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- PDB-5tgf: Crystal structure of putative beta-lactamase from Bacteroides dor... -

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Basic information

Entry
Database: PDB / ID: 5tgf
TitleCrystal structure of putative beta-lactamase from Bacteroides dorei DSM 17855
ComponentsUncharacterized protein
KeywordsHYDROLASE / beta-lactamase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase-related domain-containing protein
Similarity search - Component
Biological speciesBacteroides dorei DSM 17855 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsNocek, B. / Hatzos-Skintges, C. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of a beta-lactamase from Bacteroides dorei DSM 17855
Authors: Nocek, B. / Hatzos-Skintges, C. / Joachimaik, A. / Babnigg, G. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,51212
Polymers149,8794
Non-polymers6338
Water17,961997
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6543
Polymers37,4701
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5622
Polymers37,4701
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6944
Polymers37,4701
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6023
Polymers37,4701
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.475, 68.292, 88.216
Angle α, β, γ (deg.)103.84, 106.28, 101.20
Int Tables number1
Space group name H-MP1
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Uncharacterized protein


Mass: 37469.848 Da / Num. of mol.: 4 / Fragment: residues 23-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides dorei DSM 17855 (bacteria) / Gene: BACDOR_00452 / Production host: Escherichia coli (E. coli) / References: UniProt: B6VTD5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 997 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG 8000 0.1 M MES:NaOH pH 6 0.2 M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2016 / Details: double mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 111659 / % possible obs: 92.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.104 / Net I/av σ(I): 12 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.59 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→40 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.745 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19349 5363 5 %RANDOM
Rwork0.15201 ---
obs0.15405 101934 92.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20.01 Å20.11 Å2
2---0.28 Å2-0.01 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.81→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10245 0 38 999 11282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910642
X-RAY DIFFRACTIONr_bond_other_d0.0020.029844
X-RAY DIFFRACTIONr_angle_refined_deg1.331.95514493
X-RAY DIFFRACTIONr_angle_other_deg0.779322652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89523.82466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.277151522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4771552
X-RAY DIFFRACTIONr_chiral_restr0.0890.21566
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112245
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022503
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_it1.9631.9695367
X-RAY DIFFRACTIONr_mcbond_other1.9611.9685366
X-RAY DIFFRACTIONr_mcangle_it2.7212.9386715
X-RAY DIFFRACTIONr_mcangle_other2.7222.9396716
X-RAY DIFFRACTIONr_scbond_it2.8042.2315275
X-RAY DIFFRACTIONr_scbond_other2.7972.2315275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1223.2387770
X-RAY DIFFRACTIONr_long_range_B_refined5.49419.19447296
X-RAY DIFFRACTIONr_long_range_B_other5.49419.19447296
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.807→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 300 -
Rwork0.221 5470 -
obs--64.18 %

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