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- PDB-5vpq: Crystal structure of beta-lactamase from Burkholderia phymatum -

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Basic information

Entry
Database: PDB / ID: 5vpq
TitleCrystal structure of beta-lactamase from Burkholderia phymatum
ComponentsBeta-lactamase
KeywordsHYDROLASE / SSGCID / beta-lactamase / Burkholderia phymatum / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of beta-lactamase from Burkholderia phymatum
Authors: Conrady, D.G. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4669
Polymers61,9662
Non-polymers5007
Water12,755708
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A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3266
Polymers30,9831
Non-polymers3435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1403
Polymers30,9831
Non-polymers1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.700, 165.610, 73.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21B-467-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 12 through 14 and (name N...
21(chain B and (resid 12 through 18 or resid 21...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 12 through 14 and (name N...A12 - 14
121(chain A and ((resid 12 through 14 and (name N...A5 - 293
131(chain A and ((resid 12 through 14 and (name N...A5 - 293
141(chain A and ((resid 12 through 14 and (name N...A5 - 293
151(chain A and ((resid 12 through 14 and (name N...A5 - 293
211(chain B and (resid 12 through 18 or resid 21...B12 - 18
221(chain B and (resid 12 through 18 or resid 21...B21 - 23
231(chain B and (resid 12 through 18 or resid 21...B25 - 31
241(chain B and (resid 12 through 18 or resid 21...B33 - 43
251(chain B and (resid 12 through 18 or resid 21...B45 - 49
261(chain B and (resid 12 through 18 or resid 21...B51 - 55
271(chain B and (resid 12 through 18 or resid 21...B57 - 60
281(chain B and (resid 12 through 18 or resid 21...B62
291(chain B and (resid 12 through 18 or resid 21...B64 - 67
2101(chain B and (resid 12 through 18 or resid 21...B69 - 70
2111(chain B and (resid 12 through 18 or resid 21...B72
2121(chain B and (resid 12 through 18 or resid 21...B74 - 75
2131(chain B and (resid 12 through 18 or resid 21...B78 - 79
2141(chain B and (resid 12 through 18 or resid 21...B82 - 92
2151(chain B and (resid 12 through 18 or resid 21...B94 - 98
2161(chain B and (resid 12 through 18 or resid 21...B100 - 118
2171(chain B and (resid 12 through 18 or resid 21...B120
2181(chain B and (resid 12 through 18 or resid 21...B122 - 129
2191(chain B and (resid 12 through 18 or resid 21...B132 - 138
2201(chain B and (resid 12 through 18 or resid 21...B139
2211(chain B and (resid 12 through 18 or resid 21...B12 - 281
2221(chain B and (resid 12 through 18 or resid 21...B12 - 281
2231(chain B and (resid 12 through 18 or resid 21...B12 - 281
2241(chain B and (resid 12 through 18 or resid 21...B12 - 281

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Components

#1: Protein Beta-lactamase


Mass: 30983.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_2229 / Plasmid: BuphA.00104.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2JET9, beta-lactamase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: BuphA.00104.a.B1.PS37967 at 22.6mg/ml, mixed 1:1 with Rigaku Reagents MCSG1 A3: 0.2 M NaCl, 0.1M Sodium Phosphate pH 6.2, 10% PEG8000, cryo protected with 25% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→41.104 Å / Num. obs: 114101 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.171 % / Biso Wilson estimate: 12.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 1.07 / Net I/σ(I): 27.32 / Num. measured all: 932366 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.447.5810.5553.2483620.880.596100
1.44-1.488.1540.4214.5181490.9350.449100
1.48-1.528.1580.335.8379340.960.352100
1.52-1.578.1930.2627.4177310.9730.28100
1.57-1.628.1990.2159.1674610.9820.23100
1.62-1.678.2230.17811.0872620.9880.191100
1.67-1.748.2240.14414.0669730.9910.153100
1.74-1.818.2480.11917.0867270.9940.127100
1.81-1.898.2510.09422.0164680.9960.1100
1.89-1.988.260.0728.2661980.9980.075100
1.98-2.098.2740.05535.458720.9980.059100
2.09-2.218.2770.04641.5755800.9990.049100
2.21-2.378.2760.04146.7152850.9990.043100
2.37-2.568.2910.03651.3348990.9990.039100
2.56-2.88.2930.03257.2345220.9990.034100
2.8-3.138.2990.02664.59408710.028100
3.13-3.618.2590.02273.21363910.023100
3.61-4.438.1990.01979.16311210.02100
4.43-6.268.0690.01978.22243910.021100
6.26-41.1047.4150.0276.14140110.02199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C6Y

4c6y


Resolution: 1.4→41.104 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.55
RfactorNum. reflection% reflection
Rfree0.1611 2084 1.83 %
Rwork0.1385 --
obs0.1389 114093 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.57 Å2 / Biso mean: 19.6872 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.4→41.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 30 719 4805
Biso mean--45.87 35.53 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084507
X-RAY DIFFRACTIONf_angle_d1.076190
X-RAY DIFFRACTIONf_chiral_restr0.085708
X-RAY DIFFRACTIONf_plane_restr0.007836
X-RAY DIFFRACTIONf_dihedral_angle_d18.8521714
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1918X-RAY DIFFRACTION4.586TORSIONAL
12B1918X-RAY DIFFRACTION4.586TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.43260.2221250.193674007525
1.4326-1.46840.19141420.17173977539
1.4684-1.50810.18161330.159674377570
1.5081-1.55250.15931540.147273647518
1.5525-1.60260.16781360.145274167552
1.6026-1.65990.1681600.14373867546
1.6599-1.72630.1691310.138874357566
1.7263-1.80490.17741510.139774277578
1.8049-1.90010.1571370.140974287565
1.9001-2.01910.15761640.136974197583
2.0191-2.1750.15531120.130475147626
2.175-2.39380.14631490.131874627611
2.3938-2.74020.17451290.140275487677
2.7402-3.45210.16421350.136975727707
3.4521-41.1220.14361260.129878047930
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)
17.9026.7658-3.70277.4278-3.5261.8089-0.07380.0187-0.2489-0.0212-0.0726-0.41960.03890.10220.18580.09520.0153-0.02540.13910.00630.133-0.7735-23.59927.4187
21.0085-0.10970.12181.4977-0.27740.24990.01210.09550.0744-0.0872-0.0238-0.0204-0.02630.06050.01390.0881-0.00410.01410.090.00170.0584-15.6937-19.7622-3.426
33.85580.4815-1.4353.089-0.17254.42550.05470.30620.4747-0.0655-0.0110.1697-0.2477-0.2638-0.07430.10020.0188-0.01870.19590.04960.1903-39.2015-12.1142-7.4365
41.3553-0.37330.09281.2119-0.47430.5265-0.00070.06060.0473-0.1230.05220.04510.0281-0.0219-0.03740.1189-0.0114-0.00930.1288-0.0070.1063-26.682-22.8849-7.6287
51.59640.08690.39145.2232-1.06941.2341-0.08660.12130.1591-0.0723-0.0433-0.2265-0.14710.11420.12390.1219-0.00930.00210.12910.01740.1112-13.1792-18.0667-6.0286
66.9280.8218-3.30246.2837-0.15574.1586-0.00810.28180.243-0.30170.0682-0.1011-0.16720.0416-0.0390.1134-0.0155-0.02450.07270.01520.1037-19.1995-5.3022-7.4816
71.33910.7297-0.33242.851-0.52120.7482-0.0221-0.06470.09130.0919-0.0010.0159-0.0782-0.0130.02640.09130.0058-0.00970.0857-0.00530.0728-18.9662-18.90197.233
86.03625.3546-3.25317.2697-3.41723.5830.2267-0.57740.08980.2896-0.3149-0.1545-0.15810.28010.05520.08990.0018-0.01710.1095-0.02360.0748-10.1644-18.528712.6087
93.4725-1.66431.30121.7793-1.74152.01040.1584-0.0188-0.2034-0.2591-0.01210.22110.2492-0.2168-0.13590.1106-0.0091-0.01890.1081-0.00250.1047-45.2523-30.96124.2385
100.5539-0.19840.12380.9657-0.26160.97960.0367-0.0667-0.04230.0069-0.0065-0.05640.05250.1263-0.04640.06450.01420.00180.09880.00070.0741-25.6326-30.041528.3076
113.6437-1.82871.71366.209-1.05293.88410.1913-0.42640.24360.4392-0.0984-0.2326-0.29710.3079-0.04710.1992-0.0688-0.00170.2936-0.07550.1411-14.3092-15.039541.3177
121.18370.14280.12380.85640.04561.06720.0151-0.14010.13850.05180.0029-0.0065-0.07420.0428-0.01770.087-0.01230.00870.1157-0.01160.0936-21.1539-20.242327.9814
133.6532-2.16032.07065.0151-4.375.76620.114-0.1136-0.1948-0.0851-0.05540.04470.25570.0197-0.05940.0786-0.0018-0.00030.0749-0.00490.0809-27.1951-33.43226.4431
144.4606-1.6088-0.885.73381.89180.7648-0.0446-0.2431-0.06310.22790.0748-0.26460.14260.1719-0.020.14160.0197-0.02210.14990.03670.0859-20.1877-35.969338.9326
151.1872-0.70730.10982.6737-0.50411.38780.0146-0.12310.07150.1760.01310.1155-0.0406-0.0212-0.03010.0717-0.00070.0170.0896-0.0060.0827-36.4027-25.516935.0135
163.2892-1.16210.43786.68921.38594.23750.0231-0.2546-0.10150.1908-0.02810.42360.1331-0.17880.01410.0591-0.00130.02290.13520.01380.1053-44.8945-31.255434.0232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 27 )A5 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 73 )A28 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 107 )A74 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 168 )A108 - 168
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 183 )A169 - 183
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 202 )A184 - 202
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 265 )A203 - 265
8X-RAY DIFFRACTION8chain 'A' and (resid 266 through 281 )A266 - 281
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 39 )B12 - 39
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 74 )B40 - 74
11X-RAY DIFFRACTION11chain 'B' and (resid 75 through 107 )B75 - 107
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 168 )B108 - 168
13X-RAY DIFFRACTION13chain 'B' and (resid 169 through 183 )B169 - 183
14X-RAY DIFFRACTION14chain 'B' and (resid 184 through 202 )B184 - 202
15X-RAY DIFFRACTION15chain 'B' and (resid 203 through 265 )B203 - 265
16X-RAY DIFFRACTION16chain 'B' and (resid 266 through 281 )B266 - 281

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