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- PDB-4ben: R39-imipenem Acyl-enzyme crystal structure -

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Basic information

Entry
Database: PDB / ID: 4ben
TitleR39-imipenem Acyl-enzyme crystal structure
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASEMuramoylpentapeptide carboxypeptidase
KeywordsHYDROLASE / PENICILLIN-BINDING / ACYL-ENZYME
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region
Similarity search - Function
D-Ala-D-Ala carboxypeptidase C, peptidase S13 / Peptidase S13, D-Ala-D-Ala carboxypeptidase C / D-Ala-D-Ala carboxypeptidase 3 (S13) family / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(bba) Sandwich / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IM2 / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesACTINOMADURA SP. R39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVan Elder, D. / Sauvage, E. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P.
CitationJournal: To be Published
Title: Crystal Structures of R39-Imipenem Acyl-Enzyme.
Authors: Sauvage, E. / Van Elder, D. / Herman, R. / Kerff, F. / Pratt, R.F. / Charlier, P.
History
DepositionMar 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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_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: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,44048
Polymers190,5884
Non-polymers4,85244
Water17,475970
1
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,14616
Polymers47,6471
Non-polymers1,49915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,71710
Polymers47,6471
Non-polymers1,0709
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6219
Polymers47,6471
Non-polymers9748
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,95713
Polymers47,6471
Non-polymers1,31012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.623, 91.911, 106.924
Angle α, β, γ (deg.)90.00, 94.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / Muramoylpentapeptide carboxypeptidase / DD-CARBOXYPEPTIDASE / DD-PEPTIDASE / PENICILLIN-BINDING PROTEIN / PBP


Mass: 47647.004 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP. R39 (bacteria)
References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase

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Non-polymers , 6 types, 1014 molecules

#2: Chemical
ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form / Imipenem


Mass: 301.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 970 / 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: 2.48 Å3/Da / Density % sol: 50 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.15→25.7 Å / Num. obs: 108662 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W8Q

1w8q


Resolution: 2.15→35.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.18 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23441 5420 5 %RANDOM
Rwork0.18719 ---
obs0.18951 103175 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.552 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13394 0 273 970 14637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02113848
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9818956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90551858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53525.47574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.958151920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5711568
X-RAY DIFFRACTIONr_chiral_restr0.0880.22183
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110676
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8621.59178
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.588214556
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27434670
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7654.54400
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 394 -
Rwork0.267 7550 -
obs--99.23 %
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)
12.9198-6.8149-0.661516.66412.61172.19820.4655-0.1357-0.45-0.37540.20840.61471.0884-0.2746-0.67390.8562-0.2774-0.44250.17770.00910.5896-14.562-30.97838.17
20.93410.246-0.00430.70150.04090.66090.0124-0.01660.00170.0162-0.0068-0.00540.0499-0.0343-0.00550.13740.03310.01150.14380.00820.103912.4420.09539.673
31.1372-0.7012-0.04050.54580.150.2539-0.0039-0.01060.0599-0.0041-0.00510.0297-0.0026-0.06190.00910.1046-0.00220.0020.1032-0.00030.1114-0.04517.9741.657
40.92790.33040.08380.63540.17610.5339-0.0039-0.04520.12050.04470.0144-0.0974-0.03840.1342-0.01040.11330.0043-0.0090.12220.00230.100619.8727.58143.984
50.9680.4673-0.19690.55-0.17340.6801-0.00770.0276-0.10830.00090.0150.00230.1-0.0511-0.00730.11060.00260.00250.0975-0.00460.09443.79-11.54938.23
61.26650.8614-1.34341.2590.08153.6786-0.0827-0.0262-0.18010.05670.0015-0.04760.3578-0.19380.08110.0953-0.04710.01280.16570.00670.1533-9.696-18.40242.231
70.70880.07890.07530.5022-0.13581.6651-0.04040.08080.2162-0.05930.03380.0548-0.4079-0.17030.00650.17880.0336-0.01170.0796-0.00660.146454.32734.42927.849
80.5006-0.0683-0.02060.5839-0.1072.189-0.0072-0.1755-0.02480.1230.0125-0.06150.03420.0372-0.00540.1001-0.0035-0.01370.125-0.00250.115362.23611.78557.403
91.2072-0.1844-0.91030.14190.36041.1489-0.086-0.1388-0.08410.02340.0397-0.01470.12660.17040.04620.11020.02340.00580.13210.03220.11477.8568.42542.587
100.75370.27970.16812.057-1.5282.81480.0183-0.3033-0.03570.325-0.00160.0151-0.0248-0.0097-0.01670.12640.0240.00040.2025-0.00990.017562.27412.92165.083
110.48420.1907-0.31570.6627-0.68381.19580.0366-0.07830.10030.0796-0.01120.0096-0.2574-0.082-0.02530.12950.0141-0.00770.0806-0.02390.112356.67329.78937.52
121.9160.8422-0.01233.93190.63491.54730.0528-0.06740.33420.0054-0.0212-0.0033-0.4156-0.0271-0.03160.2030.0151-0.00130.05330.02520.125462.12839.51224.296
132.53220.3308-0.18484.18560.88542.55140.00010.23920.3622-0.3325-0.11820.0489-0.5237-0.14970.11810.188-0.0181-0.00420.12880.05290.110414.5487.505-32.296
140.7015-0.03080.00850.8322-0.45360.8896-0.0102-0.186-0.0370.11680.0193-0.0082-0.0058-0.0842-0.0090.1114-0.0288-0.00530.1634-0.05180.103312.73363.3551.754
151.1901-0.2532-0.57670.06060.13220.4773-0.0488-0.0644-0.0819-0.00010.00120.00390.08930.02130.04760.134-0.0214-0.00090.09440.00260.116227.2852.17-10.715
160.62220.0753-0.04210.7385-0.56520.9788-0.0032-0.2063-0.08470.1114-0.0034-0.04570.0579-0.04130.00670.1146-0.0255-0.01170.154-0.02210.078812.67359.7314.245
170.87710.4185-0.06170.7791-0.31830.54280.0134-0.08570.11980.09310.00290.0307-0.0849-0.1067-0.01640.11390.0042-0.00920.1066-0.02370.10913.09278.142-13.251
181.63410.43240.7253.08290.85571.7295-0.0663-0.09080.24720.0550.0687-0.1087-0.2326-0.0229-0.00240.13330.0093-0.01290.104-0.00090.114918.47586.346-21.827
191.697-0.28250.28050.8617-0.06410.8520.0373-0.0286-0.30460.0475-0.0359-0.14790.26230.2209-0.00140.17280.03210.00220.10110.01680.134351.03371.02721.749
201.2348-0.26890.31930.6247-0.17630.5517-0.00270.10070.0746-0.07270.01930.1341-0.1112-0.1448-0.01650.12240.00740.00350.11710.00880.115321.78699.3918.002
211.13070.5654-0.29830.6823-0.37210.2366-0.00410.06470.0651-0.00350.0046-0.0514-0.01690.019-0.00040.13120.0011-0.00440.08950.00260.104747.827105.1759.025
220.7239-0.11220.12820.7047-0.19960.6870.00990.10390.068-0.02350.01410.1444-0.0589-0.1727-0.0240.1133-0.00590.00430.1116-00.092228.88295.29.194
230.9382-0.1964-0.07930.47770.22440.7444-0.0064-0.0171-0.11980.01790.0135-0.02040.07320.0539-0.00710.1145-0.00260.00780.06480.0030.112143.4576.55317.563
242.0307-0.7134-0.45831.71391.23972.32790.02480.095-0.3121-0.04550.0033-0.13630.09060.1586-0.0280.08830.03990.00090.09310.01060.152557.23971.1915.325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 138
3X-RAY DIFFRACTION3A139 - 249
4X-RAY DIFFRACTION4A250 - 313
5X-RAY DIFFRACTION5A314 - 423
6X-RAY DIFFRACTION6A424 - 466
7X-RAY DIFFRACTION7B1 - 72
8X-RAY DIFFRACTION8B73 - 155
9X-RAY DIFFRACTION9B156 - 250
10X-RAY DIFFRACTION10B251 - 288
11X-RAY DIFFRACTION11B289 - 423
12X-RAY DIFFRACTION12B424 - 465
13X-RAY DIFFRACTION13C1 - 23
14X-RAY DIFFRACTION14C24 - 132
15X-RAY DIFFRACTION15C133 - 250
16X-RAY DIFFRACTION16C251 - 326
17X-RAY DIFFRACTION17C327 - 423
18X-RAY DIFFRACTION18C424 - 465
19X-RAY DIFFRACTION19D1 - 70
20X-RAY DIFFRACTION20D71 - 138
21X-RAY DIFFRACTION21D139 - 231
22X-RAY DIFFRACTION22D232 - 313
23X-RAY DIFFRACTION23D314 - 414
24X-RAY DIFFRACTION24D415 - 466

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