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

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Basic information

Entry
Database: PDB / ID: 4mph
TitleCrystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-bound
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 / Hedgehog/DD-peptidase fold / VanY-like family / MEROPS family M15B / zinc-dependent metallopeptidase / peptidoglycan metallopeptidase / BaLdcB / L / D-carboxypeptidase / tetrapeptidase / substrate L-Ala-D-iso-Gln-L-Lys-D-Ala
Function / homology
Function and homology information


carboxypeptidase activity / 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
Chem-PE3 / 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 / SAD / Resolution: 2.0301 Å
AuthorsStogios, P.J. / 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
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Structure summary
Revision 1.2Jun 18, 2014Group: Database references / Other
Revision 1.3Jul 23, 2014Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _struct_conn.ptnr2_label_asym_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

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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)44,4937
Polymers43,6572
Non-polymers8365
Water8,287460
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: D-alanyl-D-alanine carboxypeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9293
Polymers21,8281
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: D-alanyl-D-alanine carboxypeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5644
Polymers21,8281
Non-polymers7363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.831, 112.337, 125.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-643-

HOH

21A-672-

HOH

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Components

#1: Protein D-alanyl-D-alanine carboxypeptidase family protein / Serine-type D-Ala-D-Ala carboxypeptidase


Mass: 21828.436 Da / Num. of mol.: 2 / Fragment: VanY-like peptidase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: AMES / Gene: BACI_C24940, BAS2349, BA_2526, DACA3, GBAA_2526, VANY / Plasmid: PMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q81QA6, UniProt: A0A6L8PDI9*PLUS
#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.: 2 / 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.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 4K, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.282 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. obs: 35417 / % possible obs: 99.8 % / Observed criterion σ(F): -2 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rsym value: 0.101 / Net I/σ(I): 32.11
Reflection shellResolution: 2.03→2.06 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 4.23 / Num. unique all: 1708 / Rsym value: 0.511 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.solve)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.0301→28.308 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1894 3374 5 %random
Rwork0.1491 ---
obs0.1511 67494 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0301→28.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 14 460 3405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123064
X-RAY DIFFRACTIONf_angle_d0.9914148
X-RAY DIFFRACTIONf_dihedral_angle_d11.8481155
X-RAY DIFFRACTIONf_chiral_restr0.066434
X-RAY DIFFRACTIONf_plane_restr0.003533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0301-2.05910.30231350.22822578X-RAY DIFFRACTION94
2.0591-2.08980.23621380.20712548X-RAY DIFFRACTION96
2.0898-2.12250.27771340.19372590X-RAY DIFFRACTION98
2.1225-2.15720.21711450.18592743X-RAY DIFFRACTION100
2.1572-2.19440.20431410.17692662X-RAY DIFFRACTION100
2.1944-2.23430.22661410.16662670X-RAY DIFFRACTION100
2.2343-2.27730.19731410.1612687X-RAY DIFFRACTION100
2.2773-2.32370.22551420.15682702X-RAY DIFFRACTION100
2.3237-2.37420.19781410.15152701X-RAY DIFFRACTION100
2.3742-2.42940.18391400.15242633X-RAY DIFFRACTION100
2.4294-2.49020.20451390.1622697X-RAY DIFFRACTION100
2.4902-2.55740.2331450.16892717X-RAY DIFFRACTION100
2.5574-2.63260.22761430.17182667X-RAY DIFFRACTION100
2.6326-2.71760.21691400.16012707X-RAY DIFFRACTION100
2.7176-2.81460.20311370.15782662X-RAY DIFFRACTION100
2.8146-2.92720.20741430.15252687X-RAY DIFFRACTION100
2.9272-3.06030.18421450.1552686X-RAY DIFFRACTION100
3.0603-3.22140.17011420.14882671X-RAY DIFFRACTION100
3.2214-3.42290.17181460.14672697X-RAY DIFFRACTION100
3.4229-3.68670.17141400.13472687X-RAY DIFFRACTION100
3.6867-4.05670.14931390.12272688X-RAY DIFFRACTION100
4.0567-4.64150.19271380.11442680X-RAY DIFFRACTION100
4.6415-5.83930.1521410.13032698X-RAY DIFFRACTION100
5.8393-28.3110.16141380.14892662X-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)
13.80622.1788-1.45776.86361.10243.9041-0.01030.09320.5855-0.0615-0.07660.6956-0.6898-0.74220.13210.33980.1658-0.05090.32260.0890.434440.014450.218712.0458
24.40740.1396-0.2952.4590.18443.4152-0.01010.3808-0.162-0.19050.02260.03570.1462-0.2394-0.0240.1319-0.0101-0.02290.19150.02270.096245.632530.400311.3699
30.53850.757-0.71035.43630.75745.88510.0142-0.94480.25812.1249-0.254-0.3478-0.23580.78520.17070.7429-0.0444-0.06470.58320.00490.349643.933545.913327.5081
43.0217-0.718-0.21412.421-0.17872.0892-0.01860.09730.16220.1092-0.0173-0.2321-0.14740.26250.03320.1363-0.0225-0.00690.2070.06060.144455.453137.855914.4115
54.41841.39521.181.93340.15412.73480.0584-0.1301-0.04540.1772-0.0513-0.1541-0.0550.335-0.01070.16870.0126-0.02160.20960.1030.168866.517824.525744.7573
63.7351-0.26060.00821.37160.20962.952-0.02070.1772-0.2673-0.0047-0.0650.05850.2322-0.27330.07090.1652-0.0075-0.03050.19110.08270.185149.793720.112836.786
73.43731.44430.60934.7379-1.87478.2489-0.47281.10221.6794-0.41540.52410.9062-1.5769-0.9011-0.04530.5655-0.0397-0.23050.64130.35180.735164.25737.22833.6366
83.19830.59470.83551.65260.21272.2701-0.0394-0.04730.5766-0.0306-0.02960.2802-0.3613-0.56430.06740.20050.0759-0.02460.27590.06350.25147.422729.877443.1843
91.9984-0.23210.51683.179-1.11211.8301-0.08650.37960.4325-0.15830.0237-0.3047-0.41030.02740.04110.2502-0.0236-0.00510.24660.12610.267854.92546.93788.1294
103.05030.10551.03292.68280.51213.93190.0647-0.5890.25880.1503-0.16210.072-0.1309-0.10720.08590.18790.0219-0.00410.28730.00070.202953.673829.382152.5622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 55:77
2X-RAY DIFFRACTION2chain A and resi 78:126
3X-RAY DIFFRACTION3chain A and resi 127:154
4X-RAY DIFFRACTION4chain A and resi 155:208
5X-RAY DIFFRACTION5chain B and resi 52:82
6X-RAY DIFFRACTION6chain B and resi 83:129
7X-RAY DIFFRACTION7chain B and resi 130:156
8X-RAY DIFFRACTION8chain B and resi 157:208
9X-RAY DIFFRACTION9chain A and resi 209:243
10X-RAY DIFFRACTION10chain B and resi 209:243

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