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- PDB-4y7p: Structure of alkaline D-peptidase from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 4y7p
TitleStructure of alkaline D-peptidase from Bacillus cereus
ComponentsAlkaline D-peptidase
KeywordsHYDROLASE / Penicillin binding protein / apo form
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Alkaline D-peptidase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNakano, S. / Okazaki, S. / Ishitsubo, E. / Kawahara, N. / Komeda, H. / Tokiwa, H. / Asano, Y.
CitationJournal: Sci Rep / Year: 2015
Title: Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B
Authors: Nakano, S. / Okazaki, S. / Ishitsubo, E. / Kawahara, N. / Komeda, H. / Tokiwa, H. / Asano, Y.
History
DepositionFeb 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkaline D-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2534
Polymers42,0791
Non-polymers1743
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-10 kcal/mol
Surface area13980 Å2
Unit cell
Length a, b, c (Å)104.019, 104.019, 98.535
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Alkaline D-peptidase


Mass: 42078.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: adp / Production host: Escherichia coli (E. coli) / References: UniProt: P94288
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG3350, 0.2M sodium thiocyanate, 3% D-glucose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 69524 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 33.3
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.487 / Num. unique all: 69524

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HVB

1hvb


Resolution: 2.1→24.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.234 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21922 1813 5 %RANDOM
Rwork0.17395 ---
obs0.17609 69524 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.605 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 9 203 2835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192713
X-RAY DIFFRACTIONr_bond_other_d0.0010.022587
X-RAY DIFFRACTIONr_angle_refined_deg2.1191.9753666
X-RAY DIFFRACTIONr_angle_other_deg0.95635979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6795347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05424.775111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85915469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0061512
X-RAY DIFFRACTIONr_chiral_restr0.1410.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213082
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02594
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 132 -
Rwork0.261 2476 -
obs--99.58 %

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