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- PDB-4xrn: Pilz domain with c-di-gmp of a protein from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4xrn
TitlePilz domain with c-di-gmp of a protein from Pseudomonas aeruginosa
ComponentsAlginate biosynthesis protein Alg44
KeywordsUNKNOWN FUNCTION / Pilz / c-di-gmp
Function / homology
Function and homology information


mannuronan synthase / alginate synthase activity / long-chain fatty acid-CoA ligase activity / alginic acid biosynthetic process / Gram-negative-bacterium-type cell wall / cyclic-di-GMP binding / single-species biofilm formation / periplasmic space
Similarity search - Function
HlyD family secretion protein / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-C2E / Mannuronan synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsChi, K.K. / Yuan, Z.L.
CitationJournal: To Be Published
Title: Pilz domain with c-di-gmp of a protein from Pseudomonas aeruginosa
Authors: Chi, K.K. / Yuan, Z.L.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate biosynthesis protein Alg44
B: Alginate biosynthesis protein Alg44
C: Alginate biosynthesis protein Alg44
D: Alginate biosynthesis protein Alg44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,59026
Polymers48,6514
Non-polymers8,93922
Water5,062281
1
A: Alginate biosynthesis protein Alg44
C: Alginate biosynthesis protein Alg44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,66411
Polymers24,3262
Non-polymers4,3399
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-5 kcal/mol
Surface area12130 Å2
MethodPISA
2
B: Alginate biosynthesis protein Alg44
D: Alginate biosynthesis protein Alg44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,92615
Polymers24,3262
Non-polymers4,60013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-147 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.526, 75.526, 195.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-314-

HOH

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Components

#1: Protein
Alginate biosynthesis protein Alg44


Mass: 12162.848 Da / Num. of mol.: 4 / Fragment: UNP residues 16-22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: alg44, PA3542 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HY69
#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Sodium chloride, Imidazole, Hydrochloric acid, Zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39278 / % possible obs: 100 % / Redundancy: 20 % / Net I/σ(I): 74.585

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1894)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2→46.859 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2738 1983 5.1 %
Rwork0.2307 --
obs0.2328 38898 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 562 281 4115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083954
X-RAY DIFFRACTIONf_angle_d1.4965469
X-RAY DIFFRACTIONf_dihedral_angle_d19.431305
X-RAY DIFFRACTIONf_chiral_restr0.057585
X-RAY DIFFRACTIONf_plane_restr0.005619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.050.32831360.26182537X-RAY DIFFRACTION97
2.05-2.10540.28021390.25042549X-RAY DIFFRACTION98
2.1054-2.16730.27951390.23672576X-RAY DIFFRACTION99
2.1673-2.23730.29161390.25142565X-RAY DIFFRACTION99
2.2373-2.31730.311390.2462593X-RAY DIFFRACTION99
2.3173-2.410.30091390.24372623X-RAY DIFFRACTION100
2.41-2.51970.29031400.24562619X-RAY DIFFRACTION99
2.5197-2.65250.31381390.25352597X-RAY DIFFRACTION100
2.6525-2.81870.31711420.25292660X-RAY DIFFRACTION100
2.8187-3.03630.31381420.25642637X-RAY DIFFRACTION100
3.0363-3.34180.25511440.22692651X-RAY DIFFRACTION100
3.3418-3.82520.26821450.20142697X-RAY DIFFRACTION100
3.8252-4.81850.22711460.19222727X-RAY DIFFRACTION100
4.8185-46.87210.26431540.24522884X-RAY DIFFRACTION99

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