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- PDB-2zwr: Crystal structure of TTHA1623 from thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2zwr
TitleCrystal structure of TTHA1623 from thermus thermophilus HB8
ComponentsMetallo-beta-lactamase superfamily protein
KeywordsHYDROLASE / Metallo-beta-lactamase
Function / homology
Function and homology information


Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase superfamily protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsYamamura, A. / Okada, A. / Kameda, Y. / Ohtsuka, J. / Nakagawa, N. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / Nagata, K. / Tanokura, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of TTHA1623, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8
Authors: Yamamura, A. / Okada, A. / Kameda, Y. / Ohtsuka, J. / Nakagawa, N. / Ebihara, A. / Nagata, K. / Tanokura, M.
History
DepositionDec 17, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Metallo-beta-lactamase superfamily protein
B: Metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,55916
Polymers44,6432
Non-polymers91614
Water2,846158
1
A: Metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8459
Polymers22,3221
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7147
Polymers22,3221
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.136, 114.122, 114.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-266-

HOH

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Components

#1: Protein Metallo-beta-lactamase superfamily protein


Mass: 22321.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1623 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHV7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 100mM sodium cacodylate, 30% PEG200, 200mM zinc acetate, PH7.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.2829, 1.2822, 1.0000
Detector
TypeIDDetectorDate
RIGAKU JUPITER 2101CCDDec 10, 2004
RIGAKU JUPITER 2102CCDDec 10, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28291
31.28221
411
ReflectionResolution: 2.2→50 Å / Num. obs: 26556 / % possible obs: 99.4 %

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→40.46 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.899 / SU B: 4.421 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22896 1313 5 %RANDOM
Rwork0.18773 ---
obs0.18982 24819 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.312 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 14 158 3233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223162
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2252.0074344
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54723.613119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4871513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022460
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.21431
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5731.52097
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95623287
X-RAY DIFFRACTIONr_scbond_it1.45731194
X-RAY DIFFRACTIONr_scangle_it2.2224.51057
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 74 -
Rwork0.196 1679 -
obs--90.27 %

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