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- PDB-4oak: Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pe... -

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Basic information

Entry
Database: PDB / ID: 4oak
TitleCrystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II)
ComponentsD,D-dipeptidase/D,D-carboxypeptidase
KeywordsHYDROLASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID / ALPHA+BETA PROTEIN / METALLOPEPTIDASE / HEDGEHOG/DD-PEPTIDASE FOLD / MEROPS M15B SUBFAMILY / ZN2+-DEPENDENT / VANCOMYCIN RESISTANCE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


D-Ala-D-Ala dipeptidase / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / carboxypeptidase activity / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Peptidase M15B / : / D-alanyl-D-alanine carboxypeptidase / 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
COPPER (II) ION / D-ALANINE / Chem-PE3 / Bifunctional D-Ala-D-Ala dipeptidase and D-Ala-D-Ala carboxypeptidase VanXYC
Similarity search - Component
Biological speciesEnterococcus gallinarum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStogios, P.J. / Evdokimova, E. / Meziane-Cherif, D. / Di Leo, R. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the evolution of vancomycin resistance D,D-peptidases.
Authors: Meziane-Cherif, D. / Stogios, P.J. / Evdokimova, E. / Savchenko, A. / Courvalin, P.
History
DepositionJan 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Other
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3May 14, 2014Group: Database references
Revision 1.4Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 1.5Oct 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,D-dipeptidase/D,D-carboxypeptidase
B: D,D-dipeptidase/D,D-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,08022
Polymers49,5322
Non-polymers3,54820
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-118 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.939, 43.083, 66.316
Angle α, β, γ (deg.)80.53, 74.52, 64.01
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D,D-dipeptidase/D,D-carboxypeptidase / D / D-dipeptidase/D / D-carboxypeptidase VanXYc


Mass: 24765.953 Da / Num. of mol.: 2 / Fragment: VanXYc / Mutation: D59S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus gallinarum (bacteria) / Strain: BM4174 / Gene: vanXYc / Plasmid: P15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JN36

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Non-polymers , 7 types, 344 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H58O15
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M MgCl2, 0.05 M MES, 20% PEG8K and 0.1 M phenantroline, 2 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K and 1 mM CuCl2, 1.5 h incubation, ...Details: 0.1 M MgCl2, 0.05 M MES, 20% PEG8K and 0.1 M phenantroline, 2 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K and 1 mM CuCl2, 1.5 h incubation, transferred crystal to new drop with 0.1 M MgCl2, 0.05 M MES, 22% PEG8K, 1 mM CuCl2 and 20 mM D-Ala-D-Ala. Cryoprotectant: paratone, pH 5.6, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.33 Å / Num. obs: 25760 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 11
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.3 / % possible all: 92.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: dev_1538)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4MUR

4mur


Resolution: 2→19.33 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 1218 5.05 %random
Rwork0.1886 ---
obs0.191 22801 94.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 84 324 3558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183330
X-RAY DIFFRACTIONf_angle_d0.814482
X-RAY DIFFRACTIONf_dihedral_angle_d12.7761260
X-RAY DIFFRACTIONf_chiral_restr0.045464
X-RAY DIFFRACTIONf_plane_restr0.004578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03630.36971300.32457X-RAY DIFFRACTION91
2.0363-2.07550.32221320.28642503X-RAY DIFFRACTION92
2.0755-2.11780.29681280.26292501X-RAY DIFFRACTION93
2.1178-2.16380.28351220.2522531X-RAY DIFFRACTION92
2.1638-2.2140.22951340.24532498X-RAY DIFFRACTION93
2.214-2.26930.3181300.25262567X-RAY DIFFRACTION93
2.2693-2.33060.27291210.22632551X-RAY DIFFRACTION94
2.3306-2.3990.30051380.22872505X-RAY DIFFRACTION94
2.399-2.47630.30151260.22682583X-RAY DIFFRACTION94
2.4763-2.56460.24251320.21622543X-RAY DIFFRACTION94
2.5646-2.66710.31471360.21762630X-RAY DIFFRACTION95
2.6671-2.78810.29441280.20712568X-RAY DIFFRACTION95
2.7881-2.93460.22181500.20032555X-RAY DIFFRACTION96
2.9346-3.11780.25651630.22567X-RAY DIFFRACTION96
3.1178-3.35740.22541560.17792612X-RAY DIFFRACTION97
3.3574-3.69310.23211260.15242655X-RAY DIFFRACTION97
3.6931-4.22260.19921400.14152658X-RAY DIFFRACTION98
4.2226-5.30190.15341460.13442652X-RAY DIFFRACTION98
5.3019-19.33460.18211550.15122664X-RAY DIFFRACTION99
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)
16.6105-0.0563-1.45487.7366-4.97513.8025-0.0018-0.3780.78430.1465-0.2332-0.9574-0.12850.2550.32710.2806-0.00150.00260.2004-0.04450.2691-35.72311.0866-21.6175
21.2676-1.16730.50655.5745-2.21762.91430.07360.04040.0108-0.2451-0.1405-0.1750.25280.20270.07810.13910.03110.01480.2015-0.03070.1408-37.5589-3.7123-32.1257
32.1113-0.1155-0.33772.7406-2.21922.15350.10810.131-0.1346-0.4222-0.05770.2470.4214-0.2837-0.06760.26670.0233-0.05490.1957-0.02480.1901-48.07290.5007-34.4863
42.0398-0.21130.65442.04270.81434.3701-0.0007-0.02190.03850.0561-0.090.17590.0234-0.390.08460.124-0.01690.00550.20430.00660.1323-47.9121.1503-17.1603
56.74033.34990.1286.96295.76747.9831-0.0635-0.17490.56350.5086-0.0582-0.4484-0.0990.02870.10160.17380.0091-0.00920.22230.05820.2049-17.86223.4249-50.4244
64.2583-2.1731.81692.7587-0.94294.0644-0.05590.0623-0.14760.09720.07780.1654-0.0505-0.432-0.03780.1574-0.00010.05140.1647-0.0120.1627-34.5491-2.5797-45.9737
73.3765-1.94442.84221.0555-1.71033.89120.2074-0.2078-0.4697-0.0130.02060.31730.5966-0.4563-0.19070.3004-0.04620.0120.2004-0.01320.2682-29.6456-13.0725-45.4764
83.36671.1175-1.37422.9004-1.07824.3734-0.21290.2147-0.3127-0.04870.0192-0.08590.36530.03590.150.18510.0302-0.00090.155-0.03980.1471-24.1515-7.5939-60.9609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1:19
2X-RAY DIFFRACTION2chain A and resi 20:76
3X-RAY DIFFRACTION3chain A and resi 77:124
4X-RAY DIFFRACTION4chain A and resi 125:190
5X-RAY DIFFRACTION5chain B and resi 1:19
6X-RAY DIFFRACTION6chain B and resi 20:76
7X-RAY DIFFRACTION7chain B and resi 77:124
8X-RAY DIFFRACTION8chain B and resi 125:190

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