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- PDB-4k7c: Crystal structure of pepw from lactobacillus rhamnosis hn001 (dr2... -

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Basic information

Entry
Database: PDB / ID: 4k7c
TitleCrystal structure of pepw from lactobacillus rhamnosis hn001 (dr20) determined as the selenomet derivative
ComponentsAminopeptidase C
KeywordsHYDROLASE / aminopeptidase cysteine peptidase
Function / homologyCysteine proteinases / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / :
Function and homology information
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsWebby, C. / Knapp, K.M. / Anderson, B.F. / Norris, G.E.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of pepw from lactobacillus rhamnosis hn001 (dr20) determined as the selenomet derivative
Authors: Webby, C. / Knapp, K.M. / Anderson, B.F. / Norris, G.E.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminopeptidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8869
Polymers51,1491
Non-polymers7378
Water9,278515
1
A: Aminopeptidase C
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)311,31754
Polymers306,8976
Non-polymers4,42148
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area30860 Å2
ΔGint-176 kcal/mol
Surface area95360 Å2
MethodPISA
2
A: Aminopeptidase C
hetero molecules

A: Aminopeptidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,77218
Polymers102,2992
Non-polymers1,47416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area7200 Å2
ΔGint-45 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.432, 143.432, 97.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1067-

HOH

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Components

#1: Protein Aminopeptidase C


Mass: 51149.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Modified pET32 in which the Trx-His-Thrombin-Stag-Enterokinase sequence has been replaced by His-tag-rTEV
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: HN001 taxon-486408 / Gene: LRH 13711, LRH_13711 / Plasmid: pET32a / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): Cremoris NZ9000
References: UniProt: B5QNU9, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.1M NaAc, 11% Peg 4K, 30% glycerol protectant, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2006 / Details: Capilliary
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.49→33.76 Å / Num. all: 84251 / Num. obs: 84251 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.22 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.9
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 1.12 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.2 / % possible all: 23.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zuk

3zuk


Resolution: 1.66→33.76 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.199 / SU ML: 0.069 / Isotropic thermal model: Isotopic / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20968 3497 5.1 %RANDOM
Rwork0.17685 ---
obs0.17854 65412 98.94 %-
all-65412 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.437 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.66→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 48 515 4120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023783
X-RAY DIFFRACTIONr_bond_other_d0.0010.023567
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.9755123
X-RAY DIFFRACTIONr_angle_other_deg0.93238256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74225.618178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73415622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4531512
X-RAY DIFFRACTIONr_chiral_restr0.1230.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02848
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 237 -
Rwork0.364 4541 -
obs--94.18 %

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