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- PDB-5i0p: Crystal Structure of a Beta-lactamase domain protein from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 5i0p
TitleCrystal Structure of a Beta-lactamase domain protein from Burkholderia ambifaria
ComponentsBeta-lactamase domain protein
KeywordsHYDROLASE / SSGCID / Beta-lactamase / Burkholderia ambifaria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyMetallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Winged helix-like DNA-binding domain superfamily / metal ion binding / Beta-lactamase domain protein
Function and homology information
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Beta-lactamase domain protein from Burkholderia ambifaria
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionFeb 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_oper_list / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase domain protein
B: Beta-lactamase domain protein
C: Beta-lactamase domain protein
D: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,44612
Polymers163,9234
Non-polymers5238
Water5,837324
1
A: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1113
Polymers40,9811
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1113
Polymers40,9811
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1113
Polymers40,9811
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1113
Polymers40,9811
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.170, 141.230, 236.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5:8 or (resid 9 and (name...
21(chain B and ((resid 5:6 and (name N or name...
31(chain C and ((resid 5:6 and (name N or name...
41(chain D and ((resid 5:6 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEU(chain A and (resid 5:8 or (resid 9 and (name...AA5 - 813 - 16
12ASPASPASPASP(chain A and (resid 5:8 or (resid 9 and (name...AA917
13GLUGLUZNZN(chain A and (resid 5:8 or (resid 9 and (name...AA - F5 - 40113
14GLUGLUZNZN(chain A and (resid 5:8 or (resid 9 and (name...AA - F5 - 40113
15GLUGLUZNZN(chain A and (resid 5:8 or (resid 9 and (name...AA - F5 - 40113
16GLUGLUZNZN(chain A and (resid 5:8 or (resid 9 and (name...AA - F5 - 40113
21GLUGLUHISHIS(chain B and ((resid 5:6 and (name N or name...BB5 - 613 - 14
22ALAALAZNZN(chain B and ((resid 5:6 and (name N or name...BB - H3 - 40111
23ALAALAZNZN(chain B and ((resid 5:6 and (name N or name...BB - H3 - 40111
24ALAALAZNZN(chain B and ((resid 5:6 and (name N or name...BB - H3 - 40111
25ALAALAZNZN(chain B and ((resid 5:6 and (name N or name...BB - H3 - 40111
31GLUGLUHISHIS(chain C and ((resid 5:6 and (name N or name...CC5 - 613 - 14
32HISHISZNZN(chain C and ((resid 5:6 and (name N or name...CC - J-1 - 4017
33HISHISZNZN(chain C and ((resid 5:6 and (name N or name...CC - J-1 - 4017
34HISHISZNZN(chain C and ((resid 5:6 and (name N or name...CC - J-1 - 4017
35HISHISZNZN(chain C and ((resid 5:6 and (name N or name...CC - J-1 - 4017
41GLUGLUHISHIS(chain D and ((resid 5:6 and (name N or name...DD5 - 613 - 14
42ASNASNZNZN(chain D and ((resid 5:6 and (name N or name...DD - L2 - 40110
43ASNASNZNZN(chain D and ((resid 5:6 and (name N or name...DD - L2 - 40110
44ASNASNZNZN(chain D and ((resid 5:6 and (name N or name...DD - L2 - 40110
45ASNASNZNZN(chain D and ((resid 5:6 and (name N or name...DD - L2 - 40110

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Components

#1: Protein
Beta-lactamase domain protein


Mass: 40980.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria)
Strain: MC40-6 / Gene: BamMC406_2837 / Plasmid: BuamA.15997.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1YNR3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BuamA.15997.a.B1.PW37786 at 26 mg/ml, protein was mixed 1:1 with Morpheus (a1): 10% (w/v) PEG-20000, 20% (v/v) PEG MME 500, 100 mM MES/imidazole, pH = 6.5, 0.03 M each magnesium chloride, ...Details: BuamA.15997.a.B1.PW37786 at 26 mg/ml, protein was mixed 1:1 with Morpheus (a1): 10% (w/v) PEG-20000, 20% (v/v) PEG MME 500, 100 mM MES/imidazole, pH = 6.5, 0.03 M each magnesium chloride, sodium fluoride, sodium bromide, sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 53685 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.560.5293.011100
2.56-2.640.4383.641100
2.64-2.710.3664.45199.9
2.71-2.80.3135.12199.9
2.8-2.890.2496.471100
2.89-2.990.1958.07199.9
2.99-3.10.179.281100
3.1-3.230.13811.27199.9
3.23-3.370.10814.39199.9
3.37-3.540.09116.61199.9
3.54-3.730.08118.27199.9
3.73-3.950.0720.59199.9
3.95-4.230.06422.05199.7
4.23-4.560.05923.7199.9
4.56-50.05724.34199.9
5-5.590.0622.77199.8
5.59-6.460.05922.59199.9
6.46-7.910.05124.61199.9
7.91-11.180.04128.38199.2
11.18-500.04128.16195.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2299refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MR-Rosettaphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZO4

2zo4


Resolution: 2.5→44.935 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.74
RfactorNum. reflection% reflection
Rfree0.2285 1999 3.72 %
Rwork0.1663 --
obs0.1686 53673 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.97 Å2 / Biso mean: 39.0261 Å2 / Biso min: 12.74 Å2
Refinement stepCycle: final / Resolution: 2.5→44.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10201 0 8 324 10533
Biso mean--43.79 33 -
Num. residues----1328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110509
X-RAY DIFFRACTIONf_angle_d1.21114339
X-RAY DIFFRACTIONf_chiral_restr0.0661574
X-RAY DIFFRACTIONf_plane_restr0.0081870
X-RAY DIFFRACTIONf_dihedral_angle_d16.4566145
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5629X-RAY DIFFRACTION9.115TORSIONAL
12B5629X-RAY DIFFRACTION9.115TORSIONAL
13C5629X-RAY DIFFRACTION9.115TORSIONAL
14D5629X-RAY DIFFRACTION9.115TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.56260.29891390.20335893728100
2.5626-2.63190.30771410.20336403781100
2.6319-2.70930.28141400.203936313771100
2.7093-2.79670.26191420.196736543796100
2.7967-2.89670.25021400.188236193759100
2.8967-3.01260.25751440.186637023846100
3.0126-3.14970.28971390.201436183757100
3.1497-3.31570.24411410.18636613802100
3.3157-3.52340.21521430.172736913834100
3.5234-3.79530.22311440.160137063850100
3.7953-4.1770.19061430.133836963839100
4.177-4.78080.20031440.120837253869100
4.7808-6.0210.17521460.146937733919100
6.021-44.94220.22551530.17483969412299
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)
15.26241.57251.65115.04921.66452.6439-0.00060.0597-0.16020.342-0.06880.272-0.2448-0.01670.07010.45810.16820.09670.2511-0.00250.254821.727457.0082159.1738
21.9262-0.52780.64562.2483-0.4491.689-0.0267-0.2520.1630.59450.0468-0.2287-0.38130.03970.00120.4039-0.0019-0.00020.26230.01920.230533.72846.0326170.7776
32.2808-0.0644-0.09651.6346-0.3770.10340.1610.3839-0.1712-0.0653-0.1207-0.43230.12990.1631-0.11570.3103-0.04050.00060.5039-0.01490.383743.117532.0062157.5442
40.2231-0.12960.20822.49750.58891.86770.06790.0101-0.0543-0.04120.0210.2721-0.0358-0.2493-0.07920.2160.03490.0060.30690.06810.301621.513837.0999157.1178
57.4692-1.5613-0.135.67340.22195.00060.04940.0697-0.1307-0.31160.04060.002-0.61730.7588-0.10660.3364-0.0869-0.04440.42750.02570.191431.284525.6731137.7489
62.49640.2458-0.31092.8258-0.80242.323-0.08240.0335-0.29370.0518-0.083-0.27630.95450.38460.18620.57850.1422-0.00980.39140.03060.31134.3362.717161.7045
71.30960.2458-0.53232.0907-0.53764.5205-0.0351-0.1371-0.11360.0245-0.02120.01630.3265-0.08350.00460.26890.0243-0.01310.26140.05640.276226.04812.8696172.4848
84.4783-0.38162.07146.76360.26444.2960.4997-0.7980.09640.5129-0.5211-0.0656-0.23660.04430.12850.4135-0.16010.01930.47240.00440.254332.219422.4241192.6316
93.3865-1.1157-0.28221.8590.14642.2667-0.1661-0.43860.040.40930.1223-0.0298-0.1470.21960.07360.27360.0037-0.00710.2786-0.0120.168635.449571.2812153.7282
101.9771-0.9559-0.15761.6918-0.25071.528-0.0733-0.13280.28990.24230.0241-0.3991-0.37430.27060.12810.2058-0.0439-0.02730.306-0.03980.332945.376675.8244141.5625
111.3386-0.001-0.25481.0525-0.52181.3787-0.0164-0.00250.00310.08670.02160.0927-0.1863-0.115-0.01730.14640.00350.01880.2402-0.00180.222326.152776.7637138.8563
124.56111.1390.32015.64592.92735.60130.13750.07350.64460.07470.05830.0879-0.26910.2163-0.12060.28460.03540.04480.20750.05430.332426.914799.2173133.2371
132.35130.22390.48942.26420.05181.86380.14860.25940.1815-0.5574-0.0637-0.2378-0.29810.135-0.06470.364-0.04820.07690.32990.06130.244643.043581.5669101.3456
140.5876-0.14240.05111.79770.14771.42510.15510.01090.1245-0.0434-0.0078-0.3074-0.25670.3498-0.02950.2509-0.09430.02330.31560.03230.34749.181880.9875116.8029
150.4226-0.4873-0.23081.69070.02151.6153-0.03210.0431-0.009-0.05190.02210.0264-0.0216-0.034-0.00340.1292-0.04340.02670.24150.0170.234139.103168.7506113.6114
166.51750.00070.53854.27280.91044.42210.0581-0.06040.00560.23910.0979-0.19330.42570.2947-0.05750.2250.0126-0.04140.18760.00140.208154.191754.1237121.0108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 22 )A5 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 133 )A23 - 133
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 181 )A134 - 181
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 300 )A182 - 300
5X-RAY DIFFRACTION5chain 'A' and (resid 301 through 358 )A301 - 358
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 133 )B3 - 133
7X-RAY DIFFRACTION7chain 'B' and (resid 134 through 297 )B134 - 297
8X-RAY DIFFRACTION8chain 'B' and (resid 298 through 357 )B298 - 357
9X-RAY DIFFRACTION9chain 'C' and (resid -1 through 80 )C-1 - 80
10X-RAY DIFFRACTION10chain 'C' and (resid 81 through 181 )C81 - 181
11X-RAY DIFFRACTION11chain 'C' and (resid 182 through 300 )C182 - 300
12X-RAY DIFFRACTION12chain 'C' and (resid 301 through 358 )C301 - 358
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 80 )D2 - 80
14X-RAY DIFFRACTION14chain 'D' and (resid 81 through 164 )D81 - 164
15X-RAY DIFFRACTION15chain 'D' and (resid 165 through 300 )D165 - 300
16X-RAY DIFFRACTION16chain 'D' and (resid 301 through 358 )D301 - 358

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