[English] 日本語
Yorodumi
- PDB-8ewa: Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (UDP-N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ewa
TitleCrystal Structure of UDP-N-acetylmuramate-L-alanine ligase (UDP-N-acetylmuramoyl-L-alanine synthetase, MurC) Pseudomonas aeruginosa in complex with ligand AZ-13644923
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / SSGCID / murC / Cell wall biogenesis / peptidoglycan biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic 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
Chem-WYI / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)75N93022C00036 United States
CitationJournal: to be published
Title: Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (UDP-N-acetylmuramoyl-L-alanine synthetase, MurC) Pseudomonas aeruginosa in complex with ligand AZ-13644923
Authors: Abendroth, J. / Hill, P. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylmuramate--L-alanine ligase
B: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2787
Polymers67,9532
Non-polymers1,3255
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-51 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.270, 76.950, 110.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein UDP-N-acetylmuramate--L-alanine ligase / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 33976.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: murC, PA4411 / Plasmid: PsaeA.00137.b.B5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HW02, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-WYI / (2R)-2-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2-phenylethyl (2R)-2-(aminomethyl)morpholine-4-carboxylate


Mass: 548.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H36N10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 477 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: Molecular Dimensions Morpheus II, optimization screen around condition A1 and A10: 100mM Tris base/HCl pH 8.6, 11% (w/V) PEG 4000, 18% (V/V) 1,2,4-butanetriol, 30mM lithum sulfate, 30mM ...Details: Molecular Dimensions Morpheus II, optimization screen around condition A1 and A10: 100mM Tris base/HCl pH 8.6, 11% (w/V) PEG 4000, 18% (V/V) 1,2,4-butanetriol, 30mM lithum sulfate, 30mM potassium sulfate: PseaA.00137.b.B5.PW39129 at 12mg/ml + 1mM BSI111803 / AZ13644923: tray: 325495b11: cryo: direct: puck tui7-6

-
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: Oct 6, 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: 1.85→50 Å / Num. obs: 52456 / % possible obs: 100 % / Redundancy: 7.314 % / Biso Wilson estimate: 32.163 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.079 / Χ2: 0.931 / Net I/σ(I): 16.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.97.3870.6343.3338360.9090.682100
1.9-1.957.3940.4744.3737300.9410.51100
1.95-2.017.390.3735.5236290.9560.401100
2.01-2.077.4020.2847.0835460.9740.306100
2.07-2.147.3930.2328.5834090.9820.24999.9
2.14-2.217.3980.18610.3933070.9880.2100
2.21-2.297.3940.15812.1632170.990.17100
2.29-2.397.3940.13313.8930950.9930.143100
2.39-2.497.3810.11415.5729720.9940.123100
2.49-2.627.3880.10217.5428240.9950.109100
2.62-2.767.3530.08520.2927140.9960.09199.9
2.76-2.937.3350.07523.2525740.9960.08100
2.93-3.137.2850.06625.8124060.9970.071100
3.13-3.387.2820.05529.1122710.9980.06100
3.38-3.77.2140.0531.7320710.9980.054100
3.7-4.147.150.04633.919080.9980.05100
4.14-4.787.0880.04435.516990.9970.048100
4.78-5.857.0060.04335.0114440.9980.04799.9
5.85-8.276.8490.04434.3511310.9970.048100
8.27-506.1830.04235.046730.9950.04699

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1 4742refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EGN, same crystal form

8egn


Resolution: 1.85→47.24 Å / SU ML: 0.2126 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 2037 3.88 %0
Rwork0.1672 50416 --
obs0.169 52453 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.73 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 91 477 5050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834752
X-RAY DIFFRACTIONf_angle_d0.95676494
X-RAY DIFFRACTIONf_chiral_restr0.0647758
X-RAY DIFFRACTIONf_plane_restr0.0083852
X-RAY DIFFRACTIONf_dihedral_angle_d14.47821724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.32371440.26663304X-RAY DIFFRACTION100
1.89-1.940.26871480.2133307X-RAY DIFFRACTION99.94
1.94-1.990.20841300.18413313X-RAY DIFFRACTION100
1.99-2.050.24911500.17443305X-RAY DIFFRACTION100
2.05-2.120.23591160.1793341X-RAY DIFFRACTION100
2.12-2.190.23241610.19163299X-RAY DIFFRACTION99.91
2.19-2.280.21381270.17443354X-RAY DIFFRACTION100
2.28-2.390.25971470.17273318X-RAY DIFFRACTION100
2.39-2.510.28151370.17543322X-RAY DIFFRACTION99.97
2.51-2.670.21411440.18463349X-RAY DIFFRACTION100
2.67-2.870.22021420.17423361X-RAY DIFFRACTION99.94
2.87-3.160.20241240.16873388X-RAY DIFFRACTION100
3.16-3.620.20221040.15333429X-RAY DIFFRACTION100
3.62-4.560.15211250.1393444X-RAY DIFFRACTION99.97
4.56-47.240.21571380.15913582X-RAY DIFFRACTION99.87
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)
11.896867348740.00129138550895-0.06786464764362.63444570179-0.6157673165212.121860639240.01840186780160.0502116657307-0.082976905691-0.2150637315660.05699892126610.02992329471960.1560549477570.02913462504-0.04373916370720.145259354199-0.0274379018371-0.0314788134360.143467455565-0.03498050589230.131270803478-24.05322491784.0961536963131.0865568403
24.09195165237-0.00615697314214-1.108130109474.755122434557.51691535158E-53.08036937143-0.0897276339818-0.08238059008430.317534769085-0.0915265460470.1175419503970.454649586733-0.316756104829-0.210004665636-0.02669773855940.1518393385770.000194049752421-0.01130329817630.139055600175-0.002983111625390.177047526556-33.846065132712.299170586538.8700787797
34.717771576581.769440553641.00285660092.004593675030.1843744582393.681382263240.07312522724-0.03918311651990.01839062525510.0282174066078-0.02968129730310.0802867105122-0.0399108981912-0.137529155829-0.04757233911960.1757560715470.0587888906305-0.006446652550770.177663373616-0.02778826782070.1411497034-2.20577493182-1.9003113133148.33862069
42.62375261816-0.017760711814-0.2890382511071.627795534860.1105924513662.725868565990.0495203897756-0.166672726314-0.08285585582890.0356350991962-0.101276848127-0.002845510086810.03803404855030.003972932551010.03468066904520.119223980453-0.002816312052180.000362687592560.09544066976690.03422689165380.13538258124212.2412059503-1.0782242735420.5916387091
52.9389389024-0.474920525993-1.311549896473.978975858320.4087412148513.913226581080.005567871362050.09348951791250.198982784417-0.2620996221260.1075364060770.116208889304-0.3027212829490.131938474716-0.09675621423150.203518497714-0.0429179355611-0.02314600177520.1313327980960.002383242098750.167472755718-10.648525275213.87743947067.34637793997
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 115 through 264 )BD115 - 264103 - 245
22chain 'B' and (resid 265 through 322 )BD265 - 322246 - 303
33chain 'A' and (resid 13 through 114 )AA13 - 1141 - 102
44chain 'A' and (resid 115 through 322 )AA115 - 322103 - 302
55chain 'B' and (resid 13 through 114 )BD13 - 1141 - 102

+
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