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- PDB-3ws4: N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER S... -

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Basic information

Entry
Database: PDB / ID: 3ws4
TitleN288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-2A)
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
STRONTIUM ION / Beta-lactamase
Similarity search - Component
Biological speciesChromohalobacter sp. 560 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 28, 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)119,59614
Polymers118,7883
Non-polymers80711
Water9,152508
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8945
Polymers39,5961
Non-polymers2984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8074
Polymers39,5961
Non-polymers2113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8945
Polymers39,5961
Non-polymers2984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.019, 115.019, 67.800
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: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA8 - 3638 - 363
21ALAALABB8 - 3638 - 363
12ALAALAAA8 - 3638 - 363
22ALAALACC8 - 3638 - 363
13ILEILEBB8 - 3648 - 364
23ILEILECC8 - 3648 - 364

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-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystal was grown in a solution containing 100 mM MES-NaOH buffer (pH 6.5), 200 mM Ca acetate hydrate and 18% PEG8000. Obtained crystal was soaked into a solution containing 100mM MES-NaOH ...Details: Crystal was grown in a solution containing 100 mM MES-NaOH buffer (pH 6.5), 200 mM Ca acetate hydrate and 18% PEG8000. Obtained crystal was soaked into a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate, 200mM Sr acetate 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: AR-NW12A / Wavelength: 1.000, 0.769
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 21, 2013
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.7691
ReflectionResolution: 1.9→50 Å / Num. obs: 77242 / % possible obs: 97.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.09 / % possible all: 97.2

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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: 1.9→28.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.051 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4015 5.1 %RANDOM
Rwork0.182 ---
obs0.184 74882 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.896 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-0 Å2-0 Å2
2---2.12 Å2-0 Å2
3---4.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8135 0 11 508 8654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198375
X-RAY DIFFRACTIONr_bond_other_d0.0090.027844
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.97911431
X-RAY DIFFRACTIONr_angle_other_deg1.429318105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73351087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67924.786374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.724151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5881554
X-RAY DIFFRACTIONr_chiral_restr0.1110.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219650
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021758
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_it2.0682.0774318
X-RAY DIFFRACTIONr_mcbond_other2.0612.0764317
X-RAY DIFFRACTIONr_mcangle_it2.933.1025397
X-RAY DIFFRACTIONr_mcangle_other2.9313.1045398
X-RAY DIFFRACTIONr_scbond_it2.7362.394057
X-RAY DIFFRACTIONr_scbond_other2.7352.3884055
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0723.4856028
X-RAY DIFFRACTIONr_long_range_B_refined6.08820.04737476
X-RAY DIFFRACTIONr_long_range_B_other6.06119.99237152
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 / Rms dev position: 0.1 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A21291
12B21291
21A21044
22C21044
31B21271
32C21271
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 276 -
Rwork0.158 5594 -
obs--99.76 %
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)
10.4471-0.05370.19080.418-0.1150.52080.00810.0417-0.04830.0019-0.0298-0.09730.0163-0.03240.02170.02680.0131-0.00030.02130.00140.0375-42.009520.69720.9844
20.43590.0476-0.05380.185-0.04240.337-0.0185-00.0620.0172-0.0351-0.0160.030.01810.05360.0085-0.0085-0.00710.04320.00830.054-48.038-15.488827.6638
30.0769-0.1870.04650.54470.02110.46580.01710.01540.0076-0.009-0.02560.0043-0.00250.01330.00850.03680.0089-0.00730.01040.00470.0549-7.600718.5318-28.4131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 364
2X-RAY DIFFRACTION2B8 - 366
3X-RAY DIFFRACTION3C8 - 365

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