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

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Basic information

Entry
Database: PDB / ID: 4mur
TitleCrystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant
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 / 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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Structure summary
Revision 1.2Jan 22, 2014Group: Other
Revision 1.3Apr 23, 2014Group: Database references
Revision 1.4May 14, 2014Group: Database references
Revision 1.5Sep 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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)52,51115
Polymers49,5322
Non-polymers2,97913
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-178 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.239, 44.725, 62.519
Angle α, β, γ (deg.)86.27, 77.70, 63.74
Int Tables number1
Space group name H-MP1
Detailsdimer is in the asymmetric unit.

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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 , 5 types, 601 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 43.76 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M magnesium chloride, 0.05 M MES, 20% PEG 8K, pH 5.6, VAPOR DIFFUSION, HANGING 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: 1.63→40.09 Å / Num. obs: 50465 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 18
Reflection shellResolution: 1.63→1.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13646 / % possible all: 92.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.8.3_1479)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4F78

4f78


Resolution: 1.65→34.449 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2480 5.16 %random
Rwork0.1553 ---
obs0.1575 46109 95.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→34.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 38 588 3766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123385
X-RAY DIFFRACTIONf_angle_d1.0724614
X-RAY DIFFRACTIONf_dihedral_angle_d15.5221310
X-RAY DIFFRACTIONf_chiral_restr0.071479
X-RAY DIFFRACTIONf_plane_restr0.005598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66880.34161490.27912578X-RAY DIFFRACTION83
1.6688-1.68840.27721450.2483000X-RAY DIFFRACTION93
1.6884-1.7090.25361700.23572900X-RAY DIFFRACTION91
1.709-1.73060.25591710.22733057X-RAY DIFFRACTION93
1.7306-1.75340.27581520.21062867X-RAY DIFFRACTION92
1.7534-1.77740.24241840.20282968X-RAY DIFFRACTION94
1.7774-1.80280.23591380.2123012X-RAY DIFFRACTION92
1.8028-1.82970.24271720.19132925X-RAY DIFFRACTION94
1.8297-1.85830.21492060.18413051X-RAY DIFFRACTION95
1.8583-1.88880.21831770.16953053X-RAY DIFFRACTION96
1.8888-1.92130.16221580.16833083X-RAY DIFFRACTION96
1.9213-1.95630.20661610.17363130X-RAY DIFFRACTION96
1.9563-1.99390.21051760.17962992X-RAY DIFFRACTION97
1.9939-2.03460.22041710.16813138X-RAY DIFFRACTION97
2.0346-2.07880.22221540.17163083X-RAY DIFFRACTION96
2.0788-2.12720.23941450.16433133X-RAY DIFFRACTION97
2.1272-2.18040.20951600.15433033X-RAY DIFFRACTION97
2.1804-2.23930.23051940.15993167X-RAY DIFFRACTION98
2.2393-2.30520.19781590.15923061X-RAY DIFFRACTION97
2.3052-2.37960.21191670.14863115X-RAY DIFFRACTION98
2.3796-2.46460.19532020.1473126X-RAY DIFFRACTION98
2.4646-2.56320.2261640.15633112X-RAY DIFFRACTION98
2.5632-2.67990.1911710.15693124X-RAY DIFFRACTION98
2.6799-2.82110.20571580.15843181X-RAY DIFFRACTION98
2.8211-2.99770.19191560.15613163X-RAY DIFFRACTION98
2.9977-3.2290.20051710.14943115X-RAY DIFFRACTION98
3.229-3.55370.17911620.13273098X-RAY DIFFRACTION98
3.5537-4.06720.15671690.1233205X-RAY DIFFRACTION99
4.0672-5.12160.16241930.1193116X-RAY DIFFRACTION98
5.1216-34.45680.18671370.14913162X-RAY DIFFRACTION98
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)
10.035-0.0493-0.01560.03150.00150.0008-0.03330.2920.24310.16680.10250.22130.0729-0.14240.00140.15750.01270.03290.12470.03160.236632.796315.453123.801
20.51140.3502-0.48860.1795-0.19460.39820.03070.0847-0.01660.0755-0.01150.08520.0037-0.07170.04130.0890.0031-0.00950.076100.108235.00331.744634.5365
30.13550.1886-0.18960.19460.0370.03480.0707-0.04-0.00290.1023-0.03980.0033-0.01520.01730.01760.12840.0118-0.00790.0964-0.00330.12644.29426.356137.7111
40.10740.0449-0.15150.2241-0.07680.4018-0.01060.0453-0.0183-0.0324-0.0037-0.043-0.0062-0.0112-0.04770.078-0.00130.00560.0811-0.00630.076746.45936.686520.4984
50.0219-0.0050.02350.0019-0.00710.0031-0.01960.04910.01010.08410.08220.0848-0.1542-0.16600.16230.0005-0.02670.159-0.00860.15712.9767.291850.0944
60.76130.0069-0.60780.12050.00910.6190.0145-0.07140.0214-0.0213-0.01080.0692-0.04090.1685-0.01850.07160.001-0.00740.06050.00520.065927.88550.991847.6558
70.003-0.0155-0.00360.00810.02390.00410.02880.0647-0.1384-0.044-0.0893-0.06540.03180.01700.2970.1061-0.010.2853-0.00830.315634.4754-11.139847.4335
80.2276-0.1731-0.23710.162-0.23120.69490.0154-0.216-0.0673-0.044-0.0302-0.0050.08680.0199-0.05120.1097-0.00910.00190.15530.01350.081519.9905-2.361762.1564
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 125:189
5X-RAY DIFFRACTION5chain B and resi 1:18
6X-RAY DIFFRACTION6chain B and resi 19:106
7X-RAY DIFFRACTION7chain B and resi 107:117
8X-RAY DIFFRACTION8chain B and resi 118:189

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