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- PDB-3fg8: Crystal structure of PAS domain of RHA05790 -

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Basic information

Entry
Database: PDB / ID: 3fg8
TitleCrystal structure of PAS domain of RHA05790
Componentsuncharacterized protein RHA05790
Keywordsstructural genomics / unknown function / PAS domain / uncharacterized protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / PAS fold-4 / PAS fold / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase ...: / PAS fold-4 / PAS fold / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(3R)-3-(phosphonooxy)butanoic acid / Diguanylate cyclase (GGDEF) domain-containing protein
Similarity search - Component
Biological speciesRhodococcus sp. RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of PAS domain of RHA05790
Authors: Chang, C. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: uncharacterized protein RHA05790
B: uncharacterized protein RHA05790
C: uncharacterized protein RHA05790
D: uncharacterized protein RHA05790
E: uncharacterized protein RHA05790
F: uncharacterized protein RHA05790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,90112
Polymers79,7976
Non-polymers1,1056
Water13,908772
1
A: uncharacterized protein RHA05790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4842
Polymers13,2991
Non-polymers1841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein RHA05790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4842
Polymers13,2991
Non-polymers1841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: uncharacterized protein RHA05790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4842
Polymers13,2991
Non-polymers1841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: uncharacterized protein RHA05790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4842
Polymers13,2991
Non-polymers1841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: uncharacterized protein RHA05790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4842
Polymers13,2991
Non-polymers1841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: uncharacterized protein RHA05790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4842
Polymers13,2991
Non-polymers1841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.695, 55.889, 101.856
Angle α, β, γ (deg.)90.00, 132.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-547-

HOH

21F-748-

HOH

Detailsmonomer

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Components

#1: Protein
uncharacterized protein RHA05790


Mass: 13299.428 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. RHA1 (bacteria) / Strain: strain RHA1 / Gene: RHA1_ro04714 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0S7I6
#2: Chemical
ChemComp-3PB / (3R)-3-(phosphonooxy)butanoic acid


Mass: 184.084 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H9O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-tris pH6.5, 28%PEG2KMME, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 27, 2008
RadiationMonochromator: Si(III) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 57672 / Num. obs: 57336 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 30.94
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 4.27 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.081 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22259 2907 5.1 %RANDOM
Rwork0.16796 ---
obs0.17074 54377 99.26 %-
all-57284 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å2-0.9 Å2
2--0.26 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 66 772 5752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9737826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.61821.229301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.86615102
X-RAY DIFFRACTIONr_chiral_restr0.1090.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024546
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9051.53477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58225654
X-RAY DIFFRACTIONr_scbond_it2.51932251
X-RAY DIFFRACTIONr_scangle_it4.0684.52141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 182 -
Rwork0.205 4011 -
obs--98.38 %
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)
11.870.1640.37281.68550.37030.8719-0.00580.08190.0665-0.12570.0088-0.0649-0.04450.0469-0.0030.05260.00840.00180.0074-0.00040.019172.973611.975231.7645
22.57011.97771.23494.09990.54863.02640.0293-0.163-0.14080.12290.0543-0.13530.03250.171-0.08360.05570.0188-0.00790.05710.00210.060878.08357.893841.4939
31.48020.11190.04651.856-0.05552.10150.074-0.0080.24010.0796-0.0812-0.0185-0.1631-0.15910.00710.04320.00960.00690.01940.01150.076953.493729.126825.8805
43.3776-0.4631-0.45512.9463-0.75823.5487-0.0713-0.0440.19350.2477-0.0446-0.401-0.30340.21680.1160.0569-0.021-0.0420.01420.01070.099564.487328.319329.0293
52.36160.4720.25461.37260.03182.75760.03620.07440.1736-0.0105-0.01310.0112-0.24120.1131-0.02310.0408-0.00990.02150.0106-0.00610.048962.08641.31319.9311
65.07441.15551.27462.34451.21564.5698-0.19970.03870.4128-0.04240.11980.2167-0.1402-0.25990.07990.02620.0133-0.00850.03650.01390.075750.72810.8317.5773
71.9337-0.17760.39690.97240.29341.60830.00660.05830.046-0.0424-0.0084-0.11520.03880.11950.00180.02530.00720.01360.0291-0.00690.02532.286112.564-4.685
83.5573-0.45150.88011.732-1.30533.4185-0.1686-0.3647-0.2180.00890.1447-0.21710.14720.15160.02390.05160.0404-0.00530.0916-0.00420.062437.78858.74794.7001
92.5961-0.18271.36661.9511-0.56092.35180.17940.2377-0.0537-0.161-0.188-0.08380.29150.39120.00860.05550.05980.0180.09840.00730.01881.5465-15.428716.441
104.5564-0.59060.47752.1553-1.17153.96370.09380.4601-0.0284-0.2708-0.12860.16650.09610.38610.03480.09170.04520.00220.1330.01760.028675.4868-10.83687.971
112.0781-0.03810.28420.7421-0.07621.59130.1009-0.0862-0.12140.046-0.0565-0.00260.1662-0.0231-0.04440.0423-0.03660.00050.08120.01620.030632.550313.882621.9193
128.7333-1.52311.53093.18520.45112.2972-0.0644-0.57230.15910.15230.0458-0.0406-0.1441-0.03710.01860.0475-0.04520.00310.121-0.0080.009338.993518.921829.9817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A119 - 163
2X-RAY DIFFRACTION1A187 - 222
3X-RAY DIFFRACTION2A164 - 186
4X-RAY DIFFRACTION3B119 - 163
5X-RAY DIFFRACTION3B187 - 222
6X-RAY DIFFRACTION4B164 - 186
7X-RAY DIFFRACTION5C119 - 163
8X-RAY DIFFRACTION5C187 - 222
9X-RAY DIFFRACTION6C164 - 186
10X-RAY DIFFRACTION7D119 - 163
11X-RAY DIFFRACTION7D187 - 222
12X-RAY DIFFRACTION8D164 - 186
13X-RAY DIFFRACTION9E119 - 163
14X-RAY DIFFRACTION9E187 - 222
15X-RAY DIFFRACTION10E164 - 186
16X-RAY DIFFRACTION11F119 - 163
17X-RAY DIFFRACTION11F187 - 222
18X-RAY DIFFRACTION12F164 - 186

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