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- PDB-6jkv: PppA, a key regulatory component of T6SS in Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6jkv
TitlePppA, a key regulatory component of T6SS in Pseudomonas aeruginosa
ComponentsPppA
KeywordsHYDROLASE / Phosphatase / T6SS regulatory component
Function / homology
Function and homology information


protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / negative regulation of protein secretion / metal ion binding
Similarity search - Function
Protein phosphatase 2C / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / protein-serine/threonine phosphatase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, T. / Liu, L. / Wu, Y. / Li, D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of PppA from Pseudomonas aeruginosa, a key regulatory component of type VI secretion systems.
Authors: Wu, Y. / Gong, J. / Liu, S. / Li, D. / Wu, Y. / Zhang, X. / Ren, Y. / Xu, S. / Sun, J. / Wang, T. / Lin, Q. / Liu, L.
History
DepositionMar 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: PppA
B: PppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4336
Polymers56,2132
Non-polymers2204
Water6,612367
1
A: PppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2163
Polymers28,1071
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-12 kcal/mol
Surface area10470 Å2
MethodPISA
2
B: PppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2163
Polymers28,1071
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-12 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.541, 80.253, 59.084
Angle α, β, γ (deg.)90.00, 111.81, 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: 4 - 242 / Label seq-ID: 24 - 262

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

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Components

#1: Protein PppA


Mass: 28106.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I757
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.14 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Calcium acetate hydrate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→24.28 Å / Num. obs: 25293 / % possible obs: 98.6 % / Redundancy: 2.03 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 4.9
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TXO

1txo


Resolution: 2.1→24.08 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.874 / SU B: 18.198 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28332 1228 4.9 %RANDOM
Rwork0.23292 ---
obs0.23529 23846 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.226 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0.12 Å2
2---0.8 Å2-0 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.1→24.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 4 367 3803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133487
X-RAY DIFFRACTIONr_bond_other_d0.0090.0173278
X-RAY DIFFRACTIONr_angle_refined_deg1.141.6224737
X-RAY DIFFRACTIONr_angle_other_deg1.4121.5737520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.02519.895191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4515547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0191538
X-RAY DIFFRACTIONr_chiral_restr0.0560.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
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_it0.7941.3441824
X-RAY DIFFRACTIONr_mcbond_other0.7941.3441823
X-RAY DIFFRACTIONr_mcangle_it1.0822.0162273
X-RAY DIFFRACTIONr_mcangle_other1.0822.0162274
X-RAY DIFFRACTIONr_scbond_it0.7281.411663
X-RAY DIFFRACTIONr_scbond_other0.7281.411664
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9472.0962465
X-RAY DIFFRACTIONr_long_range_B_refined2.57817.4483952
X-RAY DIFFRACTIONr_long_range_B_other2.25216.8543876
X-RAY DIFFRACTIONr_rigid_bond_restr0.79436765
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6890 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 94 -
Rwork0.209 1778 -
obs--99.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.758-0.25670.08511.1785-0.2481.5066-0.0176-0.0617-0.01330.0898-0.0011-0.10210.02470.06630.01870.0252-0.00770.01390.0325-0.0060.03870.25368.4213-12.3129
21.92690.07230.09541.081-0.22311.5073-0.01630.03910.02330.0061-0.0208-0.0957-0.05550.07450.03710.0065-0.00810.01060.0262-0.00780.0423-3.2298-4.5127-41.6003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 242
2X-RAY DIFFRACTION2B4 - 242

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