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- PDB-3sho: Crystal structure of RpiR transcription factor from Sphaerobacter... -

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Basic information

Entry
Database: PDB / ID: 3sho
TitleCrystal structure of RpiR transcription factor from Sphaerobacter thermophilus (sugar isomerase domain)
ComponentsTranscriptional regulator, RpiR familyTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / transcription factor / sugar isomerase / oxidized cysteine
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding / DNA-binding transcription factor activity
Similarity search - Function
Helix-turn-helix protein RpiR / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily ...Helix-turn-helix protein RpiR / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, RpiR family
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMichalska, K. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of RpiR transcription factor from Sphaerobacter thermophilus (sugar isomerase domain)
Authors: Michalska, K. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, RpiR family
B: Transcriptional regulator, RpiR family
C: Transcriptional regulator, RpiR family
D: Transcriptional regulator, RpiR family


Theoretical massNumber of molelcules
Total (without water)80,4814
Polymers80,4814
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-78 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.194, 77.816, 71.157
Angle α, β, γ (deg.)90.00, 94.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Transcriptional regulator, RpiR family / Transcriptional regulation


Mass: 20120.373 Da / Num. of mol.: 4 / Fragment: sugar isomerase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / Gene: Sthe_3042 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: D1C9F1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M sodium malonate, 20% PEG3350, in situ proteolysis with chymotrypsin, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 4, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 68746 / Num. obs: 68642 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.98 Å2 / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2 / Num. unique all: 3358 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9387 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
Details: The crystals were obtain by in situ proteolysis with chymotrypsin, which apparently cut the N-terminal DNA-binding domain (residues ~ 1-90) prior to crystal formation. The precise location ...Details: The crystals were obtain by in situ proteolysis with chymotrypsin, which apparently cut the N-terminal DNA-binding domain (residues ~ 1-90) prior to crystal formation. The precise location of the cleavage site has not been determined. The region near residues 191-193 contains unknown density that has not been modeled.
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 1198 1.75 %thin resolution shells
Rwork0.1729 ---
all0.1735 68604 --
obs0.1735 68604 99.8 %-
Displacement parametersBiso mean: 34.96 Å2
Baniso -1Baniso -2Baniso -3
1--8.0909 Å20 Å2-0.7281 Å2
2--0.3685 Å20 Å2
3---7.7224 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5443 0 0 304 5747
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0155557HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.177609HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2571SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes129HARMONIC2
X-RAY DIFFRACTIONt_gen_planes828HARMONIC5
X-RAY DIFFRACTIONt_it5537HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion2.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion774SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6822SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2138 64 1.27 %
Rwork0.2183 4957 -
all0.2182 5021 -
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)
18.4755-1.7109-0.77212.3448-0.06583.1038-0.0360.1406-0.1985-0.0519-0.0607-0.06050.14170.1340.09670.16220.03530.0288-0.1025-0.0047-0.139354.568315.4882-19.2329
21.68770.17920.11761.5696-0.13581.13310.03870.07020.01150.0343-0.02170.0358-0.1068-0.1451-0.0170.04030.02660.0056-0.0754-0.006-0.073138.327423.7179-1.2132
31.51380.6195-2.260.08241.07917.74960.0049-0.28690.17450.5327-0.11820.05840.4170.01710.11330.1983-0.0473-0.0273-0.07-0.0413-0.094534.970716.780411.2441
41.44210.6884-0.3792.0071-0.5542.15530.03690.0836-0.0959-0.0144-0.0647-0.0510.2666-0.12790.02780.0604-0.0277-0.0059-0.09-0.0201-0.054237.404410.6501-2.6752
50.98010.0253-0.60850.81930.80281.4588-0.06510.1217-0.08150.1017-0.13150.09340.0365-0.11660.19670.07960.02920.0009-0.06790.0137-0.084443.269527.1866-6.7123
60.8886-1.34960.31780.97251.89050.7580.0150.18830.10410.0373-0.0421-0.017-0.04480.08470.02710.2588-0.0337-0.0265-0.16810.0732-0.066548.123445.66379.1655
73.1157-1.57271.1650.009-0.78620.2349-0.00320.22780.1003-0.24240.0490.0991-0.0781-0.2275-0.04580.150.0733-0.0182-0.00240.0271-0.086142.628428.3422-19.0655
82.7065-0.3310.09261.318-0.09811.90680.05440.13090.0503-0.1421-0.0005-0.02660.04940.0338-0.05390.07450.00160.0371-0.16070.0069-0.072963.947422.3917-6.8423
90.18871.63330.89754.64371.43673.66130.1247-0.0687-0.1570.4275-0.06610.2141-0.2027-0.1286-0.05870.16280.01750.067-0.04590.026-0.063362.546820.5767.8469
101.6553-0.06360.78582.33460.34212.9092-0.0491-0.03350.01130.19420.0432-0.0293-0.33910.21070.00590.0938-0.04260.0299-0.1150.0142-0.053167.073330.80130.2615
111.2614-0.80080.18163.3029-0.21851.34220.01670.0810.2028-0.1115-0.1371-0.0327-0.10720.0320.12030.07750.00670.0062-0.0931-0.0001-0.076256.914423.8481-10.2514
123.48610.6933-2.64781.82281.62951.23530.01240.1894-0.06520.2095-0.21830.04920.10930.02220.20580.16560.05390.041-0.1271-0.0034-0.035262.62631.2495-0.1948
133.5109-1.24742.13861.5567-0.39090.7566-0.01870.01350.0863-0.0654-0.14350.11910.055-0.12280.16210.1128-0.01630.03320.0227-0.0151-0.144136.864322.000842.3061
140.9991-0.8943-0.43080.87950.68513.2633-0.0698-0.1713-0.07260.0290.02330.05670.09750.11390.04650.1639-0.00130.0153-0.11740.0313-0.124959.405811.736831.212
150.49540.62330.16180.32050.03363.77850.0274-0.00810.0242-0.12490.02290.0727-0.1525-0.1315-0.05020.17010.0189-0.004-0.09250.0359-0.111361.520412.34115.8728
163.0084-0.0494-1.5632.71031.45874.5047-0.11580.1892-0.30490.1964-0.14330.32890.368-0.30950.25910.2126-0.00720.0446-0.15550.0229-0.101854.09632.265323.5302
171.6278-1.3601-0.80990.90030.39622.2229-0.07-0.1119-0.24490.046-0.09730.18890.023-0.01930.16730.16120.01530.0383-0.11750.0149-0.153455.125513.417433.0639
182.04062.2102-1.2110.0226-1.48220.76820.0432-0.07720.25970.03110.1322-0.1589-0.17750.1372-0.17540.2909-0.15390.0329-0.13340.0161-0.190270.781730.544222.3119
192.2855-2.86081.23631.23760.0282.35690.0022-0.0228-0.08260.10120.0232-0.08750.08230.1261-0.02540.16760.00070.005-0.00820.0303-0.116562.928218.636742.2267
202.9911-1.13240.22191.4587-0.39652.1187-0.1078-0.29890.03090.23020.12390.0710.0388-0.2139-0.01610.14760.00020.0214-0.117-0.0125-0.15342.197129.513530.6476
210.62170.5006-0.59960.923-0.50213.1045-0.0180.0531-0.0275-0.1027-0.02180.02440.2746-0.20870.03980.12820.01170.0206-0.0575-0.0263-0.113440.879929.355716.251
223.8433-0.7070.56971.446-0.31532.94590.05280.0220.17710.0788-0.0603-0.0678-0.32860.10320.00750.1849-0.00520.0021-0.1054-0.0263-0.108547.815839.244124.5562
233.8073-0.81240.37160.9930.01461.2992-0.0564-0.27340.16760.0569-0.0261-0.11460.0507-0.11870.08260.16650.01270.0174-0.0760.0113-0.174347.532726.81233.5803
242.1327-0.76322.7690.08610.12441.157-0.0273-0.1612-0.09060.01860.08140.04490.1188-0.1263-0.05410.2169-0.15870.1137-0.15450.0726-0.040930.354112.871623.7535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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