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- PDB-1u10: MEPA, active form with ZN in P1 -

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Basic information

Entry
Database: PDB / ID: 1u10
TitleMEPA, active form with ZN in P1
ComponentsPenicillin-insensitive murein endopeptidase
KeywordsHYDROLASE / LAS enzyme / metallopeptidase / peptidoglycan hydrolase
Function / homology
Function and homology information


peptidoglycan metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / peptidoglycan biosynthetic process / metalloendopeptidase activity / peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / response to xenobiotic stimulus / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M74, penicillin-insensitive murein endopeptidase / Penicillin-insensitive murein endopeptidase / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin-insensitive murein endopeptidase / Penicillin-insensitive murein endopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD combined with molecular replacement / Resolution: 2.4 Å
AuthorsMarcyjaniak, M. / Odintsov, S.G. / Sabala, I. / Bochtler, M.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Peptidoglycan amidase MepA is a LAS metallopeptidase
Authors: Marcyjaniak, M. / Odintsov, S.G. / Sabala, I. / Bochtler, M.
#1: Journal: Protein Sci. / Year: 2004
Title: Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases
Authors: Bochtler, M. / Odintsov, S.G. / Marcyjaniak, M. / Sabala, I.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn_type / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-insensitive murein endopeptidase
B: Penicillin-insensitive murein endopeptidase
C: Penicillin-insensitive murein endopeptidase
D: Penicillin-insensitive murein endopeptidase
E: Penicillin-insensitive murein endopeptidase
F: Penicillin-insensitive murein endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,84221
Polymers171,6776
Non-polymers1,16515
Water99155
1
A: Penicillin-insensitive murein endopeptidase
B: Penicillin-insensitive murein endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6147
Polymers57,2262
Non-polymers3885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-69 kcal/mol
Surface area21130 Å2
MethodPISA
2
C: Penicillin-insensitive murein endopeptidase
D: Penicillin-insensitive murein endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6147
Polymers57,2262
Non-polymers3885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-68 kcal/mol
Surface area21780 Å2
MethodPISA
3
E: Penicillin-insensitive murein endopeptidase
F: Penicillin-insensitive murein endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6147
Polymers57,2262
Non-polymers3885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-68 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.613, 77.988, 127.663
Angle α, β, γ (deg.)93.15, 95.93, 90.75
Int Tables number1
Space group name H-MP1
DetailsDimer in three different crystal forms. Oligomeric state in solution not characterized.

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Components

#1: Protein
Penicillin-insensitive murein endopeptidase / D-alanyl-D-alanine-endopeptidase / DD-endopeptidase


Mass: 28612.814 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mepA / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14007, UniProt: P0C0T5*PLUS, EC: 3.4.99.-
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.22 %
Description: The number of reflections reported here include anomalous data.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, MES, PEG monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9791, 0.9793, 1.2810
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 27, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
31.2811
ReflectionResolution: 2.4→20 Å / Num. all: 103423 / Num. obs: 103423 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4 / Num. unique all: 4917 / Rsym value: 0.151 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD combined with molecular replacement
Starting model: MepA in the P21 form (1TZP)

1tzp


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.918 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 2658 5.1 %RANDOM
Rwork0.23393 ---
all0.23551 49711 --
obs0.23551 49711 98.17 %-
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 mean: 24.954 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.31 Å2-0.09 Å2
2---0.15 Å2-0.68 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11217 0 39 55 11311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111547
X-RAY DIFFRACTIONr_bond_other_d00.0210378
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.94915688
X-RAY DIFFRACTIONr_angle_other_deg3.527324195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.53151421
X-RAY DIFFRACTIONr_chiral_restr0.1020.21697
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212819
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022275
X-RAY DIFFRACTIONr_nbd_refined0.2380.22632
X-RAY DIFFRACTIONr_nbd_other0.2970.210970
X-RAY DIFFRACTIONr_nbtor_other0.1070.25571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2226
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.251
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3610.2147
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.25
X-RAY DIFFRACTIONr_mcbond_it1.6881.57166
X-RAY DIFFRACTIONr_mcangle_it2.625211566
X-RAY DIFFRACTIONr_scbond_it2.54934381
X-RAY DIFFRACTIONr_scangle_it3.6694.54122
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 168
Rwork0.257 3598

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