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- PDB-7cfj: Crystal structure of housekeeping sortase SrtA from Lactobacillus... -

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Basic information

Entry
Database: PDB / ID: 7cfj
TitleCrystal structure of housekeeping sortase SrtA from Lactobacillus rhamnosus GG
ComponentsClass A sortase
KeywordsHYDROLASE / housekeeping sortase / cysteine-transpeptidase / pilus assembly / lactobacillar pilus / SpaCBA pilus / probiotics
Function / homologySortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / Sortase
Function and homology information
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsPratap, S. / Megta, A.K. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5891/BRB/10/1098/2012 India
CitationJournal: To Be Published
Title: Crystal structure of housekeeping sortase SrtA from Lactobacillus rhamnosus GG
Authors: Pratap, S. / Megta, A.K. / Krishnan, V.
History
DepositionJun 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class A sortase
B: Class A sortase


Theoretical massNumber of molelcules
Total (without water)36,9712
Polymers36,9712
Non-polymers00
Water1267
1
A: Class A sortase


Theoretical massNumber of molelcules
Total (without water)18,4851
Polymers18,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class A sortase


Theoretical massNumber of molelcules
Total (without water)18,4851
Polymers18,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.006, 55.557, 74.897
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 89 - 232 / Label seq-ID: 26 - 169

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Class A sortase / Sortase


Mass: 18485.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria)
Gene: F8M46_11135, FEZ43_04140, GKD02_05185, GKD07_00565, GKD11_09430, GKD12_00565, GKD15_01240, GMB04_10630, LRHP344_01784, LRHP540_01088, PY91_04000
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3D3H8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.97 Å3/Da / Density % sol: 37.47 % / Description: Plate-like
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M Citric Bis-Tris Propane, pH 5.0 and 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.636→72.712 Å / Num. obs: 3890 / % possible obs: 62.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.071 / Rrim(I) all: 0.116 / Net I/σ(I): 6.1
Reflection shellResolution: 2.636→2.879 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 205 / CC1/2: 0.532 / Rpim(I) all: 0.459 / Rrim(I) all: 0.839 / % possible all: 63.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 2.64→72.71 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.849 / SU B: 20.179 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27634 182 4.7 %RANDOM
Rwork0.23895 ---
obs0.24074 3708 45.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.248 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20.02 Å2
2---0.81 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 2.64→72.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 0 7 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132064
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171862
X-RAY DIFFRACTIONr_angle_refined_deg1.441.6312821
X-RAY DIFFRACTIONr_angle_other_deg1.2741.5714298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.56826.05671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71615306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.051152
X-RAY DIFFRACTIONr_chiral_restr0.0510.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
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_it3.2364.3881150
X-RAY DIFFRACTIONr_mcbond_other3.2364.3891149
X-RAY DIFFRACTIONr_mcangle_it5.2626.5771434
X-RAY DIFFRACTIONr_mcangle_other5.2616.5761435
X-RAY DIFFRACTIONr_scbond_it3.1084.5914
X-RAY DIFFRACTIONr_scbond_other3.1074.501915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0556.6831388
X-RAY DIFFRACTIONr_long_range_B_refined9.3683.0868342
X-RAY DIFFRACTIONr_long_range_B_other9.35983.098342
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4028 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.64→2.705 Å
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.292 13 -
obs--2.1 %

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