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- PDB-4r8z: Crystal Structure of PA4781 HD-GYP domain from Pseudomonas aerugi... -

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Basic information

Entry
Database: PDB / ID: 4r8z
TitleCrystal Structure of PA4781 HD-GYP domain from Pseudomonas aeruginosa at 2.2A resolution showing a bi-metallic Ni ion center
ComponentsCyclic di-GMP phosphodiesterase
KeywordsHYDROLASE / bimetallic / c-di-GMP / PDE / phosphdiesterase / cyclic-di-GMP / biofilm
Function / homology
Function and homology information


regulation of single-species biofilm formation on inanimate substrate / cyclic-guanylate-specific phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / positive regulation of cell motility / phosphorelay signal transduction system / metal ion binding
Similarity search - Function
: / HD-GYP domain / HD domain / HD-GYP domain profile. / Hypothetical protein af1432 / Hypothetical protein af1432 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...: / HD-GYP domain / HD domain / HD-GYP domain profile. / Hypothetical protein af1432 / Hypothetical protein af1432 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Cyclic di-GMP phosphodiesterase PA4781
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsGiardina, G. / Cutruzzolaa, F. / Rinaldo, S. / Stelitano, V.
CitationJournal: J.Bacteriol. / Year: 2015
Title: Structural basis of functional diversification of the HD-GYP domain revealed by the Pseudomonas aeruginosa PA4781 protein, which displays an unselective bimetallic binding site.
Authors: Rinaldo, S. / Paiardini, A. / Stelitano, V. / Brunotti, P. / Cervoni, L. / Fernicola, S. / Protano, C. / Vitali, M. / Cutruzzola, F. / Giardina, G.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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 / _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

Downloads & links

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Assembly

Deposited unit
A: Cyclic di-GMP phosphodiesterase
B: Cyclic di-GMP phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3228
Polymers48,0162
Non-polymers3066
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-90 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.984, 93.984, 78.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 151 - 366 / Label seq-ID: 1 - 216

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

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Components

#1: Protein Cyclic di-GMP phosphodiesterase


Mass: 24008.107 Da / Num. of mol.: 2 / Fragment: HD-GYP domain, UNP residues 151-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4781 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HV27, phosphodiesterase I
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 3.61 Å3/Da / Density % sol: 65.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodilate 0.1M pH 6.5, KSCN 0.25M, KBr 0.2M, PEG 20K 3%, PGA 3%, cryo 20% glycerol, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→46.99 Å / Num. obs: 34840 / % possible obs: 100 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.256 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.016 / Mean I/σ(I) obs: 2.4 / Num. measured all: 46360 / Num. unique all: 3024 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
MOLREPphasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2046 / WRfactor Rwork: 0.1675 / FOM work R set: 0.849 / SU B: 4.646 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1708 / SU Rfree: 0.1555 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 1750 5 %RANDOM
Rwork0.1769 ---
obs0.1787 33063 99.99 %-
all-33066 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100 Å2 / Biso mean: 34.955 Å2 / Biso min: 13.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 6 198 3589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193409
X-RAY DIFFRACTIONr_bond_other_d0.0060.023286
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9674598
X-RAY DIFFRACTIONr_angle_other_deg1.20837469
X-RAY DIFFRACTIONr_chiral_restr0.1090.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213916
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02819
X-RAY DIFFRACTIONr_mcbond_it3.1713.1711733
X-RAY DIFFRACTIONr_mcbond_other3.173.1691732
X-RAY DIFFRACTIONr_mcangle_it4.5914.7252161
Refine LS restraints NCS

Ens-ID: 1 / Number: 12195 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 135 -
Rwork0.293 2452 -
all-2587 -
obs--100 %

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