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- PDB-3pfe: Crystal structure of a M20A metallo peptidase (dapE, lpg0809) fro... -

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Basic information

Entry
Database: PDB / ID: 3pfe
TitleCrystal structure of a M20A metallo peptidase (dapE, lpg0809) from Legionella pneumophila subsp. pneumophila str. philadelphia 1 at 1.50 A resolution
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / METAL BINDING / MEROPS M20 FAMILIY / PHOSPHORYLASE/HYDROLASE-LIKE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


peptidase activity / proteolysis / metal ion binding
Similarity search - Function
: / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich ...: / Alpha-Beta Plaits - #360 / Peptidase M20, 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
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a M20A metallo peptidase (dapE, lpg0809) from Legionella pneumophila subsp. pneumophila str. philadelphia 1 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)54,95325
Polymers53,3121
Non-polymers1,64124
Water9,476526
1
A: Succinyl-diaminopimelate desuccinylase
hetero molecules

A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,90650
Polymers106,6232
Non-polymers3,28348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area16680 Å2
ΔGint-472 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.388, 178.600, 50.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Succinyl-diaminopimelate desuccinylase


Mass: 53311.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: dapE, lpg0809 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5ZXC3

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Non-polymers , 6 types, 550 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20.00% polyethylene glycol 6000, 1.00M lithium chloride, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.5→29.767 Å / Num. all: 87563 / Num. obs: 87563 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.089 Å2 / Rsym value: 0.098 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.544.90.77213106563860.772100
1.54-1.584.90.6251.23010861930.625100
1.58-1.634.90.5241.52966060790.524100
1.63-1.684.90.4211.82873658790.421100
1.68-1.734.90.3532.22806857320.353100
1.73-1.794.90.2892.72717455370.289100
1.79-1.864.90.2243.42643853670.224100
1.86-1.944.90.1834.12522751240.183100
1.94-2.024.90.1445.12456049790.144100
2.02-2.124.90.1265.72347347670.126100
2.12-2.244.90.1146.22218545000.114100
2.24-2.374.90.1076.42117642880.107100
2.37-2.544.90.1046.51990640260.104100
2.54-2.744.90.097.71849637650.09100
2.74-34.90.0768.91735435140.076100
3-3.354.90.079.21549231590.07100
3.35-3.874.90.0639.91372128220.063100
3.87-4.744.80.05411.81156924030.054100
4.74-6.714.70.06110.5898019220.061100
6.71-29.7674.30.0649.7483811210.06498.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.767 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.029 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.059 / Phase error: 0.056
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.CHLORIDE (CL) AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.GLYCEROL (GOL) FROM THE CRYOPROTECTANT AND IMIDAZOLE (IMD) FROM THE PURIFICATION BUFFER HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 7.ZINC (ZN) HAS BEEN MODELED BASED ON AN ANOMALOUS DIFFERENCE FOURIER MAP AND X-RAY FLUORESCENCE EXCITATION SCAN.
RfactorNum. reflection% reflectionSelection details
Rfree0.163 4389 5 %RANDOM
Rwork0.1376 ---
obs0.1389 87480 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 73.75 Å2 / Biso mean: 21.667 Å2 / Biso min: 8.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 84 526 4286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224172
X-RAY DIFFRACTIONr_bond_other_d0.0010.022889
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9855708
X-RAY DIFFRACTIONr_angle_other_deg0.92737141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4825.112178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15915729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7381516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214701
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02791
X-RAY DIFFRACTIONr_mcbond_it1.51932547
X-RAY DIFFRACTIONr_mcbond_other0.46331017
X-RAY DIFFRACTIONr_mcangle_it2.50154157
X-RAY DIFFRACTIONr_scbond_it4.19981625
X-RAY DIFFRACTIONr_scangle_it6.137111518
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 298 -
Rwork0.248 6060 -
all-6358 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: 43.4328 Å / Origin y: 21.5784 Å / Origin z: 36.2128 Å
111213212223313233
T0.0256 Å20.0043 Å20.0066 Å2-0.0213 Å2-0.0027 Å2--0.0088 Å2
L0.3861 °2-0.1848 °20.1503 °2-0.3289 °2-0.1788 °2--0.1693 °2
S-0.0119 Å °0.0181 Å °0.0087 Å °0.011 Å °0.019 Å °0.0056 Å °0.0086 Å °-0.0155 Å °-0.0072 Å °

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