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- PDB-3x30: Crystal structure of metallo-beta-lactamase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3x30
TitleCrystal structure of metallo-beta-lactamase from Thermotoga maritima
ComponentsUPF0173 metal-dependent hydrolase TM_1162
KeywordsHYDROLASE
Function / homology
Function and homology information


Protein of unknown funcion UPF0173 / Beta-lactamase superfamily domain / 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
: / NICKEL (II) ION / UPF0173 metal-dependent hydrolase TM_1162
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.921 Å
AuthorsChoi, H.J. / Kim, H.J. / Matsuura, A. / Mikami, B. / Yoon, H.J. / Lee, H.H.
CitationJournal: To be Published
Title: Crystal structure of metallo-beta-lactamase from Thermotoga maritima
Authors: Choi, H.J. / Kim, H.J. / Matsuura, A. / Mikami, B. / Yoon, H.J. / Lee, H.H.
History
DepositionJan 7, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0173 metal-dependent hydrolase TM_1162
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2233
Polymers25,1091
Non-polymers1142
Water2,828157
1
A: UPF0173 metal-dependent hydrolase TM_1162
hetero molecules

A: UPF0173 metal-dependent hydrolase TM_1162
hetero molecules

A: UPF0173 metal-dependent hydrolase TM_1162
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6689
Polymers75,3273
Non-polymers3416
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6980 Å2
ΔGint-65 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.727, 98.727, 45.255
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-527-

HOH

31A-530-

HOH

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Components

#1: Protein UPF0173 metal-dependent hydrolase TM_1162


Mass: 25108.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_1162 / Plasmid: pHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q9X0P5
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 55% 2-Methyl-2,4-pentanediol(MPD), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9789 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 37623 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.92→1.95 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.921→28.5 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 1005 5.12 %RANDOM
Rwork0.1564 ---
all0.1577 19623 --
obs0.1577 19623 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.921→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 2 157 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081772
X-RAY DIFFRACTIONf_angle_d1.0922393
X-RAY DIFFRACTIONf_dihedral_angle_d12.387650
X-RAY DIFFRACTIONf_chiral_restr0.046271
X-RAY DIFFRACTIONf_plane_restr0.005304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.921-2.02220.17871410.1446260799
2.0222-2.14890.17461360.13892649100
2.1489-2.31470.16711630.13782611100
2.3147-2.54760.17131500.1432634100
2.5476-2.91590.19211310.15432671100
2.9159-3.67250.20851430.16472670100
3.6725-28.50320.17361410.16722776100

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