[English] 日本語
Yorodumi
- PDB-8dp2: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dp2
TitleCrystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine)
ComponentsUDP-N-acetylmuramoylalanine--D-glutamate ligase
KeywordsLIGASE / SSGCID / UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase / MurD / UMA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
ACETATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / PHOSPHATE ION / SUCCINIC ACID / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine)
Authors: Abendroth, J. / DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9509
Polymers48,3481
Non-polymers1,6028
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.460, 95.460, 99.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase


Mass: 48348.320 Da / Num. of mol.: 1 / Fragment: PsaeA.17938.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: murD, PA4414 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HVZ9, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

-
Non-polymers , 8 types, 524 molecules

#2: Chemical ChemComp-UMA / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE


Type: L-peptide linking / Mass: 750.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36N4O20P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#7: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RigakuReagents JCSG Top96 screen, condition b1: 100mM HEPES free acid / sodium hydroxide pH 7.5, 30% (V/V) PEG 400, 5% (w/V) PEG 3000, 10% (V/V) Glycerol: PsaeA.17938.a.B2.PS38065 at 40mg/ml ...Details: RigakuReagents JCSG Top96 screen, condition b1: 100mM HEPES free acid / sodium hydroxide pH 7.5, 30% (V/V) PEG 400, 5% (w/V) PEG 3000, 10% (V/V) Glycerol: PsaeA.17938.a.B2.PS38065 at 40mg/ml + 3mM UMA (BSI102034) and MgCl2: tray: 325018b1: cryo: direct, puck: tua1-2. SIN is modeled tenatively based on density only, it was not added to the crystallizaton buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 9, 2022
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 67812 / % possible obs: 100 % / Redundancy: 8.964 % / Biso Wilson estimate: 28.069 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Χ2: 0.952 / Net I/σ(I): 20.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.645.8310.5932.3150050.8090.653100
1.64-1.697.4920.4893.4348750.9020.526100
1.69-1.749.0810.44.8947250.9510.424100
1.74-1.799.4310.3026.6246140.9760.32100
1.79-1.859.4350.2368.5344440.9850.25100
1.85-1.919.4570.17911.3343330.990.19100
1.91-1.989.4610.13814.7541550.9940.146100
1.98-2.079.4670.10918.5840250.9960.115100
2.07-2.169.4610.09322.0538470.9970.099100
2.16-2.269.4520.08125.2336840.9970.085100
2.26-2.399.4480.07228.2135110.9980.076100
2.39-2.539.4370.06431.233040.9980.067100
2.53-2.79.3980.05733.8631150.9980.06100
2.7-2.929.3780.0537.9729080.9990.053100
2.92-3.29.2810.04641.1626850.9990.048100
3.2-3.589.1740.0445.3224100.9990.043100
3.58-4.139.10.03847.2821400.9990.04100
4.13-5.069.1340.03548.7818280.9990.037100
5.06-7.169.2860.03348.4314110.9990.035100
7.16-508.8280.03248.67930.9990.03499.4

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ADP-bound MurD, pdb entry 7U35, in three domains

7u35


Resolution: 1.6→41.34 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 1964 2.9 %0
Rwork0.15 65778 --
obs0.1506 67742 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.91 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 104 516 3994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893651
X-RAY DIFFRACTIONf_angle_d1.04794967
X-RAY DIFFRACTIONf_chiral_restr0.0688566
X-RAY DIFFRACTIONf_plane_restr0.0091659
X-RAY DIFFRACTIONf_dihedral_angle_d14.49351387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.24941370.21724681X-RAY DIFFRACTION99.96
1.64-1.680.21371350.18174706X-RAY DIFFRACTION99.98
1.68-1.730.21360.17814671X-RAY DIFFRACTION100
1.73-1.790.19861150.1724696X-RAY DIFFRACTION99.96
1.79-1.850.20311460.17784671X-RAY DIFFRACTION100
1.85-1.930.19611330.14754683X-RAY DIFFRACTION100
1.93-2.020.17191610.14774690X-RAY DIFFRACTION100
2.02-2.120.17751340.14194731X-RAY DIFFRACTION100
2.12-2.260.15341260.14994672X-RAY DIFFRACTION100
2.26-2.430.16691440.14284705X-RAY DIFFRACTION100
2.43-2.670.18021580.16034665X-RAY DIFFRACTION100
2.67-3.060.18921270.14964751X-RAY DIFFRACTION100
3.06-3.850.14171370.14014713X-RAY DIFFRACTION100
3.86-41.340.15611750.14084743X-RAY DIFFRACTION99.94
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)
12.852158278240.146724373796-0.3080066347962.92231697210.618208085653.63450637783-0.1786649509840.02185188213440.4900785855720.04179259493940.158121948762-0.290861407974-0.352583102730.6160594041180.02212440843420.199133939258-0.0453365196218-0.06113002153950.241766420663-0.01870741093320.28928967728865.97557971529.719871048259.79152770562
21.19504512172-0.1720079593090.18969993510.7359989394440.1014775807051.04082784086-0.0275402777265-0.0064153682085-0.08243712540640.00752035208542-0.01232554699170.01028503768550.0145476776354-0.05613442603950.03733922483740.1372763623720.0004514532819980.003765419592590.0842999091304-0.001792273545820.10590813525740.3584387816-2.218285589520.367960683994
31.71598332864-0.5714946455180.04327097699051.464575206440.1605170091663.711673119880.08083183026980.03492007625420.0438033270981-0.06425032228520.0112367141856-0.0645446134090.0208101188760.0500138679297-0.07971321267580.1155024726940.008647410286750.02803927108590.0890918786101-0.008631900787860.16360119972854.7648114508-16.5788757365-18.4868892316
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 75 )3 - 751 - 73
22chain 'A' and (resid 76 through 310 )76 - 31074 - 308
33chain 'A' and (resid 311 through 448 )311 - 448309 - 446

+
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