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- PDB-3adr: The first crystal structure of an archaeal metallo-beta-lactamase... -

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Basic information

Entry
Database: PDB / ID: 3adr
TitleThe first crystal structure of an archaeal metallo-beta-lactamase superfamily protein; ST1585 from Sulfolobus tokodaii
ComponentsPutative uncharacterized protein ST1585
KeywordsSIGNALING PROTEIN / quorum sensing / quinolone signal / metallo-beta-lactamase fold / conserved hypothetical protein / archaea
Function / homology
Function and homology information


ST1585, MBL-fold / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase fold-containing protein ST1585
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsShimada, A. / Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
CitationJournal: Proteins / Year: 2010
Title: The first crystal structure of an archaeal metallo-beta-lactamase superfamily protein; ST1585 from Sulfolobus tokodaii
Authors: Shimada, A. / Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJan 28, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 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: Putative uncharacterized protein ST1585
B: Putative uncharacterized protein ST1585
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,77120
Polymers59,2882
Non-polymers1,48318
Water5,459303
1
A: Putative uncharacterized protein ST1585
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,51012
Polymers29,6441
Non-polymers86611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein ST1585
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2618
Polymers29,6441
Non-polymers6177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.970, 45.230, 110.890
Angle α, β, γ (deg.)90.000, 131.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21B-375-

HOH

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Components

#1: Protein Putative uncharacterized protein ST1585


Mass: 29644.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST1585 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: Q970L2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.59 Å3/Da / Density % sol: 52.54 % / Mosaicity: 0.267 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M HEPES, 10% PEG 8000, 8% ethylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9794, 0.9791, 0.9000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2007
RadiationMonochromator: transparent diamond double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97911
30.91
ReflectionRedundancy: 7.1 % / Av σ(I) over netI: 28.9 / Number: 399949 / Rmerge(I) obs: 0.097 / Χ2: 2.05 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 56067 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.910.0582.6847.3
3.083.8810010.082.7037.6
2.693.0810010.1153.1357.6
2.442.6910010.1422.8067.6
2.272.4410010.1652.3937.6
2.132.2710010.1851.897.6
2.032.1310010.2041.3767.6
1.942.0310010.2390.9527.4
1.861.9497.810.2830.86.1
1.81.8684.710.2890.6574.6
ReflectionResolution: 1.8→50 Å / Num. obs: 56293 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.101 / Χ2: 2.496 / Net I/σ(I): 28.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.272 / Num. unique all: 4929 / Χ2: 0.743 / % possible all: 87.5

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97915.4-7.42
3 wavelength120.97944-7.99
3 wavelength130.91.82-2.96
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se13.2360.0830.0010.0810.676
2Se16.1770.9720.2970.3860.7
3Se14.9790.4570.2710.3610.665
4Se16.9890.0960.4750.080.619
5Se21.1560.8780.2090.2670.512
6Se22.4870.1070.3240.1770.517
7Se22.3120.1770.2490.2080.652
8Se17.4260.0360.3350.10.392
9Se26.1780.5440.1320.4850.606
10Se24.2950.4740.0440.2790.62
11Se14.650.5280.1190.3920.452
12Se30.480.6360.410.0450.65
13Se30.3530.650.3560.0950.633
14Se30.6710.9070.1550.2690.634
15Se33.2660.9370.2570.2130.316
16Se1.7540.130.2210.0390.099
17Se44.2890.7140.4670.2140.373
Phasing dmFOM : 0.7 / FOM acentric: 0.7 / FOM centric: 0.72 / Reflection: 53344 / Reflection acentric: 50617 / Reflection centric: 2727
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.1-19.9910.960.970.9524252058367
3.2-5.10.960.960.9173586742616
2.6-3.20.880.890.7793848838546
2.3-2.60.780.790.6794048966438
1.9-2.30.590.60.481629215686606
1.8-1.90.350.350.3484818327154

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
CNS1.1refinement
PDB_EXTRACT3.005data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.99 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2517646 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5428 10.2 %RANDOM
Rwork0.199 ---
obs-53344 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.909 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 61.37 Å2 / Biso mean: 22.67 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å20 Å21.79 Å2
2---3.03 Å20 Å2
3---0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 82 303 4431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it3.842.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 747 10 %
Rwork0.215 6697 -
all-7444 -
obs--79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_st1585.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top

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