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- PDB-3x2x: Crystal structure of metallo-beta-lactamase H48A from Thermotoga ... -

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Basic information

Entry
Database: PDB / ID: 3x2x
TitleCrystal structure of metallo-beta-lactamase H48A 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / UPF0173 metal-dependent hydrolase TM_1162
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 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 H48A 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
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,1656
Polymers74,0003
Non-polymers1653
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-37 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.164, 143.164, 149.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UPF0173 metal-dependent hydrolase TM_1162


Mass: 24666.717 Da / Num. of mol.: 3 / Mutation: H48A
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X0P5
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.17 Å3/Da / Density % sol: 76.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-HCl, 60% 2-Methyl-2,4-pentanediol(MPD), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2014
RadiationMonochromator: Si 111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 23779 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.3→3.36 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→47.06 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.897 / SU B: 16.412 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20913 2003 9.4 %RANDOM
Rwork0.17338 ---
all0.17677 19299 --
obs0.17677 19299 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.481 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.42→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 3 14 5207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195298
X-RAY DIFFRACTIONr_bond_other_d0.0050.025235
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.9777155
X-RAY DIFFRACTIONr_angle_other_deg0.666312123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.135678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93825.224201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83715945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.188159
X-RAY DIFFRACTIONr_chiral_restr0.0460.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021071
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_it1.2343.2642721
X-RAY DIFFRACTIONr_mcbond_other1.2323.2632720
X-RAY DIFFRACTIONr_mcangle_it2.1564.8923396
X-RAY DIFFRACTIONr_mcangle_other2.1564.8933397
X-RAY DIFFRACTIONr_scbond_it1.2933.4532577
X-RAY DIFFRACTIONr_scbond_other1.2933.4542578
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.295.1093760
X-RAY DIFFRACTIONr_long_range_B_refined5.03930.92322109
X-RAY DIFFRACTIONr_long_range_B_other5.03930.92422110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.422→3.511 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 156 -
Rwork0.225 1410 -
obs--99.62 %

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