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- PDB-3zcz: Crystal structure of a complex between Actinomadura R39 DD-peptid... -

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Basic information

Entry
Database: PDB / ID: 3zcz
TitleCrystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE
KeywordsHYDROLASE / INHIBITOR / PEPTIDOGLYCAN
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-TFR / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesACTINOMADURA SP. R39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6 Å
AuthorsSauvage, E. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P.
CitationJournal: Biochemistry / Year: 2013
Title: Inhibition of Dd-Peptidases by a Specific Trifluoroketone: Crystal Structure of a Complex with the Actinomadura R39 Dd-Peptidase.
Authors: Dzhekieva, L. / Adediran, S.A. / Herman, R. / Kerff, F. / Duez, C. / Charlier, P. / Sauvage, E. / Pratt, R.F.
History
DepositionNov 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
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 / pdbx_struct_conn_angle / struct_conn / 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 / _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
Revision 1.3Nov 13, 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)193,84430
Polymers190,8164
Non-polymers3,02726
Water5,819323
1
A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5339
Polymers47,7041
Non-polymers8298
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)48,3896
Polymers47,7041
Non-polymers6855
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)48,4857
Polymers47,7041
Non-polymers7816
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)48,4378
Polymers47,7041
Non-polymers7337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.653, 91.727, 106.882
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 47704.055 Da / Num. of mol.: 4 / Fragment: RESIDUES 50-516 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP. R39 (bacteria)
References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-TFR / (2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid


Type: D-peptide linking / Mass: 300.275 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H19F3N2O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.61 Å3/Da / Density % sol: 52.42 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorDate: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.6→48.9 Å / Num. obs: 61653 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: PDB ENTRY 2XDM

2xdm


Resolution: 2.6→47.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 25.69 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 1.115 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3120 5.1 %RANDOM
Rwork0.193 ---
obs0.195 58482 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20.53 Å2
2--0.75 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13394 0 174 323 13891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02113782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.97518868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.251858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86825.47574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.837151920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2121568
X-RAY DIFFRACTIONr_chiral_restr0.0610.22182
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110660
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_it0.3771.59194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.709214584
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.90834588
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5664.54284
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 247 -
Rwork0.256 4268 -
obs--99.93 %
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)
143.25163.029517.50710.64221.57317.3719-0.5044-0.038-0.7650.01920.30180.4708-0.12280.11980.20270.9131-0.3578-0.05490.28980.2680.7794-16.038-27.33137.585
20.93990.8040.06011.20270.40260.7769-0.08710.1461-0.1525-0.0160.0701-0.06240.1695-0.04920.0170.4348-0.02-0.10680.1432-0.01980.32871.313-13.38635.388
35.3272.1345-0.1522.66250.6892.3460.1632-0.37860.34060.1139-0.0198-0.1044-0.08940.1805-0.14350.35410.0192-0.14370.1398-0.0590.370727.87417.14349.056
41.4817-0.54290.12770.62040.24260.2907-0.0173-0.00970.1377-0.03370.0204-0.0243-0.02560.0027-0.0030.42940.0051-0.12860.1344-0.00070.3538.31415.99441.66
51.62920.5903-0.2810.7204-0.24060.9935-0.01070.0313-0.10180.00780.0543-0.01430.0384-0.0001-0.04360.42660.0167-0.13030.1271-0.00770.33554.737-9.59138.876
61.05020.9375-1.62312.5356-1.2455.8652-0.11090.0968-0.0196-0.030.18580.12240.3186-0.5849-0.07490.3474-0.0356-0.14810.15440.01580.3479-11.167-16.66841.818
70.79710.24120.01460.7667-0.58922.49240.01060.04040.2148-0.01370.1340.1363-0.3967-0.359-0.14460.47520.1025-0.07430.06350.03120.400254.44334.35228.05
81.4272-0.2818-0.03323.791-2.71976.4982-0.0355-0.2847-0.12560.32810.11220.00240.0237-0.3172-0.07670.4159-0.0272-0.12070.2107-0.01940.264361.13311.03368.837
90.5666-0.212-0.8210.28810.09611.49450.0225-0.11980.01490.027-0.004-0.02340.09590.1611-0.01840.4217-0.0298-0.13750.16840.00250.365472.02310.07746.726
100.89320.00450.05852.4572-2.26834.33030.0919-0.18480.2410.1685-0.0218-0.0001-0.12230.0456-0.07010.3795-0.0331-0.11450.1244-0.0890.268162.6617.19258.198
111.15420.6391-0.51231.8578-1.17492.20060.0834-0.02790.03340.06190.06160.0461-0.3648-0.2816-0.1450.43410.0679-0.07730.04860.00050.35155.90130.0336.709
123.30041.7330.5768.3895-0.1582.281-0.05520.17680.3635-0.10820.1391-0.0764-0.4487-0.068-0.0840.48630.0499-0.06070.02230.05750.382262.20639.52124.426
131.0202-5.9894-1.955758.8316-22.724854.75890.91660.07280.44881.5712.53550.093-5.3113-2.9003-3.45220.99270.46550.49910.63720.53791.27412.23898.189-29.685
140.81480.1047-0.08351.0269-0.52680.8066-0.0218-0.15190.14240.08570.10150.1075-0.1375-0.3006-0.07970.39540.0071-0.11020.1962-0.06470.289611.00372.33-9.074
151.1736-0.0725-0.22890.787-0.65062.34560.0823-0.2082-0.0089-0.02580.04160.00570.0144-0.071-0.12390.4062-0.0626-0.11590.2039-0.02670.283616.93456.3520.517
161.7311-0.7175-1.61990.39130.52331.9669-0.0064-0.1653-0.1079-0.01020.0067-0.01040.1410.1294-0.00030.4585-0.0487-0.12560.15150.02270.382331.30550.277-9.768
170.46360.201-0.25270.7664-0.75441.24650.0153-0.15990.10160.0930.04580.0296-0.1223-0.173-0.06120.4128-0.0167-0.1020.1948-0.08380.325312.06870.74-5.066
182.91561.02831.02384.39671.48322.1779-0.03580.00760.1932-0.14870.1154-0.0803-0.2516-0.2481-0.07970.43280.0192-0.10190.0737-0.04850.338617.78184.471-21.651
191.5068-0.24070.02050.781-0.34920.5132-0.2115-0.0799-0.4272-0.1763-0.0409-0.2840.3567-0.05510.25230.53990.00520.04190.0520.04120.531650.67171.79321.342
203.0132-1.3620.79323.2985-0.30133.5042-0.20090.26850.2159-0.4290.42580.3568-0.2605-0.565-0.22490.448-0.1013-0.19020.30770.2210.29619.011101.7483.775
212.99580.0512-0.24581.2634-1.72083.70880.0673-0.4170.12680.2968-0.0068-0.161-0.1524-0.1491-0.06050.46650.0307-0.0980.1082-0.02620.333736.50895.56923.503
222.31230.69180.0571.3012-0.92480.8359-0.09620.26320.1521-0.06770.0188-0.1180.07190.00910.07740.4788-0.0121-0.07310.13910.05250.345846.191105.6848.45
231.4198-0.0629-0.19271.8481-1.22161.0544-0.23120.0148-0.133-0.2120.2256-0.02450.1717-0.26470.00560.4715-0.045-0.08060.1024-0.04230.306432.49885.40115.852
242.5204-0.8981-0.0290.5253-0.43063.6557-0.08260.1365-0.5218-0.1723-0.0834-0.0663-0.10590.27060.1660.4860.01260.16660.0346-0.05810.61655.97174.20211.861
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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