesium chloride, 0.06 M calcium chloride, 0.1 M TRIS-Bicine, 37.5% MPD/PEG1000/PEG3350, 20.26 mg/ml BuamA.00119.a.A1 PS01236, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 76670 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.182 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 17.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.690.4782.2914782554297.9
1.69-1.740.3553.0614515540097.7
1.74-1.790.2673.9814219526497.5
1.79-1.840.2264.6913758508197.5
1.84-1.910.1716.2112996483296.2
1.91-1.970.1238.3912709468596.4
1.97-2.050.09410.5612598458996.4
2.05-2.130.07213.5111736428995.7
2.13-2.220.05616.6111581417895.4
2.22-2.330.04719.7710847390494.5
2.33-2.460.03922.7810547376894.4
2.46-2.610.03525.629888350893.8
2.61-2.790.02929.449300328293.5
2.79-3.010.02733.588619304492.4
3.01-3.30.02338.17810275891.8
3.3-3.690.02243.17056248690.6
3.69-4.260.02245.976134218590.6
4.26-5.220.0248.685457185090.1
5.22-7.380.02148.84260141088.8
7.380.01850.71204670579.6

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IOV

1iov


Resolution: 1.65→40.978 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8723 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 3840 5.02 %RANDOM
Rwork0.1733 ---
obs0.1747 76559 99.87 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.279 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 90.24 Å2 / Biso mean: 31.1757 Å2 / Biso min: 10.71 Å2
Baniso -1Baniso -2Baniso -3
1-6.1947 Å2-0 Å2-1.6442 Å2
2---6.1428 Å20 Å2
3----0.0519 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 20 387 4678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184448
X-RAY DIFFRACTIONf_angle_d1.746058
X-RAY DIFFRACTIONf_chiral_restr0.131697
X-RAY DIFFRACTIONf_plane_restr0.009797
X-RAY DIFFRACTIONf_dihedral_angle_d12.5771601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.67080.29781500.276127562906100
1.6708-1.69280.2821360.256826222758100
1.6928-1.71590.28561390.253527122851100
1.7159-1.74050.23741300.216326942824100
1.7405-1.76640.27121370.219826812818100
1.7664-1.7940.22851350.21127292864100
1.794-1.82350.24231490.207426472796100
1.8235-1.85490.261480.215127012849100
1.8549-1.88860.23361490.185627072856100
1.8886-1.9250.22761310.183126662797100
1.925-1.96420.22381320.172126852817100
1.9642-2.0070.2221500.177826852835100
2.007-2.05360.19911210.174627272848100
2.0536-2.1050.19511480.168727112859100
2.105-2.16190.19941330.166826662799100
2.1619-2.22550.20851500.173326832833100
2.2255-2.29730.21721360.160626942830100
2.2973-2.37940.19651450.171226922837100
2.3794-2.47470.18321420.169926852827100
2.4747-2.58730.20231450.167227002845100
2.5873-2.72370.20831460.17126902836100
2.7237-2.89430.18891430.177426862829100
2.8943-3.11770.20161270.183627102837100
3.1177-3.43130.19011660.175626832849100
3.4313-3.92750.1941720.157426812853100
3.9275-4.94690.15941420.138727282870100
4.9469-40.9780.18951380.17532698283698
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)
15.16770.0757-0.40573.6227-0.40462.7681-0.0973-0.533-0.09840.92840.1043-0.01290.1223-0.169-0.02220.41090.00460.03940.1905-0.02260.13458.872119.650435.1807
21.0264-0.5283-0.30890.94050.67061.7065-0.1514-0.1267-0.08140.23110.05620.07610.20840.15280.09280.14950.01350.01280.11730.01480.161718.588411.899618.692
35.15350.51871.87643.8370.24582.74550.3565-0.0858-0.37760.3551-0.1733-0.42130.2103-0.0403-0.15810.1092-0.0301-0.03210.23370.02220.288439.334918.11088.819
41.1329-0.3263-1.81712.8727-0.35243.82190.1006-0.04620.2089-0.0380.00960.1086-0.2821-0.0126-0.09910.07820.0004-0.01880.11870.00570.143315.156830.217.4168
51.39510.0896-1.26181.4311-0.62233.47790.0364-0.00690.04620.136-0.03030.214-0.2319-0.19980.01140.08670.0092-0.00090.1344-0.0110.155211.508722.885413.7283
63.4961-0.28640.8794.07140.8424.7198-0.2088-0.56760.12350.71530.14020.1706-0.36270.26670.07790.43710.0525-0.02720.16180.00260.171728.4035-7.314336.4414
70.7484-1.62760.1883.9479-0.05220.3659-0.4003-0.393-0.08851.12630.34480.6103-0.2937-0.166-0.04190.53170.10830.10260.25950.06440.245723.2645-9.77538.2643
80.8358-0.1634-0.16720.8813-0.38932.3193-0.072-0.1170.01280.33480.0794-0.1007-0.1559-0.0745-0.00510.23580.0307-0.01340.1063-0.00630.127722.6637-0.312221.5891
90.51710.31590.25422.8949-0.24682.93240.21250.2421-0.0588-0.1356-0.20731.50020.0347-1.2976-0.04870.1640.024-0.08710.4659-0.10950.55947.8102-6.56960.6447
100.958-0.60210.24012.59870.54613.62690.0005-0.0281-0.10110.1808-0.0213-0.03040.1995-0.01990.00270.1141-0.01280.00290.11370.00630.11930.2011-14.82814.3651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:64)A4 - 64
2X-RAY DIFFRACTION2(chain A and resid 65:121)A65 - 121
3X-RAY DIFFRACTION3(chain A and resid 122:184)A122 - 184
4X-RAY DIFFRACTION4(chain A and resid 185:240)A185 - 240
5X-RAY DIFFRACTION5(chain A and resid 241:311)A241 - 311
6X-RAY DIFFRACTION6(chain B and resid 4:21)B4 - 21
7X-RAY DIFFRACTION7(chain B and resid 22:62)B22 - 62
8X-RAY DIFFRACTION8(chain B and resid 63:117)B63 - 117
9X-RAY DIFFRACTION9(chain B and resid 118:185)B118 - 185
10X-RAY DIFFRACTION10(chain B and resid 186:311)B186 - 311

+
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