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

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Basic information

Entry
Database: PDB / ID: 4mus
TitleCrystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Ala-D-Ala phosphinate analog
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 D / D-DIPEPTIDASE / D-PENTAPEPTIDASE / ANTIBIOTIC RESISTANCE / VANCOMYCIN 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
Chem-2D8 / Chem-LY0 / Bifunctional D-Ala-D-Ala dipeptidase and D-Ala-D-Ala carboxypeptidase VanXYC
Similarity search - Component
Biological speciesEnterococcus gallinarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.675 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
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 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_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_alt_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_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_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _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,D-dipeptidase/D,D-carboxypeptidase
B: D,D-dipeptidase/D,D-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,66711
Polymers49,5322
Non-polymers1,1359
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-32 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.256, 44.780, 62.407
Angle α, β, γ (deg.)86.84, 77.29, 64.15
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 / 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, 521 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-2D8 / (2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid


Mass: 195.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14NO4P
#4: Chemical ChemComp-LY0 / (2R)-3-[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid


Mass: 195.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14NO4P
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M magnesium chloride, 0.05 M MES, 20% PEG 8K, 50 mM PHY D-Ala-D-Ala phosphinate analog, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27696 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 26, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27696 Å / Relative weight: 1
ReflectionResolution: 1.67→38.67 Å / Num. obs: 47059 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.6
Reflection shellResolution: 1.67→1.87 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 4.9 / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4F78

4f78


Resolution: 1.675→37.198 Å / SU ML: 0.17 / σ(F): 1.98 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 4023 4.31 %
Rwork0.168 --
obs0.1697 46627 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.675→37.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 62 512 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073330
X-RAY DIFFRACTIONf_angle_d1.2894533
X-RAY DIFFRACTIONf_dihedral_angle_d16.0641320
X-RAY DIFFRACTIONf_chiral_restr0.055467
X-RAY DIFFRACTIONf_plane_restr0.005585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6749-1.69460.27431460.25112936X-RAY DIFFRACTION90
1.6946-1.71530.29431300.24722870X-RAY DIFFRACTION91
1.7153-1.7370.23941080.23632888X-RAY DIFFRACTION91
1.737-1.75980.2691300.22812928X-RAY DIFFRACTION92
1.7598-1.78390.24011340.21572990X-RAY DIFFRACTION93
1.7839-1.80940.27521180.22672996X-RAY DIFFRACTION95
1.8094-1.83640.25781500.21483104X-RAY DIFFRACTION96
1.8364-1.86510.2521320.20413032X-RAY DIFFRACTION96
1.8651-1.89570.25871580.18563000X-RAY DIFFRACTION96
1.8957-1.92840.23131300.19573044X-RAY DIFFRACTION96
1.9284-1.96340.22441440.18793088X-RAY DIFFRACTION96
1.9634-2.00120.22131420.17463104X-RAY DIFFRACTION96
2.0012-2.04210.24431340.17563076X-RAY DIFFRACTION97
2.0421-2.08650.23651380.17283050X-RAY DIFFRACTION97
2.0865-2.1350.20051420.16343168X-RAY DIFFRACTION97
2.135-2.18840.15961440.1643056X-RAY DIFFRACTION97
2.1884-2.24750.18741480.16543100X-RAY DIFFRACTION97
2.2475-2.31370.22351200.16643112X-RAY DIFFRACTION98
2.3137-2.38830.20021600.16143106X-RAY DIFFRACTION97
2.3883-2.47370.22491440.173170X-RAY DIFFRACTION98
2.4737-2.57270.21681260.16033090X-RAY DIFFRACTION98
2.5727-2.68970.18651420.16763134X-RAY DIFFRACTION99
2.6897-2.83150.21961520.16443174X-RAY DIFFRACTION99
2.8315-3.00880.21041320.16613190X-RAY DIFFRACTION99
3.0088-3.2410.2281460.15853100X-RAY DIFFRACTION99
3.241-3.5670.17931480.14913152X-RAY DIFFRACTION99
3.567-4.08250.17861420.14643202X-RAY DIFFRACTION100
4.0825-5.14140.16191400.13823170X-RAY DIFFRACTION100
5.1414-37.2070.21681430.1773192X-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)
15.83630.01242.26392.065-2.73185.8361-0.21970.24720.6773-0.08070.25410.3984-0.7707-0.1307-0.10830.28030.01170.01550.2601-0.01260.278515.88891.859851.0712
23.81391.152.1541.62451.29534.93850.049-0.1690.12420.0868-0.0213-0.0971-0.16310.4671-0.02850.1146-0.02010.02720.17850.01330.11533.2279-2.356649.7899
31.85991.44431.62171.22911.02692.86150.22740.0391-0.50170.1635-0.0035-0.23940.60060.4587-0.20030.24510.0735-0.0130.21160.00530.246129.6712-13.06149.2503
43.9063-0.7376-1.98112.66760.42824.2712-0.0075-0.3136-0.20.076-0.03580.09910.1938-0.15630.04970.1421-0.02860.00810.17730.03050.086421.66-7.78863.235
52.44820.3377-4.00218.40252.45067.63480.00310.7370.57020.15130.06921.3575-0.3258-1.3266-0.0570.27410.06580.03960.38970.06670.386535.27289.831625.3483
62.81130.7318-0.83575.0321.74013.47310.01890.0603-0.02310.1294-0.00230.1511-0.0312-0.0892-0.00610.0873-0.01670.01410.1170.03540.091437.7072-4.11535.8393
73.1158-0.2086-0.49462.61381.86511.5235-0.0492-0.3746-0.10210.44220.0773-0.13130.03470.1174-0.03420.1829-0.0036-0.00990.15660.03930.117746.91020.809139.0399
83.20540.3126-0.11644.1145-0.84685.5265-0.04330.25030.1183-0.20110.0067-0.1496-0.1456-0.00090.03940.0617-0.00450.02070.1363-0.00790.099348.81850.967722.4488
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 125:188
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 125:188

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