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- PDB-2xdm: Crystal structure of a complex between Actinomadura R39 DD peptid... -

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Basic information

Entry
Database: PDB / ID: 2xdm
TitleCrystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic boronate inhibitor
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / BORONIC ACID / PEPTIDOGLYCAN / HYDROLASE
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
(D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONIC ACID / : / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesACTINOMADURA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRocaboy, M. / Sauvage, E. / Herman, R. / Kerff, F. / Charlier, P.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal Structure of a Complex between the Actinomadura R39 Dd-Peptidase and a Peptidoglycan- Mimetic Boronate Inhibitor: Interpretation of a Transition State Analogue in Terms of Catalytic Mechanism.
Authors: Dzhekieva, L. / Rocaboy, M. / Kerff, F. / Charlier, P. / Sauvage, E. / Pratt, R.F.
History
DepositionMay 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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: 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)193,46631
Polymers190,5884
Non-polymers2,87827
Water9,998555
1
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2458
Polymers47,6471
Non-polymers5987
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)48,3907
Polymers47,6471
Non-polymers7436
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)48,3907
Polymers47,6471
Non-polymers7436
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)48,4409
Polymers47,6471
Non-polymers7938
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.308, 91.568, 106.871
Angle α, β, γ (deg.)90.00, 94.37, 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 / DD-PEPTIDASE / DD-CARBOXYPEPTIDASE / PENICILLIN-BINDING PROTEIN / PBP


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

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Non-polymers , 5 types, 582 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-BO8 / (D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONIC ACID


Mass: 263.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20BN2O6
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97969
DetectorType: MARRESEARCH SX-165 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionResolution: 2.4→33 Å / Num. obs: 77588 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 99.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WK0

2wk0


Resolution: 2.4→32.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.546 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26225 3901 5 %RANDOM
Rwork0.19948 ---
obs0.20265 73667 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.566 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å21.27 Å2
2--2.04 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13391 0 150 555 14096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02113753
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.97218820
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26151858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08725.47574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.103151920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9141568
X-RAY DIFFRACTIONr_chiral_restr0.0790.22177
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210634
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.26168
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.29196
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2749
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4391.59347
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.775214564
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.20334904
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9684.54256
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 299 -
Rwork0.251 5393 -
obs--99.44 %
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)
16.56326.55665.06076.54995.05563.9022-0.2903-0.2761-1.4515-0.58030.32990.83361.1184-0.1282-0.03960.3189-0.227-0.020.05980.03980.2179-16.038-27.33137.585
20.69740.7147-0.02690.88920.29840.6783-0.03810.2118-0.1189-0.02320.0251-0.08020.1632-0.0590.0130.1974-0.0235-0.095-0.0813-0.02680.10031.313-13.38635.388
34.24541.4506-0.2931.3804-0.14641.99380.1314-0.23090.34280.17690.0329-0.0434-0.06590.1973-0.16420.12950.0147-0.1013-0.066-0.06710.129827.87417.14349.056
41.2004-0.51880.17090.62590.24080.2709-0.02590.01860.112-0.03690.0052-0.021-0.0279-0.01040.02070.17910.0124-0.1131-0.07550.00220.11698.31415.99441.66
51.25830.629-0.28690.5048-0.22160.70580.01040.0708-0.11290.020.0181-0.03290.0388-0.0203-0.02860.18260.0052-0.1149-0.0786-0.02110.10664.737-9.59138.876
61.29070.6845-1.68291.9158-0.62624.7822-0.03640.1771-0.0421-0.0450.11710.03040.3104-0.5029-0.08070.1207-0.0421-0.1326-0.0904-0.00180.1074-11.167-16.66841.818
70.45380.09010.04220.73-0.44062.22930.0440.00360.1516-0.03690.09280.1082-0.3827-0.2652-0.13680.22110.0816-0.0556-0.12860.01760.152254.44334.35228.05
81.08910.05530.13873.6011-1.79813.91240.0011-0.2098-0.07230.39320.0504-0.0933-0.03-0.4344-0.05150.1882-0.0299-0.1058-0.02-0.00420.038961.13311.03368.837
90.3558-0.0804-0.60450.26410.09871.03270.0213-0.13120.0440.0248-0.0285-0.03780.09590.11180.00730.1715-0.0028-0.1155-0.03620.00940.110672.02310.07746.726
100.8370.40370.2132.3661-2.68584.45050.1179-0.10530.18960.1489-0.0604-0.0209-0.10270.0057-0.05750.1341-0.0159-0.0816-0.085-0.07990.030762.6617.19258.198
110.81610.4314-0.38441.2555-1.07111.74580.0831-0.00610.00750.06570.0404-0.0134-0.339-0.2539-0.12350.19050.0592-0.0555-0.10640.01120.092855.90130.0336.709
122.2841.2828-0.05516.9899-0.75872.2844-0.0010.10530.28790.02810.0844-0.1245-0.4059-0.0272-0.08330.22650.0482-0.0565-0.18910.06590.145162.20639.52124.426
1347.8702-14.028-27.0166.5102-57.891384.63921.19841.39935.11553.98681.1527-2.1305-6.6812-0.9559-2.35120.3531-0.0061-0.00590.36970.00150.352412.23898.189-29.685
140.68830.0254-0.08911.0321-0.69670.8279-0.0191-0.10510.10710.06690.06010.0409-0.1011-0.2591-0.04090.15720.0025-0.1137-0.0599-0.05810.064111.00372.33-9.074
150.75-0.0962-0.44820.6693-0.66192.23590.0399-0.1737-0.0425-0.01880.0607-0.04820.0054-0.1336-0.10060.1586-0.0359-0.1064-0.0186-0.02090.055716.93456.3520.517
161.4453-0.6439-1.2890.34660.71621.4872-0.0002-0.1332-0.09940.0013-0.0116-0.03720.11870.02640.01170.2074-0.016-0.1051-0.07640.01430.108531.30550.277-9.768
170.37050.1429-0.11990.4179-0.39530.8977-0.0267-0.10070.07650.0610.0561-0.0082-0.0863-0.1578-0.02950.16210.0086-0.1035-0.018-0.05560.086712.06870.74-5.066
182.20780.90991.58353.14451.23962.0632-0.06780.03130.1556-0.16440.0164-0.0168-0.2023-0.18450.05140.17980.0087-0.0879-0.1093-0.03690.090817.78184.471-21.651
192.0341-0.60860.20450.774-0.24090.3495-0.0527-0.0819-0.2736-0.1088-0.0406-0.13710.28620.02090.09330.26790.0324-0.0186-0.1220.05930.160550.67171.79321.342
203.0628-2.16270.48883.0483-1.30643.8963-0.01120.09280.0526-0.44710.36230.2908-0.2738-0.4304-0.35110.2179-0.0709-0.1818-0.03730.12190.064419.011101.7483.775
213.97170.5798-0.39461.4224-1.32743.01570.0474-0.30690.07960.1793-0.0415-0.1873-0.2435-0.0986-0.00590.21450.0184-0.0875-0.0872-0.02690.072336.50895.56923.503
221.26070.33660.21140.742-0.66630.8365-0.05810.22970.0957-0.0299-0.0285-0.12330.09560.00360.08660.2151-0.0024-0.0834-0.08850.04390.100846.191105.6848.45
231.0214-0.0288-0.12411.3739-1.12240.955-0.1351-0.0398-0.0391-0.22620.1317-0.00560.1831-0.14920.00340.2235-0.0288-0.0838-0.1116-0.03130.083532.49885.40115.852
242.5128-0.6685-0.18521.05620.36422.7184-0.05120.0905-0.3206-0.1546-0.0007-0.1472-0.00870.08740.05190.15990.01480.006-0.1548-0.02540.202655.97174.20211.861
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 74
3X-RAY DIFFRACTION3A75 - 122
4X-RAY DIFFRACTION4A123 - 290
5X-RAY DIFFRACTION5A291 - 427
6X-RAY DIFFRACTION6A428 - 466
7X-RAY DIFFRACTION7B1 - 72
8X-RAY DIFFRACTION8B73 - 97
9X-RAY DIFFRACTION9B98 - 249
10X-RAY DIFFRACTION10B250 - 304
11X-RAY DIFFRACTION11B305 - 423
12X-RAY DIFFRACTION12B424 - 465
13X-RAY DIFFRACTION13C1 - 7
14X-RAY DIFFRACTION14C8 - 91
15X-RAY DIFFRACTION15C92 - 162
16X-RAY DIFFRACTION16C163 - 255
17X-RAY DIFFRACTION17C256 - 410
18X-RAY DIFFRACTION18C411 - 465
19X-RAY DIFFRACTION19D1 - 71
20X-RAY DIFFRACTION20D72 - 126
21X-RAY DIFFRACTION21D127 - 141
22X-RAY DIFFRACTION22D142 - 249
23X-RAY DIFFRACTION23D250 - 380
24X-RAY DIFFRACTION24D381 - 466

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