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- PDB-3ws0: N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER S... -

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Basic information

Entry
Database: PDB / ID: 3ws0
TitleN288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-1A)
ComponentsBeta-lactamase
KeywordsHYDROLASE / CEPHALOSPORINASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesChromohalobacter sp. 560 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Tokunaga, H. / Ishibashi, M. ...Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Tokunaga, M. / Kuroki, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of a highly acidic beta-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site
Authors: Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shibazaki, C. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Kawamoto, M. / Tokunaga, H. / Ishibashi, M. / Blaber, M. / Tokunaga, M. / Kuroki, R.
History
DepositionFeb 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,59719
Polymers118,7883
Non-polymers80816
Water10,106561
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9257
Polymers39,5961
Non-polymers3296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7525
Polymers39,5961
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9207
Polymers39,5961
Non-polymers3246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.393, 115.393, 67.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLYAA8 - 3628 - 362
21GLNGLNGLYGLYBB8 - 3628 - 362
12THRTHRALAALAAA9 - 3639 - 363
22THRTHRALAALACC9 - 3639 - 363
13THRTHRGLYGLYBB9 - 3629 - 362
23THRTHRGLYGLYCC9 - 3629 - 362

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Beta-lactamase


Mass: 39596.098 Da / Num. of mol.: 3 / Fragment: UNP residues 22-388 / Mutation: N288Q, N321Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter sp. 560 (bacteria) / Gene: bla / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI BL21 STAR (DE3) / References: UniProt: Q76LX5, beta-lactamase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18% PEG 8000. Obtained crystal was soaked into a solution containing 100mM MES-NaOH ...Details: Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18% PEG 8000. Obtained crystal was soaked into a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate, 100mM CsCl and 18% PEG8000., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.000, 2.066
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2013
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.0661
ReflectionResolution: 2→50 Å / Num. all: 66954 / Num. obs: 66954 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 7.9 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WRZ

3wrz


Resolution: 2→29.88 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.011 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 3389 5.1 %RANDOM
Rwork0.1903 ---
obs0.19202 66954 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8114 0 16 561 8691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198283
X-RAY DIFFRACTIONr_bond_other_d0.0050.027766
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.97911295
X-RAY DIFFRACTIONr_angle_other_deg1.13317916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39851068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16624.753364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.302151309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8511552
X-RAY DIFFRACTIONr_chiral_restr0.0910.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219515
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021735
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_it0.9081.5774281
X-RAY DIFFRACTIONr_mcbond_other0.9061.5764280
X-RAY DIFFRACTIONr_mcangle_it1.5042.3595346
X-RAY DIFFRACTIONr_mcangle_other1.5042.3595347
X-RAY DIFFRACTIONr_scbond_it1.1931.7564002
X-RAY DIFFRACTIONr_scbond_other1.1891.7544000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9492.5745949
X-RAY DIFFRACTIONr_long_range_B_refined5.75413.7999942
X-RAY DIFFRACTIONr_long_range_B_other5.68313.479721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A214040.09
12B214040.09
21A212800.09
22C212800.09
31B208750.1
32C208750.1
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 263 -
Rwork0.219 4741 -
obs--99.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0589-0.25460.02821.202-0.57641.9750.02920.04510.0429-0.1327-0.0598-0.13710.15670.07580.03070.04460.02540.01550.01540.00750.0166-42.596120.47570.9453
21.9835-0.53430.80052.2415-0.52321.9649-0.07890.03030.17550.1193-0.194-0.2744-0.02620.040.2730.0191-0.02980.00110.08970.05010.1708-47.873-15.820927.3982
31.0779-0.40620.26671.36040.22822.06080.05660.08090.103-0.08-0.028-0.0286-0.0626-0.0089-0.02860.01440.01110.01190.01270.01460.018-7.938518.401-28.1649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 364
2X-RAY DIFFRACTION2B7 - 363
3X-RAY DIFFRACTION3C9 - 365

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