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- PDB-4jid: Crystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc... -

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Basic information

Entry
Database: PDB / ID: 4jid
TitleCrystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-free
ComponentsD-alanyl-D-alanine carboxypeptidase family protein
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / D-alanyl-D-alanine carboxypeptidase / BaLdcB / L / D-carboxypeptidase / tetrapeptidase / substrate L-Ala-D-iso-Gln-L-Lys-D-Ala
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / carboxypeptidase activity / membrane => GO:0016020 / proteolysis / membrane / metal ion binding
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
D-alanyl-D-alanine carboxypeptidase family protein / D-alanyl-D-alanine carboxypeptidase family protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMinasov, G. / Wawrzak, Z. / Onopriyenko, O. / Skarina, T. / Shatsman, S. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Structure / Year: 2014
Title: Structure of the LdcB LD-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition.
Authors: Hoyland, C.N. / Aldridge, C. / Cleverley, R.M. / Duchene, M.C. / Minasov, G. / Onopriyenko, O. / Sidiq, K. / Stogios, P.J. / Anderson, W.F. / Daniel, R.A. / Savchenko, A. / Vollmer, W. / Lewis, R.J.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Other / Structure summary
Revision 1.2Feb 19, 2014Group: Structure summary
Revision 1.3Jun 18, 2014Group: Database references
Revision 1.4Jul 23, 2014Group: Database references
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Sep 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 / 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 / _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-alanyl-D-alanine carboxypeptidase family protein
B: D-alanyl-D-alanine carboxypeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7426
Polymers48,6002
Non-polymers1424
Water3,855214
1
A: D-alanyl-D-alanine carboxypeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4425
Polymers24,3001
Non-polymers1424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-alanyl-D-alanine carboxypeptidase family protein


Theoretical massNumber of molelcules
Total (without water)24,3001
Polymers24,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.576, 112.996, 124.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein D-alanyl-D-alanine carboxypeptidase family protein


Mass: 24300.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BACI_c24940, dacA3, VanY / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: D8GYY2, UniProt: A0A6L8PDI9*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 2.3mg/mL, 0.3M Sodium cloride, 0.1M 0.1M HEPES pH 7.5; Screen: 0.1M HEPES pH 7.0, 30% Jeffamine ED-2001; Cryo: paraton., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 24059 / Num. obs: 24059 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.4 / % possible all: 94.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F78

4f78


Resolution: 2.3→29.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.586 / SU ML: 0.175 / Isotropic thermal model: Individually Refined / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25873 1226 5.1 %RANDOM
Rwork0.19099 ---
obs0.19442 22730 98.16 %-
all-22730 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.013 Å2
Baniso -1Baniso -2Baniso -3
1--4.27 Å2-0 Å20 Å2
2--7.02 Å2-0 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 4 214 3130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223120
X-RAY DIFFRACTIONr_bond_other_d0.0010.022162
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9584226
X-RAY DIFFRACTIONr_angle_other_deg0.79735281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6555390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.00924.706153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48815557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9021515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02643
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_it1.2211.51898
X-RAY DIFFRACTIONr_mcbond_other0.3591.5766
X-RAY DIFFRACTIONr_mcangle_it2.06523055
X-RAY DIFFRACTIONr_scbond_it3.61931222
X-RAY DIFFRACTIONr_scangle_it5.234.51171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 60 -
Rwork0.262 1585 -
obs--93.25 %
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)
15.9844-1.03551.35450.1872-0.05315.4423-0.0330.53420.08470.0026-0.12610.0018-0.2988-0.39070.15910.1603-0.0317-0.0360.1954-0.09470.144747.490426.635416.9492
23.36270.26490.37461.767-0.06195.03550.0031-0.2435-0.53950.09530.02670.01720.2960.3091-0.02980.17420.0034-0.03380.1455-0.07150.239365.283819.123525.8753
32.8685-3.9086-3.66745.6784.14646.8270.0713-0.23950.33650.18190.2528-0.4653-1.04340.3038-0.32410.581-0.0348-0.18130.4456-0.12170.375150.95736.86130.4087
47.2406-0.52140.30411.26310.41642.7239-0.0280.46980.7187-0.0160.0265-0.2806-0.36210.44740.00140.1389-0.055-0.01780.1723-0.01920.169367.506730.124719.1808
53.23640.31981.29480.9188-0.41544.2891-0.10950.78280.3094-0.05250.11120.011-0.25160.3142-0.00170.1027-0.0307-0.00620.3237-0.04590.144561.676329.489110.1869
615.7197-4.47640.30586.2003-1.75525.4774-0.0131-0.23471.3496-0.1522-0.1842-0.7295-0.78451.23320.19730.3933-0.198-0.04320.2947-0.04160.539575.386850.004749.8818
76.15890.2426-0.57042.09450.16593.08310.0279-0.4828-0.18750.05250.011-0.03930.25040.3137-0.0390.10330.0006-0.01040.103-0.03260.058769.597331.690450.1955
814.1909-7.3139-1.38511.6279-0.06461.25520.54922.2894-0.1624-1.1957-0.46870.121-0.1857-0.2859-0.08050.574-0.01550.01150.61120.06770.400270.893946.619335.4309
94.79690.33620.8332.73340.19452.01110.0227-0.15520.2502-0.0805-0.03360.0972-0.1888-0.58880.01090.14770.00140.03050.227-0.06440.125658.805437.965348.3415
103.396-0.6192.15214.07740.4457.3413-0.0745-0.59980.65410.25350.01040.1716-0.7351-0.23280.06410.1363-0.01670.04470.1474-0.15740.197760.097347.032354.2813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 77
2X-RAY DIFFRACTION2A78 - 126
3X-RAY DIFFRACTION3A127 - 154
4X-RAY DIFFRACTION4A155 - 208
5X-RAY DIFFRACTION5A209 - 243
6X-RAY DIFFRACTION6B56 - 78
7X-RAY DIFFRACTION7B79 - 129
8X-RAY DIFFRACTION8B130 - 156
9X-RAY DIFFRACTION9B157 - 208
10X-RAY DIFFRACTION10B209 - 243

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