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- PDB-3pbi: Structure of the peptidoglycan hydrolase RipB (Rv1478) from Mycob... -

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Basic information

Entry
Database: PDB / ID: 3pbi
TitleStructure of the peptidoglycan hydrolase RipB (Rv1478) from Mycobacterium tuberculosis at 1.6 resolution
ComponentsINVASION PROTEIN
KeywordsHYDROLASE / peptidoglycan hydrolase / extracellular / invasion related protein / cell wall / NlpC-like module
Function / homology
Function and homology information


cell wall organization or biogenesis / cell wall / N-acetylmuramoyl-L-alanine amidase activity / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / peptidoglycan-based cell wall / cell wall organization / proteolysis
Similarity search - Function
: / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan endopeptidase RipB / Peptidoglycan endopeptidase RipB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchnell, R. / Both, D. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Peptidoglycan Remodeling in Mycobacterium tuberculosis: Comparison of Structures and Catalytic Activities of RipA and RipB.
Authors: Both, D. / Schneider, G. / Schnell, R.
History
DepositionOct 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INVASION PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,7331
Polymers21,7331
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.980, 92.980, 53.192
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein INVASION PROTEIN / NLP/P60 family protein


Mass: 21733.350 Da / Num. of mol.: 1 / Fragment: unp residues 30-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1525, Rv1478 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53169, UniProt: P9WHU5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.2 M NaCl 0.1 M HEPES, 30% v/v PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009 / Details: MIRRORS
RadiationMonochromator: SI (311) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 32063 / % possible obs: 92.3 % / Observed criterion σ(I): 2.5 / Redundancy: 7.4 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 19.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.411 / % possible all: 63.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HBW

2hbw


Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.332 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 2.5 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1604 5 %RANDOM
Rwork0.159 ---
obs0.161 32063 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0.37 Å20 Å2
2---0.74 Å20 Å2
3---1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.078 Å0.071 Å
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 0 242 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221487
X-RAY DIFFRACTIONr_bond_other_d0.0010.021019
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.9692024
X-RAY DIFFRACTIONr_angle_other_deg1.13232473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51822.67956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23915217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8031513
X-RAY DIFFRACTIONr_chiral_restr0.1370.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02307
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_it1.4591.5986
X-RAY DIFFRACTIONr_mcbond_other0.471.5421
X-RAY DIFFRACTIONr_mcangle_it2.19221562
X-RAY DIFFRACTIONr_scbond_it2.9093501
X-RAY DIFFRACTIONr_scangle_it4.6464.5458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 78 -
Rwork0.247 1370 -
obs--57.05 %

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