[English] 日本語
Yorodumi
- PDB-9erq: Citramalate lyase - AMPPNP- citramalate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9erq
TitleCitramalate lyase - AMPPNP- citramalate complex
Components
  • Acyclic terpene utilization AtuA family protein
  • DUF4387 domain-containing protein
KeywordsLYASE / aldolase / ATP / citramalate / glutamate fermentation
Function / homologyAcyclic terpene utilisation / Protein of unknown function DUF4387 / Acyclic terpene utilisation family protein AtuA / Domain of unknown function (DUF4387) / : / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / (2S)-2-HYDROXYPENTANEDIOIC ACID / DUF4387 domain-containing protein / Acyclic terpene utilization AtuA family protein
Function and homology information
Biological speciesKlebsiella michiganensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsErmler, U. / Berg, I.A. / Demmer, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Novel citramalate lyase involved in glutamate fermentation of enterobacteria
Authors: Eggers, J. / Schaefer, L. / Cassens, E.A. / Schmid, L. / Simon, S.A. / Probst, A.J. / Koenig, S. / Demmer, U. / Ermler, U. / Berg, I.A.
History
DepositionMar 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyclic terpene utilization AtuA family protein
B: DUF4387 domain-containing protein
C: Acyclic terpene utilization AtuA family protein
D: DUF4387 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,09319
Polymers121,9174
Non-polymers2,17715
Water16,105894
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.240, 107.290, 98.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-945-

HOH

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Acyclic terpene utilization AtuA family protein


Mass: 48954.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella michiganensis (bacteria) / Gene: CWM85_18250, CWN49_12110, PTQ40_16850 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2K0K9V8
#2: Protein DUF4387 domain-containing protein


Mass: 12003.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella michiganensis (bacteria) / Gene: CWN49_12105, GW952_12775, L373_04358 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A249WD43

-
Non-polymers , 7 types, 909 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-A1H6S / (2~{S})-2-methyl-2-oxidanyl-butanedioic acid


Mass: 148.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-S2G / (2S)-2-HYDROXYPENTANEDIOIC ACID


Mass: 148.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 894 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: PEP 629, MES pH 6.5, MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 349643 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.105 / Net I/σ(I): 9.94
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.2-1.32.869726910.5993.1421
1.3-1.51.652959630.8251.7961
1.5-1.80.493756830.9760.5341
1.8-2.30.108543740.9960.1171
2.3-2.90.061252850.9970.0661
2.9-3.50.044108650.9980.0481
3.5-4.50.03776970.9990.041
4.5-5.70.03335190.9990.0361
5.7-80.0322340.9990.0321
8-120.0279270.9990.0291
12-500.0264050.9980.0291

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→44.73 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 17519 5.02 %
Rwork0.1626 --
obs0.1638 349194 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8570 0 133 894 9597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.25
X-RAY DIFFRACTIONf_dihedral_angle_d14.5813447
X-RAY DIFFRACTIONf_chiral_restr0.0851393
X-RAY DIFFRACTIONf_plane_restr0.0121694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.48335000.4519925X-RAY DIFFRACTION90
1.21-1.230.42775730.413210570X-RAY DIFFRACTION96
1.23-1.240.41945990.389210956X-RAY DIFFRACTION99
1.24-1.260.38656060.358310936X-RAY DIFFRACTION99
1.26-1.280.36575750.339911112X-RAY DIFFRACTION100
1.28-1.290.3395610.323411000X-RAY DIFFRACTION100
1.29-1.310.32916650.296110984X-RAY DIFFRACTION100
1.31-1.330.31035350.278311034X-RAY DIFFRACTION100
1.33-1.350.2775670.258511070X-RAY DIFFRACTION100
1.35-1.370.30276390.246810989X-RAY DIFFRACTION100
1.37-1.40.27615870.227810988X-RAY DIFFRACTION100
1.4-1.420.24676130.205111032X-RAY DIFFRACTION100
1.42-1.450.25145890.197211050X-RAY DIFFRACTION100
1.45-1.480.23025990.180511029X-RAY DIFFRACTION100
1.48-1.510.19095760.157811087X-RAY DIFFRACTION100
1.51-1.550.18754910.145611196X-RAY DIFFRACTION100
1.55-1.590.18235860.136711079X-RAY DIFFRACTION100
1.59-1.630.16716240.131711061X-RAY DIFFRACTION100
1.63-1.680.17715400.130111182X-RAY DIFFRACTION100
1.68-1.730.17715890.130711076X-RAY DIFFRACTION100
1.73-1.790.1845970.130111129X-RAY DIFFRACTION100
1.79-1.860.1646110.129211085X-RAY DIFFRACTION100
1.86-1.950.16995650.129811188X-RAY DIFFRACTION100
1.95-2.050.16525620.137111178X-RAY DIFFRACTION100
2.05-2.180.16585930.133311168X-RAY DIFFRACTION100
2.18-2.350.1525220.132911232X-RAY DIFFRACTION100
2.35-2.590.1646290.140611151X-RAY DIFFRACTION100
2.59-2.960.17275420.156311309X-RAY DIFFRACTION100
2.96-3.730.16446430.152911241X-RAY DIFFRACTION99
3.73-44.730.14886410.145611638X-RAY DIFFRACTION100

+
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