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- PDB-4jxb: RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic N... -

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Basic information

Entry
Database: PDB / ID: 4jxb
TitleRipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein, adaptation to peptidoglycan-binding function
ComponentsInvasion-associated protein
KeywordsCELL INVASION / cell wall / envelope biogenesis / NlpC/p60
Function / homology
Function and homology information


: / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / 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
ACETATE ION / Possible Inv protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBoth, D. / Steiner, E.M. / Schnell, R. / Schneider, G.
CitationJournal: Biochem.J. / Year: 2014
Title: RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.
Authors: Both, D. / Steiner, E.M. / Izumi, A. / Schneider, G. / Schnell, R.
History
DepositionMar 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Invasion-associated protein
B: Invasion-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6059
Polymers28,1922
Non-polymers4137
Water4,161231
1
A: Invasion-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3325
Polymers14,0961
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Invasion-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2734
Polymers14,0961
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.822, 56.114, 57.157
Angle α, β, γ (deg.)90.00, 109.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Invasion-associated protein


Mass: 14096.059 Da / Num. of mol.: 2 / Fragment: UNP residues 38-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1566c, RVBD_1566c / Plasmid: pNIC28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL31(DE3) / References: UniProt: O06624
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Bis-Tris propane/HCl, pH 4.5, 3.5 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2012 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.56→56.11 Å / Num. all: 38284 / Num. obs: 37671 / % possible obs: 98.4 % / Observed criterion σ(F): 3.9 / Observed criterion σ(I): 3.9 / Redundancy: 3.2 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 21
Reflection shellResolution: 1.56→1.64 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.9 / Num. unique all: 5551 / % possible all: 91.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→56.1 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.789 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20406 1903 5.1 %RANDOM
Rwork0.16905 ---
obs0.17083 37671 98.39 %-
all-38284 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.18 Å2
2---0.3 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.56→56.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 28 231 2181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222026
X-RAY DIFFRACTIONr_bond_other_d0.0010.021371
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9812750
X-RAY DIFFRACTIONr_angle_other_deg0.94633354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32623.67179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6715327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0681514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
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_it1.3471.51311
X-RAY DIFFRACTIONr_mcbond_other0.5871.5555
X-RAY DIFFRACTIONr_mcangle_it2.02222084
X-RAY DIFFRACTIONr_scbond_it2.9043715
X-RAY DIFFRACTIONr_scangle_it4.2334.5657
X-RAY DIFFRACTIONr_rigid_bond_restr1.38533397
X-RAY DIFFRACTIONr_sphericity_free6.9933231
X-RAY DIFFRACTIONr_sphericity_bonded2.58433359
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 100 -
Rwork0.207 2364 -
obs-2364 87.1 %

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