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- PDB-3wrt: Wild type beta-lactamase DERIVED FROM CHROMOHALOBACTER SP.560 -

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Basic information

Entry
Database: PDB / ID: 3wrt
TitleWild type beta-lactamase DERIVED FROM CHROMOHALOBACTER SP.560
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: 2.9 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 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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


Theoretical massNumber of molelcules
Total (without water)118,7043
Polymers118,7043
Non-polymers00
Water41423
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5681
Polymers39,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5681
Polymers39,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5681
Polymers39,5681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.171, 116.171, 68.032
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: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA8 - 3628 - 362
21GLYGLYBB8 - 3628 - 362
12GLYGLYAA8 - 3628 - 362
22GLYGLYCC8 - 3628 - 362
13ALAALABB8 - 3638 - 363
23ALAALACC8 - 3638 - 363

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Beta-lactamase


Mass: 39568.043 Da / Num. of mol.: 3 / Fragment: UNP residues 22-388
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / pH: 7
Details: 0.2M NACL, 0.2M MAGNESIUM FORMATE, 30% PEG3350, 50MM HEPES BUFFER, PH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 17, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 21572 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.5
Reflection shellResolution: 2.9→3.007 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 5.16 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZKJ

1zkj


Resolution: 2.9→40.45 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.892 / SU B: 30.816 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1163 5.1 %RANDOM
Rwork0.171 ---
obs0.174 21572 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: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å2-0 Å2
2--0.11 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8093 0 0 23 8116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198260
X-RAY DIFFRACTIONr_bond_other_d0.0080.027739
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.97911264
X-RAY DIFFRACTIONr_angle_other_deg1.327317850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90951065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12624.738363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.184151300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4061552
X-RAY DIFFRACTIONr_chiral_restr0.0810.21271
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219490
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021732
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_it2.0062.7974272
X-RAY DIFFRACTIONr_mcbond_other2.0062.7974271
X-RAY DIFFRACTIONr_mcangle_it3.2594.195333
X-RAY DIFFRACTIONr_mcangle_other3.2594.1915334
X-RAY DIFFRACTIONr_scbond_it2.3073.0363988
X-RAY DIFFRACTIONr_scbond_other2.3063.0363989
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.784.4675932
X-RAY DIFFRACTIONr_long_range_B_refined6.85726.535967
X-RAY DIFFRACTIONr_long_range_B_other6.85726.535968
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)
11A207140.12
12B207140.12
21A208540.11
22C208540.11
31B209100.11
32C209100.11
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 93 -
Rwork0.293 1598 -
obs--99.41 %
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)
11.3405-0.56730.38970.9081-0.48420.61740.05410.10560.0787-0.0477-0.0694-0.1630.14430.00620.01530.10210.0483-0.01170.1010.02010.0433-42.770220.58881.0968
20.738-0.00040.0281.106-0.03980.3166-0.08270.12120.06220.0883-0.0126-0.08060.02-0.04470.09530.0359-0.0654-0.02120.15730.03330.0673-48.2572-15.939327.8984
31.2566-0.5660.0540.5405-0.07310.48140.00670.09880.4136-0.01780.0749-0.11480.1406-0.0567-0.08160.0557-0.0024-0.05270.07610.0440.2081-8.088718.6013-28.5029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 364
2X-RAY DIFFRACTION2B8 - 363
3X-RAY DIFFRACTION3C7 - 363

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