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- PDB-2wuq: Crystal structure of BlaB protein from Streptomyces cacaoi -

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Basic information

Entry
Database: PDB / ID: 2wuq
TitleCrystal structure of BlaB protein from Streptomyces cacaoi
ComponentsBETA-LACTAMASE REGULATORY PROTEIN BLAB
KeywordsTRANSCRIPTION / CLASS A BETA-LACTAMASE FOLD / TRANSCRIPTION REGULATION / BETA-LACTAMASE INDUCTION / RESISTANCE MECHANISM
Function / homologyBeta-lactamase enzyme family / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta / Beta-lactamase regulatory protein BlaB
Function and homology information
Biological speciesSTREPTOMYCES CACAOI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDandois, S. / Herman, R. / Sauvage, E. / Charlier, P. / Joris, B. / Kerff, F.
CitationJournal: To be Published
Title: The Crystal Structure of Blab Protein from Streptomyces Cacaoi
Authors: Dandois, S. / Moutzourelis, G. / Herman, R. / Sauvage, E. / Charlier, P. / Joris, B. / Kerff, F.
History
DepositionOct 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: BETA-LACTAMASE REGULATORY PROTEIN BLAB
B: BETA-LACTAMASE REGULATORY PROTEIN BLAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5384
Polymers69,3542
Non-polymers1842
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-16.7 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.140, 94.580, 61.380
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-LACTAMASE REGULATORY PROTEIN BLAB / BLAB


Mass: 34677.055 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CACAOI (bacteria) / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): TK24 / References: UniProt: P33652
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.22 Å3/Da / Density % sol: 44.56 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979738
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979738 Å / Relative weight: 1
ReflectionResolution: 1.8→47.3 Å / Num. obs: 56421 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DY6

1dy6


Resolution: 1.8→47.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.95 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20099 2860 5.1 %RANDOM
Rwork0.16055 ---
obs0.1626 53512 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.969 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.16 Å2
2--0.01 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4305 0 12 420 4737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9756047
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3535564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69822.304204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84115713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7691556
X-RAY DIFFRACTIONr_chiral_restr0.0970.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22131
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22986
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2343
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0261.52877
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52124514
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.44131712
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0044.51529
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 217 -
Rwork0.224 3924 -
obs--99.64 %
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)
10.8158-0.736-0.05582.4031-0.17410.80950.028-0.075-0.19250.1058-0.01010.00890.19-0.1354-0.0179-0.0321-0.0256-0.0242-0.03470.0286-0.011342.64332.54553.974
21.13660.3604-0.90940.9579-0.02891.44380.06-0.01630.05650.1056-0.0321-0.0575-0.06020.0354-0.0279-0.0359-0.0009-0.0363-0.0606-0.0101-0.03448.96362.19556.033
37.2494-1.21191.17262.71850.13675.987-0.0493-0.0254-0.11050.11070.0503-0.04880.15410.1642-0.0010.134-0.0016-0.0070.04310.0043-0.010541.21550.97365.542
438.9197-19.87638.275318.276211.920133.84430.849-0.62980.19961.60440.0744-0.994-1.49482.037-0.92340.00110.00050.0019-0.0007-0.0005-0.001456.11542.37369.576
51.3988-0.17470.73641.2031-0.42592.5069-0.0351-0.19710.05390.0930.04210.09430.1289-0.3008-0.007-0.0629-0.0076-0.0058-0.0518-0.0192-0.024534.59844.90754.475
628.884121.627915.657129.81477.73999.65251.1117-0.53870.05650.1989-0.48141.95940.6119-0.5842-0.6303-0.0252-0.0868-0.0104-0.0604-0.0315-0.003825.61649.3854.7
71.0787-0.48120.05151.1111-0.20270.8110-0.01630.0132-0.0056-0.0448-0.0960.02280.06740.0448-0.0592-0.0069-0.03-0.05360.0058-0.026145.18841.80347
821.8587-1.311130.25135.95495.417643.3231-0.2528-0.6935-0.27740.4147-0.02461.4177-0.06-2.10330.27730.05130.0231-0.0223-0.0528-0.07350.163229.46329.21340.673
94.2517-0.58532.41592.198-0.55251.87630.32050.5514-0.4349-0.3443-0.18510.03290.36970.1039-0.1354-0.01930.0378-0.01680.0747-0.077-0.024566.12637.47823.373
101.1552-0.3833-0.55140.93520.09511.14930.04720.0730.0742-0.0055-0.0461-0.006-0.1488-0.0252-0.0012-0.0571-0.0145-0.0333-0.04630.0128-0.02659.44764.00437.234
112.20110.00750.73862.25590.20412.389-0.06430.16670.0946-0.097-0.0191-0.1061-0.04860.11580.08340.0142-0.0407-0.01750.01170.03730.020167.37566.11526.375
126.1091-1.7612.32864.73129.356624.69580.3276-0.4504-0.2069-0.2604-0.32620.3645-0.0038-1.0963-0.0014-0.0695-0.0530.00470.02550.0387-0.043551.91259.67418.111
131.3514-1.01221.25271.3329-0.74392.3751-0.05810.06560.1016-0.0502-0.0479-0.1424-0.01250.06790.106-0.0653-0.01580.0052-0.02490.01560.004168.06654.89827.23
149.38063.724-1.08655.8928-0.36542.1288-0.1576-0.04650.0907-0.14080.045-0.3937-0.15850.24180.1125-0.07190.0027-0.0441-0.0410.0127-0.013672.13157.01639.421
152.53880.12151.07561.4786-0.48571.6326-0.03590.0822-0.04970.0340.08280.09690.039-0.1092-0.0469-0.0891-0.0031-0.0243-0.03430.0065-0.031260.08445.08733.425
169.2553-1.47270.24726.8345-1.1345.3534-0.07940.401-0.8999-0.0539-0.0709-0.26150.5670.21650.15030.0320.0188-0.0058-0.0509-0.0370.065769.54834.54130.671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 4
2X-RAY DIFFRACTION2A5 - 126
3X-RAY DIFFRACTION3A127 - 146
4X-RAY DIFFRACTION4A177 - 186
5X-RAY DIFFRACTION5A187 - 209
6X-RAY DIFFRACTION6A210
7X-RAY DIFFRACTION6A218 - 220
8X-RAY DIFFRACTION7A221 - 310
9X-RAY DIFFRACTION8A311 - 315
10X-RAY DIFFRACTION9B1 - 33
11X-RAY DIFFRACTION10B34 - 118
12X-RAY DIFFRACTION11B119 - 144
13X-RAY DIFFRACTION12B145 - 147
14X-RAY DIFFRACTION12B171 - 178
15X-RAY DIFFRACTION13B179 - 210
16X-RAY DIFFRACTION14B218 - 236
17X-RAY DIFFRACTION15B237 - 299
18X-RAY DIFFRACTION16B300 - 312

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