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- PDB-7t1q: Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (... -

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Basic information

Entry
Database: PDB / ID: 7t1q
TitleCrystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic Acid
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DapE
Function / homology
Function and homology information


succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding
Similarity search - Function
Succinyl-diaminopimelate desuccinylase, proteobacteria / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / SUCCINIC ACID / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 17978 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Pshenychnyi, S. / Satchell, K.J.F. / 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) United States
CitationJournal: To be Published
Title: Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic Acid.
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Pshenychnyi, S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,70411
Polymers82,9382
Non-polymers7669
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-159 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.323, 103.460, 145.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 41468.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
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 , 5 types, 355 molecules

#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.94 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein: 10.6 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3, 2mM N6-Me-L,L-SDAP; Screen: Classics II (D5), 0.1M Sodium acetate pH 4.5, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97848 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2021 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 50400 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 45.5 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.043 / Rrim(I) all: 0.151 / Rsym value: 0.145 / Χ2: 1.068 / Net I/σ(I): 20.2
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2507 / CC1/2: 0.756 / CC star: 0.928 / Rpim(I) all: 0.607 / Χ2: 1.009 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uej

5uej


Resolution: 2.25→29.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 14.067 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 2458 5 %RANDOM
Rwork0.1878 ---
obs0.19 47108 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.64 Å2 / Biso mean: 53.815 Å2 / Biso min: 22.46 Å2
Baniso -1Baniso -2Baniso -3
1-4.81 Å2-0 Å20 Å2
2--0.49 Å2-0 Å2
3----5.31 Å2
Refinement stepCycle: final / Resolution: 2.25→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 38 350 6160
Biso mean--62.9 49.68 -
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135980
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155578
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.6428133
X-RAY DIFFRACTIONr_angle_other_deg0.3611.57412856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1125758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.93223.389301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.64515930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.051530
X-RAY DIFFRACTIONr_chiral_restr0.0580.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0520.026884
X-RAY DIFFRACTIONr_gen_planes_other0.0470.021308
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 159 -
Rwork0.346 3441 -
all-3600 -
obs--100 %
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)
12.1437-0.22731.03972.278-0.14023.4748-0.02220.68430.2982-0.00930.03850.0329-0.42750.2075-0.01640.0722-0.0061-0.00520.32150.04490.2016-34.91126.38712.167
21.94890.00160.50121.3669-0.37283.20480.01570.485-0.0068-0.01320.04750.15580.0313-0.1572-0.06320.00920.0216-0.01990.2193-0.0120.104-39.19718.88512.673
34.5819-0.4572-3.87090.83881.03323.9311-0.3276-0.1663-0.08530.2040.07870.10930.5770.1860.24890.48220.1041-0.01780.21870.00290.1961-17.885-5.2612.276
41.6192-0.29891.06941.1481-0.46433.43440.12510.3347-0.221-0.06660.01170.34990.2723-0.5442-0.13680.0846-0.0311-0.04630.3166-0.05110.232-45.23312.49313.48
51.69140.1143-0.77411.54520.55423.51130.0573-0.11150.4290.05420.3594-0.4858-0.18690.4771-0.41660.0392-0.0132-0.01390.1501-0.1130.339311.68910.168-27.532
61.034-0.0856-0.32641.83740.62892.9826-0.0239-0.15930.21870.08950.2713-0.4115-0.06180.4976-0.24740.13020.0059-0.06440.1634-0.08450.234811.6162.489-26.423
73.5638-1.6211-4.28591.60192.13425.2589-0.08230.8421-0.19760.09-0.23050.03460.1465-1.02060.31280.30590.0405-0.07470.5264-0.06910.1891-18.883-5.633-16.649
80.4670.0096-0.23370.76630.23323.9615-0.1282-0.09480.06580.09950.2214-0.33840.06360.5022-0.09320.18940.0712-0.09580.172-0.07130.203910.131-6.571-27.63
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 78
2X-RAY DIFFRACTION2A79 - 180
3X-RAY DIFFRACTION3A181 - 290
4X-RAY DIFFRACTION4A291 - 378
5X-RAY DIFFRACTION5B4 - 76
6X-RAY DIFFRACTION6B77 - 175
7X-RAY DIFFRACTION7B176 - 284
8X-RAY DIFFRACTION8B285 - 378

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