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- PDB-4ege: Crystal Structure of Dipeptidase PepE from Mycobacterium ulcerans -

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Basic information

Entry
Database: PDB / ID: 4ege
TitleCrystal Structure of Dipeptidase PepE from Mycobacterium ulcerans
ComponentsDipeptidase PepE
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 ...Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidase PepE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,45225
Polymers39,3661
Non-polymers1,08524
Water2,936163
1
A: Dipeptidase PepE
hetero molecules

A: Dipeptidase PepE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,90350
Polymers78,7332
Non-polymers2,17048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6550 Å2
ΔGint-425 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.420, 120.420, 58.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Dipeptidase PepE


Mass: 39366.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: pepE, MUL_2321 / Production host: Escherichia coli (E. coli) / References: UniProt: A0PQS3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.50, 200 mM zinc acetate, 10% (v/v) isopropanol, 40 mg/ml MyulA.01407.a.A1 PS00805, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.973962 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973962 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 22304 / Num. obs: 22015 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.851 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.260.5443.027930162399.7
2.26-2.320.4453.667633156199.9
2.32-2.390.3844.137538153199.7
2.39-2.460.334.737257148999.8
2.46-2.540.3075.17137145799.8
2.54-2.630.2476.166816138499.6
2.63-2.730.2246.76605135399.7
2.73-2.840.1728.516342130299.4
2.84-2.970.1459.76030124299.7
2.97-3.110.11511.725928121599.3
3.11-3.280.09113.945538113998.9
3.28-3.480.08115.975202107299.1
3.48-3.720.0718.14940102398.7
3.72-4.020.06419.69457895498.4
4.02-4.40.05821.56416586697.7
4.4-4.920.05322.87378879697.4
4.92-5.680.05821.04326269595.7
5.68-6.960.05920.69279859895.2
6.96-9.840.0524.36220147794.6
9.840.04326.97101023877.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1wn1

1wn1


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.184 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1133 5.1 %RANDOM
Rwork0.1883 ---
all0.1912 22304 --
obs0.1912 22014 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.57 Å2 / Biso mean: 18.0455 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 48 163 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192791
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9713810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59523110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58915383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6511523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212145
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 83 -
Rwork0.227 1380 -
all-1463 -
obs--99.59 %
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)
13.2929-0.02011.55051.2007-0.40663.34820.01380.0855-0.0515-0.08460.11050.12670.1256-0.2874-0.12420.03560.00150.01870.1660.0380.049626.607932.2564-16.585
22.6217-0.9541-0.33235.9857-1.6673.6334-0.01890.4609-0.3719-0.23230.1710.05160.133-0.3244-0.15210.0204-0.03120.01270.1774-0.04410.12535.530224.3706-15.8862
31.7230.3385-0.15262.2718-0.3891.39260.01980.1756-0.0163-0.0498-0.0162-0.0893-0.0152-0.0921-0.00360.00830.00290.00480.043-0.00130.031939.646430.997-11.1061
43.38570.9242-0.7541.6696-1.00251.63860.01430.038-0.261-0.1463-0.00170.06190.19430.0214-0.01260.04540.0397-0.02180.084800.07715.609428.0128-4.7184
52.26350.3575-0.33931.4568-0.43161.42630.128-0.30250.02850.0806-0.15680.0585-0.1218-0.00280.02890.0216-0.007-0.00990.1450.00310.03622.591836.88165.2473
62.49620.2767-0.16051.27950.23831.05350.0445-0.110.11040.0224-0.03390.0053-0.12050.0432-0.01050.02190.0052-0.00390.09090.0230.03845.544939.8487-1.2075
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 49
2X-RAY DIFFRACTION2A50 - 77
3X-RAY DIFFRACTION3A78 - 135
4X-RAY DIFFRACTION4A136 - 194
5X-RAY DIFFRACTION5A195 - 303
6X-RAY DIFFRACTION6A304 - 374

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