[English] 日本語
Yorodumi
- PDB-8f8o: Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f8o
TitleCrystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic and L-Lactic Acids
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / Center for Structural Biology of Infectious Diseases (CSBID) / DapE / Succinate / L-Lactate / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / acetylornithine deacetylase activity / L-arginine biosynthetic process / : / : / cobalt ion binding / zinc ion binding
Similarity search - Function
Succinyl-diaminopimelate desuccinylase, proteobacteria / : / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / CITRIC ACID / TRIETHYLENE GLYCOL / SUCCINIC ACID / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 17978 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Pshenychnyi, S. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: Acs Omega / Year: 2024
Title: Biochemical and Structural Analysis of the Bacterial Enzyme Succinyl-Diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii.
Authors: Kelley, E.H. / Minasov, G. / Konczak, K. / Shuvalova, L. / Brunzelle, J.S. / Shukla, S. / Beulke, M. / Thabthimthong, T. / Olsen, K.W. / Inniss, N.L. / Satchell, K.J.F. / Becker, D.P.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation_author
Revision 1.2Feb 22, 2023Group: Data collection / Experimental preparation
Category: diffrn_detector / diffrn_radiation_wavelength ...diffrn_detector / diffrn_radiation_wavelength / diffrn_source / exptl_crystal_grow
Item: _diffrn_detector.pdbx_collection_date / _diffrn_radiation_wavelength.wavelength ..._diffrn_detector.pdbx_collection_date / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _exptl_crystal_grow.pH / _exptl_crystal_grow.pdbx_details
Revision 1.3Sep 24, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinyl-diaminopimelate desuccinylase
B: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,74213
Polymers84,5272
Non-polymers1,21411
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-164 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.659, 102.533, 145.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Succinyl-diaminopimelate desuccinylase / SDAP desuccinylase / N-succinyl-LL-2 / 6-diaminoheptanedioate amidohydrolase


Mass: 42263.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria)
Gene: dapE, A1S_2810 / Plasmid: pMCSG92 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic
References: UniProt: A3M8H2, succinyl-diaminopimelate desuccinylase

-
Non-polymers , 7 types, 389 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 8.0 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3, 2mM N6-Me-L,L-SDAP; Screen: Peg's II (H1), 0.1M M tri-Sodium citrate, 33% (w/v) PEG6000.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97864 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 9, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 59464 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 37.2 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.056 / Rrim(I) all: 0.154 / Rsym value: 0.143 / Χ2: 1.025 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2947 / CC1/2: 0.492 / CC star: 0.812 / Rpim(I) all: 0.419 / Χ2: 0.987 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 14.72 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22965 3030 5.1 %RANDOM
Rwork0.18901 ---
obs0.19116 56580 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.327 Å2
Baniso -1Baniso -2Baniso -3
1-7.22 Å2-0 Å2-0 Å2
2---2.33 Å2-0 Å2
3----4.89 Å2
Refinement stepCycle: 1 / Resolution: 2.1→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5753 0 68 378 6199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125988
X-RAY DIFFRACTIONr_bond_other_d0.0140.0165384
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.6518140
X-RAY DIFFRACTIONr_angle_other_deg0.5481.56312570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9025756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.245530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.91410924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.026844
X-RAY DIFFRACTIONr_gen_planes_other0.020.021108
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9673.1073022
X-RAY DIFFRACTIONr_mcbond_other2.9673.1073023
X-RAY DIFFRACTIONr_mcangle_it4.2374.6543778
X-RAY DIFFRACTIONr_mcangle_other4.2364.6543778
X-RAY DIFFRACTIONr_scbond_it3.8143.5062966
X-RAY DIFFRACTIONr_scbond_other3.7733.4972963
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4345.1074363
X-RAY DIFFRACTIONr_long_range_B_refined8.15646.7156702
X-RAY DIFFRACTIONr_long_range_B_other8.19143.3936640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 206 -
Rwork0.4 4057 -
obs--98.14 %
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)
10.6540.16610.68472.26440.43342.2259-0.10220.23150.1016-0.08270.06270.0363-0.32180.08080.03950.0468-0.0163-0.00860.30470.01780.2745-34.33725.83512.59
20.67410.18530.26151.797-0.34222.47140.01860.12970.019-0.07710.02250.09140.097-0.0597-0.04110.00830.01-0.02430.2896-0.00410.2799-38.99819.11112.95
32.7957-0.3267-2.44320.0870.39942.5328-0.2265-0.2409-0.10560.06720.05820.04980.43370.23320.16830.22150.0428-0.00550.18740.01530.174-19.45-4.684.108
41.3909-0.077-0.34441.1883-0.68420.5615-0.01310.1339-0.0329-0.18340.160.26340.1114-0.2769-0.14690.0302-0.0231-0.06080.3921-0.00050.334-45.9313.32213.02
51.0402-0.0879-0.58681.3942-0.12761.07020.0192-0.08970.1559-0.00530.134-0.3486-0.10160.2606-0.15330.0168-0.0231-0.00790.231-0.05660.286511.85810.05-27.351
60.44320.0062-0.10681.51870.40662.3887-0.0375-0.09170.09430.09670.1395-0.30950.04440.3424-0.1020.00970.0217-0.03410.2396-0.04640.259111.6972.41-26.252
72.3555-1.3305-2.62960.79641.43333.0641-0.09960.424-0.17050.0854-0.17540.04560.1452-0.54380.27510.1093-0.0224-0.02190.2754-0.05230.1681-18.559-5.302-17.287
80.2001-0.1544-0.47261.49490.40481.2192-0.0873-0.11960.05940.0690.1551-0.33860.19620.4095-0.06780.05210.0702-0.07310.2916-0.03420.261212.909-7.206-27.311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 78
2X-RAY DIFFRACTION2A79 - 178
3X-RAY DIFFRACTION3A179 - 299
4X-RAY DIFFRACTION4A300 - 378
5X-RAY DIFFRACTION5B4 - 76
6X-RAY DIFFRACTION6B77 - 175
7X-RAY DIFFRACTION7B176 - 293
8X-RAY DIFFRACTION8B294 - 377

+
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