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- PDB-3ix7: Crystal structure of a domain of functionally unknown protein fro... -

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Basic information

Entry
Database: PDB / ID: 3ix7
TitleCrystal structure of a domain of functionally unknown protein from Thermus thermophilus HB8
ComponentsUncharacterized protein TTHA0540
KeywordsStructural Genomics / Unknown function / Thermus thermophilus HB8 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


nuclease activity / Hydrolases; Acting on ester bonds / membrane => GO:0016020 / metal ion binding
Similarity search - Function
TRAM domain / TRAM domain / TRAM domain profile. / 5'-nuclease / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Uncharacterized PIN and TRAM-domain containing protein TTHA0540
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsChang, C. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a domain of functionally unknown protein from Thermus thermophilus HB8
Authors: Chang, C. / Li, H. / Clancy, S. / Joachimiak, A.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein TTHA0540
B: Uncharacterized protein TTHA0540
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5903
Polymers29,5302
Non-polymers601
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-12 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.152, 110.152, 39.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Uncharacterized protein TTHA0540


Mass: 14764.822 Da / Num. of mol.: 2 / Fragment: sequence database residues 138-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0540 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5SKV3
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Calcium acetate, 0.1M imidazol, 10% PEG8000, pH 8.0, 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: 0.97937 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 1, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 15055 / Num. obs: 15031 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 58.18
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 6.22 / Num. unique all: 378 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.05 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25609 746 5 %RANDOM
Rwork0.20936 ---
all0.21167 15000 --
obs0.21167 15000 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.209 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 4 142 2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222113
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9862879
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08523.40791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85915361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3721520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211616
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_it0.8031.51361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46222172
X-RAY DIFFRACTIONr_scbond_it2.3263752
X-RAY DIFFRACTIONr_scangle_it3.8754.5707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 58 -
Rwork0.227 1038 -
obs-1096 99.64 %
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)
10.3949-0.6423-0.45231.0550.73080.5267-0.01630.2618-0.31050.1176-0.39120.5224-0.0327-0.27840.40760.68840.0806-0.09730.57340.03930.6979-19.501471.2621-2.3323
22.2692-1.399-0.35055.28421.18051.53650.09130.1529-0.2322-0.0256-0.23280.30450.1505-0.24610.14150.0463-0.07060.01840.1624-0.07450.068-19.068850.57180.9048
37.0916-0.3302-2.06683.0616-1.56444.73830.05530.4444-0.068-0.4915-0.0932-0.02030.1463-0.27640.03790.0966-0.02420.00640.1838-0.01540.0089-7.426261.0358-7.6587
44.45630.2922-1.25352.2542-0.6560.52250.1741-0.37630.09540.1109-0.1731-0.1139-0.07410.0824-0.00090.044-0.0328-0.01420.2252-0.00560.0399-11.13763.43018.3106
50.0191-0.22070.47414.6401-10.231822.58650.180.0014-0.0965-0.2170.45020.38780.4063-0.6779-0.63020.5501-0.13040.04760.7819-0.47461.4572-32.255370.1321-0.2446
61.4802-0.9510.28094.17910.89832.4145-0.00150.20390.18810.3915-0.0421-0.0052-0.39630.23150.04350.2946-0.0980.11130.0829-0.00420.1883-28.094979.32517.9858
72.3261-2.01791.16182.2355-2.19699.18330.14360.41290.1227-0.1973-0.13530.4166-0.2205-0.7899-0.00840.43830.0054-0.10490.31770.09840.8719-42.059678.59697.6047
87.6375-0.7391.69061.81851.38433.25650.0487-0.1313-0.2783-0.0193-0.06320.29940.004-0.05850.01440.062-0.04190.07170.0746-0.02440.2035-35.605765.592713.5355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A137 - 142
2X-RAY DIFFRACTION2A143 - 213
3X-RAY DIFFRACTION3A214 - 233
4X-RAY DIFFRACTION4A234 - 266
5X-RAY DIFFRACTION5B137 - 142
6X-RAY DIFFRACTION6B143 - 213
7X-RAY DIFFRACTION7B214 - 233
8X-RAY DIFFRACTION8B234 - 266

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