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- PDB-8f8o: Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (... -

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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 / diaminopimelate biosynthetic process / cobalt ion binding / lysine biosynthetic process via diaminopimelate / 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: To Be Published
Title: Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic and L-Lactic Acids
Authors: Minasov, 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 ...Authors: Minasov, 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)
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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.

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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

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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

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