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- PDB-3tx8: Crystal structure of a succinyl-diaminopimelate desuccinylase (Ar... -

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Entry
Database: PDB / ID: 3tx8
TitleCrystal structure of a succinyl-diaminopimelate desuccinylase (ArgE) from Corynebacterium glutamicum ATCC 13032 at 2.97 A resolution
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / peptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / metal ion binding
Similarity search - Function
Succinyl-diaminopimelate desuccinylase, DapE / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases ...Succinyl-diaminopimelate desuccinylase, DapE / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MAD / MAD / Resolution: 2.972 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Brunger, A.T. / Terwilliger, T.C. / Read, R.J. / Adams, P.D. / Levitt, M. / Schroder, G.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.
Authors: Brunger, A.T. / Das, D. / Deacon, A.M. / Grant, J. / Terwilliger, T.C. / Read, R.J. / Adams, P.D. / Levitt, M. / Schroder, G.F.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Dec 6, 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

Downloads & links

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Assembly

Deposited unit
A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4023
Polymers40,2711
Non-polymers1302
Water00
1
A: Succinyl-diaminopimelate desuccinylase
hetero molecules

A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8036
Polymers80,5422
Non-polymers2614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area3990 Å2
ΔGint-52 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.901, 82.901, 364.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Succinyl-diaminopimelate desuccinylase / SDAP desuccinylase


Mass: 40271.184 Da / Num. of mol.: 1 / Mutation: E4N, K6Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: dapE, Cgl1109, cg1260 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q59284, succinyl-diaminopimelate desuccinylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS CLEAVED WITH TEV PROTEASE LEAVING GLY(0) FOLLOWED BY THE TARGET SEQUENCE. 2. DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS TWO AMINO ACID SUBSTITUTIONS (E4N AND K6Q) AND ONE AMINO ACID DELETION (L5DEL), WHEN COMPARED TO THE AVAILABLE GENBANK SEQUENCE (NP_600337.1) FROM CORYNEBACTERIUM GLUTAMICUM 534 (ATCC 13032).

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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: 4.47 Å3/Da / Density % sol: 72.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.41
Details: 43.1% polyethylene glycol 400, 0.20M sodium chloride, 0.1M Na/K phosphate pH 6.41, Additive: 0.006 M zinc chloride, nanodrop, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97919,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979191
30.979361
ReflectionResolution: 2.97→29.543 Å / Num. obs: 16179 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 91.327 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.97-3.054.81.2481.55424113798.5
3.05-3.134.70.9391.95284111898.1
3.13-3.224.70.692.65127109198.7
3.22-3.324.70.5313.15026107499
3.32-3.434.70.41944807102598.6
3.43-3.554.70.2845.6467999398.9
3.55-3.694.70.217.2456597899.4
3.69-3.844.60.1678.8437995399.4
3.84-4.014.60.12711.3421691599.5
4.01-4.24.60.09514.3401787899.9
4.2-4.434.60.07317.9372381799.2
4.43-4.74.50.05721367180899.2
4.7-5.024.50.05822.9341875499.8
5.02-5.434.40.05122.8318171899.8
5.43-5.944.40.05223.6295667699.9
5.94-6.654.40.05323.8261660099.7
6.65-7.674.30.04229.62326547100
7.67-9.440.03137.31962485100
9.4-13.293.90.02740.81518394100
13.29-29.543.30.03137.472821887.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1refinement
PDB_EXTRACT3.1data extraction
XSCALEJanuary 30, 2009data scaling
PHASER2.3.0phasing
CNS1.3phasing
CNS1.3refinement
MolProbity3beta29model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MAD
Starting model: 1VGY

1vgy


Resolution: 2.972→29.543 Å / Occupancy max: 1 / Occupancy min: 0.75 / SU ML: 0.71 / σ(F): 1.87 / Phase error: 28.12 / Stereochemistry target values: MLHL
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. PHOSPHATE (PO4) AND CHLORIDE (CL) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. THE STRUCTURE WAS SOLVED BY A COMBINATION OF MOLECULAR REPLACEMENT USING PHASER AND DEN REFINEMENT IN CNS, IN CONJUCTION WITH MODELLER, AUTOBUILD AND EXPERIMENTAL PHASING WITH SE MAD PHASES 5.THE REFINEMENT WAS RESTRAINED WITH THE MAD PHASES.
RfactorNum. reflection% reflection
Rfree0.2566 1649 10.24 %
Rwork0.2379 --
obs0.2399 16098 99.07 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.72 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 181.59 Å2 / Biso mean: 99.6661 Å2 / Biso min: 32.71 Å2
Baniso -1Baniso -2Baniso -3
1-18.0032 Å20 Å2-0 Å2
2--18.0032 Å2-0 Å2
3----36.0064 Å2
Refinement stepCycle: LAST / Resolution: 2.972→29.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 6 0 2750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032801
X-RAY DIFFRACTIONf_angle_d0.6253809
X-RAY DIFFRACTIONf_chiral_restr0.047430
X-RAY DIFFRACTIONf_plane_restr0.002505
X-RAY DIFFRACTIONf_dihedral_angle_d11.381011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9725-3.05990.36831310.36191155128698
3.0599-3.15850.44251300.38261140127098
3.1585-3.27130.40011350.33291172130799
3.2713-3.40210.33941330.31341154128798
3.4021-3.55670.30261170.27831198131599
3.5567-3.74380.25511380.26111185132399
3.7438-3.97790.28291310.25121199133099
3.9779-4.28420.2351350.211611971332100
4.2842-4.71370.22231290.1841213134299
4.7137-5.39220.21561540.194912201374100
5.3922-6.78010.25121530.231312571410100
6.7801-29.54770.21591630.22161359152299
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)
12.4425-0.37950.17142.3110.54882.16140.1903-0.2721-0.01560.2171-0.1181-0.0426-0.3184-0.24430.00070.4078-0.030.04150.83370.13040.38877.05845.996191.6712
21.16380.05131.21642.173-0.14290.8309-0.1797-0.2428-0.335-0.17780.28960.07830.4140.03250.02440.2353-0.04420.03710.52850.07740.5478-5.418436.532158.8134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 10:175 or resseq 293:369)A10 - 175
2X-RAY DIFFRACTION1chain A and (resseq 10:175 or resseq 293:369)A293 - 369
3X-RAY DIFFRACTION2chain A and (resseq 176:292)A176 - 292

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