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

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Basic information

Entry
Database: PDB / ID: 3wrz
TitleN288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (without soaking)
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: 1.8 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_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)119,33617
Polymers118,7883
Non-polymers54714
Water15,061836
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8327
Polymers39,5961
Non-polymers2366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7124
Polymers39,5961
Non-polymers1163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7926
Polymers39,5961
Non-polymers1965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.928, 114.928, 67.567
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.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 836 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 293 K / pH: 7
Details: 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate, 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
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 wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.02
11-K, -H, -L20.372
11-h,-k,l30.02
11K, H, -L40.588
ReflectionResolution: 1.799→50 Å / Num. obs: 92589 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 15.5 / % possible all: 99.4

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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: 3WRT

3wrt


Resolution: 1.8→29.12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.253 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4609 5 %RANDOM
Rwork0.172 ---
obs0.181 87957 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2--1.38 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8107 0 14 836 8957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198283
X-RAY DIFFRACTIONr_bond_other_d0.0060.027766
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.97911295
X-RAY DIFFRACTIONr_angle_other_deg1.491317916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10651068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98224.753364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.604151309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.481552
X-RAY DIFFRACTIONr_chiral_restr0.1560.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219515
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021735
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_it0.8280.9634281
X-RAY DIFFRACTIONr_mcbond_other0.8270.9624280
X-RAY DIFFRACTIONr_mcangle_it1.4381.4395346
X-RAY DIFFRACTIONr_mcangle_other1.4381.4395347
X-RAY DIFFRACTIONr_scbond_it1.0841.1174002
X-RAY DIFFRACTIONr_scbond_other1.0841.1164000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7461.6275949
X-RAY DIFFRACTIONr_long_range_B_refined4.339.54637698
X-RAY DIFFRACTIONr_long_range_B_other4.1659.21236824
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)
11A203990.12
12B203990.12
21A203190.12
22C203190.12
31B201110.13
32C201110.13
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 316 -
Rwork0.153 6508 -
obs--99.65 %
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)
10.8502-0.122-0.0920.5717-0.18070.61570.03090.00740.0155-0.0823-0.0418-0.08090.0587-0.00020.01090.05650.01930.01910.03450.00510.0605-42.263920.48090.7741
20.9842-0.24530.30551.3744-0.56021.445-0.0111-0.02690.07480.0378-0.1957-0.1860.00740.03310.20680.0045-0.0145-0.00850.05970.04460.0993-47.5043-15.67927.4267
30.4266-0.20020.00180.4932-0.01131.47050.0132-0.01090.0295-0.00770.02820.0157-0.1340.039-0.04140.05280.00430.01320.0281-00.0524-7.936718.4145-28.0262
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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