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- PDB-2r5f: Putative sugar-binding domain of transcriptional regulator DeoR f... -

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Basic information

Entry
Database: PDB / ID: 2r5f
TitlePutative sugar-binding domain of transcriptional regulator DeoR from Pseudomonas syringae pv. tomato
ComponentsTranscriptional regulator, putative
KeywordsTRANSCRIPTION / transcription regulator / sugar-binding domain / structural genomics / pfam04198 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-templated transcription initiation / carbohydrate binding / DNA-binding transcription factor activity
Similarity search - Function
Sugar-binding domain, putative / : / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, putative
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsCuff, M.E. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Putative sugar-binding domain of trancsriptional regulator DeoR from Pseudomonas syringae pv. tomato.
Authors: Cuff, M.E. / Duggan, E. / Clancy, S. / Joachimiak, A.
History
DepositionSep 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Transcriptional regulator, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1093
Polymers28,9171
Non-polymers1922
Water1,946108
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.112, 42.112, 144.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
DetailsAuthors state that the biological unit of this polypeptide is unknown.

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Components

#1: Protein Transcriptional regulator, putative


Mass: 28917.014 Da / Num. of mol.: 1 / Fragment: Putative sugar-binding domain: Residues 57-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: DeoR, PSPTO_2395 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q883G8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97907, 0.97921
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 14, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.979211
ReflectionRedundancy: 7.7 % / Av σ(I) over netI: 10.6 / Number: 100848 / Rmerge(I) obs: 0.081 / Χ2: 1.86 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 13180 / % possible obs: 89.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.525087.210.0685.548
3.594.529210.0572.8588.3
3.143.5992.610.0711.9528.5
2.853.1495.810.0921.4068.4
2.652.8595.710.1291.2648.3
2.492.6596.110.1630.9958.4
2.372.4994.110.1980.9088.2
2.262.3788.510.250.9237.5
2.182.2679.910.3430.9945.4
2.12.1872.710.4340.8714.4
ReflectionResolution: 2.1→50 Å / Num. all: 13180 / Num. obs: 13180 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.856 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.65 / Num. unique all: 1052 / Χ2: 0.871 / % possible all: 72.7

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.1 Å / D res low: 42.11 Å / FOM : 0.296 / FOM acentric: 0.296 / FOM centric: 0.219 / Reflection: 13121 / Reflection acentric: 12982 / Reflection centric: 139
Phasing MAD set

Highest resolution: 2.1 Å / Lowest resolution: 42.11 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.5210.10.10012982139
20.930.8913.915.30.510.5110768118
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
112.45-42.112.7111.10.400511
17.31-12.451.0810.50.3002345
15.17-7.311.710.50.20055913
14-5.171.110.30.200101715
13.26-41.1710.20.100164225
12.75-3.261.8510.1000241233
12.38-2.757.1710.1000334629
12.1-2.381.9510000372118
212.45-42.110.690.5616.329.12.130.78501
27.31-12.450.680.7714.818.51.731.42335
25.17-7.310.760.7514.923.51.340.6355913
24-5.170.880.9916.515.60.890.78101715
23.26-40.920.8514.913.40.630.63164125
22.75-3.260.950.9711.713.90.470.28241233
22.38-2.750.991.0112.611.30.250.19327023
22.1-2.381116.829.60.130.0415863
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se78.31342-0.215-0.749-0.1840
2Se73.04219-0.469-0.768-0.0250
3Se86.98933-0.289-0.104-0.2510
4Se75.62676-0.189-0.546-0.2530
5Se67.71538-0.563-0.012-0.1230
6Se639.30438-0.092-0.192-0.0110
7Se77.12099-0.215-0.749-0.184-0.207
8Se60.76777-0.471-0.766-0.025-0.275
9Se84.10966-0.29-0.102-0.25-0.286
10Se76.52405-0.189-0.547-0.253-0.264
11Se67.04011-0.564-0.013-0.123-0.203
12Se620.20215-0.085-0.189-0.01-0.1
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.45-42.110.8070.8030.98752511
7.31-12.450.8030.8050.6872392345
5.17-7.310.7510.7540.58757255913
4-5.170.6720.6770.3091032101715
3.26-40.5390.5420.2911667164225
2.75-3.260.3680.370.1672445241233
2.38-2.750.150.1510.0323375334629
2.1-2.380.0590.0590.0023739372118
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 13121
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.16-10048.50.88506
4.89-6.16430.913511
4.29-4.8942.40.93508
3.9-4.2942.50.921519
3.64-3.945.50.916501
3.43-3.6447.80.908511
3.26-3.4350.80.919508
3.12-3.2655.20.863506
3.01-3.1255.60.885501
2.91-3.0162.60.875514
2.82-2.9163.20.861523
2.73-2.8264.20.816527
2.66-2.7366.80.799565
2.59-2.6671.90.81556
2.53-2.59720.812607
2.47-2.5373.90.805581
2.41-2.4777.60.818619
2.36-2.4178.10.792618
2.31-2.3682.90.723606
2.26-2.3180.60.747594
2.22-2.2679.90.668602
2.18-2.22840.758546
2.14-2.1883.20.694553
2.1-2.1484.70.671539

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.1→36.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.43 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 658 5 %RANDOM
Rwork0.195 ---
all0.197 13120 --
obs0.197 13120 89.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.944 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2--1.84 Å20 Å2
3----3.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 10 108 1753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221670
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9852250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92523.93966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22915299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1661512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021200
X-RAY DIFFRACTIONr_nbd_refined0.20.2699
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.29
X-RAY DIFFRACTIONr_mcbond_it0.9161.51112
X-RAY DIFFRACTIONr_mcangle_it1.30621702
X-RAY DIFFRACTIONr_scbond_it2.1273626
X-RAY DIFFRACTIONr_scangle_it3.24.5548
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 36 -
Rwork0.239 732 -
all-768 -
obs--72.18 %
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)
11.62040.306-0.42632.12480.34397.56570.03670.02420.07680.00270.0364-0.0506-0.35880.0422-0.0731-0.1832-0.00990.0001-0.1205-0.0205-0.081810.644618.793374.9177
20.7381-0.39760.98241.9998-1.05776.1228-0.0082-0.0068-0.0968-0.0023-0.1515-0.19780.78080.44330.1596-0.06640.02870.0194-0.09470.0086-0.11116.90936.970973.5901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA59 - 1216 - 68
2X-RAY DIFFRACTION2AA132 - 21779 - 164

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