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- PDB-2zbc: Crystal structure of STS042, a stand-alone RAM module protein, fr... -

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Basic information

Entry
Database: PDB / ID: 2zbc
TitleCrystal structure of STS042, a stand-alone RAM module protein, from hyperthermophilic archaeon Sulfolobus tokodaii strain7.
Components83aa long hypothetical transcriptional regulator asnC
KeywordsTRANSCRIPTION / SARD
Function / homologyLrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ISOLEUCINE / AsnC_trans_reg domain-containing protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsMiyazono, K. / Tsujimura, M. / Kawarabayasi, Y. / Tanokura, M.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of STS042, a stand-alone RAM module protein, from hyperthermophilic archaeon Sulfolobus tokodaii strain7
Authors: Miyazono, K. / Tsujimura, M. / Kawarabayasi, Y. / Tanokura, M.
History
DepositionOct 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 83aa long hypothetical transcriptional regulator asnC
B: 83aa long hypothetical transcriptional regulator asnC
C: 83aa long hypothetical transcriptional regulator asnC
D: 83aa long hypothetical transcriptional regulator asnC
E: 83aa long hypothetical transcriptional regulator asnC
F: 83aa long hypothetical transcriptional regulator asnC
G: 83aa long hypothetical transcriptional regulator asnC
H: 83aa long hypothetical transcriptional regulator asnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49316
Polymers75,4438
Non-polymers1,0498
Water7,314406
1
A: 83aa long hypothetical transcriptional regulator asnC
B: 83aa long hypothetical transcriptional regulator asnC
C: 83aa long hypothetical transcriptional regulator asnC
D: 83aa long hypothetical transcriptional regulator asnC
hetero molecules

A: 83aa long hypothetical transcriptional regulator asnC
B: 83aa long hypothetical transcriptional regulator asnC
C: 83aa long hypothetical transcriptional regulator asnC
D: 83aa long hypothetical transcriptional regulator asnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49316
Polymers75,4438
Non-polymers1,0498
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20750 Å2
ΔGint-109.1 kcal/mol
Surface area22160 Å2
MethodPISA
2
E: 83aa long hypothetical transcriptional regulator asnC
F: 83aa long hypothetical transcriptional regulator asnC
G: 83aa long hypothetical transcriptional regulator asnC
H: 83aa long hypothetical transcriptional regulator asnC
hetero molecules

E: 83aa long hypothetical transcriptional regulator asnC
F: 83aa long hypothetical transcriptional regulator asnC
G: 83aa long hypothetical transcriptional regulator asnC
H: 83aa long hypothetical transcriptional regulator asnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49316
Polymers75,4438
Non-polymers1,0498
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area20860 Å2
ΔGint-111.1 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.367, 61.785, 90.487
Angle α, β, γ (deg.)90.000, 94.470, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-86-

HOH

21B-90-

HOH

31G-85-

HOH

41H-88-

HOH

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Components

#1: Protein
83aa long hypothetical transcriptional regulator asnC / stand-alone RAM module protein


Mass: 9430.398 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Plasmid: pET21(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q975W5
#2: Chemical
ChemComp-ILE / ISOLEUCINE / Isoleucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9792, 0.9793, 0.9641
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97931
30.96411
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 13.5 / Number: 167795 / Rmerge(I) obs: 0.1 / Χ2: 5.57 / D res high: 1.9 Å / D res low: 25 Å / Num. obs: 45907 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.092599.510.07616.5823.7
3.254.0999.910.0879.0083.7
2.843.2510010.1087.3593.8
2.582.8410010.1325.7443.8
2.392.5810010.1484.1713.8
2.252.3910010.1613.5033.8
2.142.2510010.1842.5533.8
2.052.1499.910.1972.123.7
1.972.0598.410.2271.6263.5
1.91.9789.910.261.132.9
ReflectionResolution: 1.9→20 Å / Num. obs: 52841 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.104 / Χ2: 2.76 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9730.24451631.516196.6
1.97-2.053.10.20752591.696198.7
2.05-2.143.30.1952491.888198.9
2.14-2.253.40.1852771.952198.9
2.25-2.393.40.15852772.336198.7
2.39-2.583.40.14653112.551199
2.58-2.843.40.12952943.038199.5
2.84-3.253.40.11153183.81198.9
3.25-4.083.20.08253134.152198.6
4.08-203.40.06953804.331198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT3data extraction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.099 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2694 5.1 %RANDOM
Rwork0.17 ---
obs0.172 52841 97.95 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.425 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-2.26 Å2
2---0.69 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 72 406 5494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0225120
X-RAY DIFFRACTIONr_bond_other_d0.0020.025008
X-RAY DIFFRACTIONr_angle_refined_deg2.0811.9846888
X-RAY DIFFRACTIONr_angle_other_deg0.946311656
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD I (DEGREES)6.9265640
X-RAY DIFFRACTIONr_chiral_restr0.1250.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025408
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02888
X-RAY DIFFRACTIONr_nbd_refined0.2150.2811
X-RAY DIFFRACTIONr_nbd_other0.2510.25668
X-RAY DIFFRACTIONr_nbtor_other0.0880.23322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2302
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.2195
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.239
X-RAY DIFFRACTIONr_mcbond_it1.1821.53248
X-RAY DIFFRACTIONr_mcangle_it1.95625320
X-RAY DIFFRACTIONr_scbond_it3.38131872
X-RAY DIFFRACTIONr_scangle_it5.1724.51568
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.247 176
Rwork0.185 3356
all-3532

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