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- PDB-6ao1: Crystal structure of a beta-lactamase from Burkholderia phymatum -

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Basic information

Entry
Database: PDB / ID: 6ao1
TitleCrystal structure of a beta-lactamase from Burkholderia phymatum
ComponentsBeta-lactamase domain protein
KeywordsHYDROLASE / NIAID / structural genomics / beta-lactamase / metalloenzyme / calcium / zinc / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyMetallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Winged helix-like DNA-binding domain superfamily / Beta-lactamase domain protein
Function and homology information
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a beta-lactamase from Burkholderia phymatum
Authors: Edwards, T.E. / Delker, S.L. / Lorimer, D.D.
History
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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)162,75228
Polymers161,6364
Non-polymers1,11624
Water21,4021188
1
A: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6536
Polymers40,4091
Non-polymers2445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,81410
Polymers40,4091
Non-polymers4059
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6727
Polymers40,4091
Non-polymers2626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6135
Polymers40,4091
Non-polymers2044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.300, 70.800, 82.580
Angle α, β, γ (deg.)90.470, 98.620, 112.460
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-lactamase domain protein


Mass: 40409.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (bacteria) / Gene: Bphy_0182 / Production host: Escherichia coli (E. coli) / References: UniProt: B2JKI6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1188 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18.6 mg/mL BuphA.15997.PS38000 against MCSG screen condition C7 (200 mM calcium chloride, 0.1 M Tris, pH 8.5, 20% PEG4000), cryoprotectant: 15% ethylene glycol, crystal tracking ID 290667h5, ...Details: 18.6 mg/mL BuphA.15997.PS38000 against MCSG screen condition C7 (200 mM calcium chloride, 0.1 M Tris, pH 8.5, 20% PEG4000), cryoprotectant: 15% ethylene glycol, crystal tracking ID 290667h5, unique puck ID cho2-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→35.057 Å / Num. obs: 128398 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 2.926 % / Biso Wilson estimate: 23.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.053 / Χ2: 1.025 / Net I/σ(I): 14.85 / Num. measured all: 375743 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.852.5390.3532.7294380.870.44195.7
1.85-1.92.8450.2753.7891660.9280.3495.9
1.9-1.952.990.2224.989370.9520.27396.3
1.95-2.012.990.1646.3786850.9720.20296.3
2.01-2.082.9880.1327.7884800.9820.16296.5
2.08-2.152.9850.1039.782100.9880.12796.6
2.15-2.232.9870.08511.4979270.9910.10596.7
2.23-2.322.9790.07413.0575710.9920.09296.9
2.32-2.432.9790.06214.8973510.9950.07797
2.43-2.552.9710.05516.8769640.9950.06897.1
2.55-2.682.970.04818.7266830.9960.0697.2
2.68-2.852.9680.04221.2663010.9960.05297
2.85-3.042.9560.03823.7559070.9960.04797.2
3.04-3.292.9370.03526.155330.9970.04397.7
3.29-3.62.9360.03128.5450870.9970.03997.5
3.6-4.022.9280.0329.8346070.9970.03797.4
4.02-4.652.9360.02931.0640520.9970.03697.7
4.65-5.692.9350.0283134380.9970.03598.1
5.69-8.052.8970.02930.8226600.9970.03598
8.05-35.0572.8280.02931.6914010.9970.03694

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5U8O

5u8o


Resolution: 1.8→35.057 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.2006 1980 1.54 %
Rwork0.1636 --
obs0.1641 128371 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.8 Å2 / Biso mean: 34.3218 Å2 / Biso min: 11.79 Å2
Refinement stepCycle: final / Resolution: 1.8→35.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10847 0 45 1199 12091
Biso mean--39.45 39.25 -
Num. residues----1412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611269
X-RAY DIFFRACTIONf_angle_d0.81415351
X-RAY DIFFRACTIONf_chiral_restr0.0571685
X-RAY DIFFRACTIONf_plane_restr0.0052008
X-RAY DIFFRACTIONf_dihedral_angle_d14.6976630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8450.27931430.2278933907696
1.845-1.89480.2761430.21158948909196
1.8948-1.95060.22841230.20559017914096
1.9506-2.01360.23291550.1918928908396
2.0136-2.08550.24071560.18459013916996
2.0855-2.1690.23631250.17539066919197
2.169-2.26770.2011450.16828970911597
2.2677-2.38720.19731340.16679048918297
2.3872-2.53680.1931510.17059043919497
2.5368-2.73260.23361420.17969073921597
2.7326-3.00740.22411510.17039073922497
3.0074-3.44230.18811460.15989067921398
3.4423-4.33560.16591290.13739143927298
4.3356-35.06410.16941370.14499069920697
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)
10.89650.4499-0.47861.2748-0.91352.22670.0221-0.0804-0.0135-0.0805-0.0408-0.035-0.0439-0.048-0.00540.13750.031-0.02780.1528-0.0120.1413-21.1044-0.497844.5439
24.22480.1068-0.41023.8187-1.12015.2011-0.112-0.1861-0.4743-0.3339-0.0472-0.35040.34510.32720.09820.16170.02850.03620.21630.05570.2398-1.0607-1.470132.342
30.49120.0256-0.43721.53520.27571.69750.329-0.04820.29830.0336-0.0568-0.0528-0.91540.1125-0.190.7463-0.05790.18130.1951-0.02930.3158-6.849432.812836.184
42.0558-0.38080.59692.0209-1.53291.4476-0.28110.8285-0.3884-0.44460.31060.3386-0.48870.2363-0.09770.54210.00010.15740.56460.0180.4561-38.754532.240325.9443
51.1857-0.3765-0.35660.796-0.18810.62750.1359-0.01940.08190.21460.01860.147-0.3818-0.0837-0.12440.66180.07140.1540.20150.00510.2786-25.560230.561444.3395
60.7513-0.07380.5932.1442-0.59043.16920.05730.0152-0.1944-0.09320.0138-0.05860.43140.1314-0.05240.3023-0.0737-0.01960.22230.0020.2912-10.3209-26.8757-2.3986
70.85150.15960.24292.0762-0.14142.58370.020.0663-0.0374-0.20050.01830.1360.1705-0.2351-0.02720.1425-0.0429-0.03140.1662-0.01320.1845-12.4785-12.2939-12.865
86.58261.4741-0.24050.8371-0.51686.7776-0.47450.9867-0.1963-1.4620.0628-0.22660.53470.65790.41570.6222-0.02110.04840.4343-0.00850.291821.778-15.2827-9.4216
90.78430.42430.37081.6568-0.23622.2859-0.01350.0529-0.0341-0.2238-0.0413-0.0352-0.0450.1210.02920.1683-0.005-0.01540.17230.00290.1963-6.9132-5.5329-8.1948
101.8068-0.03470.3931.1706-0.0691.28270.0261-0.03960.0372-0.0003-0.02950.0220.1219-0.11210.02230.188-0.01890.00040.1632-0.00490.2063-2.9547-12.7744.3098
112.98590.42110.51870.7848-0.07880.9601-0.00190.0416-0.20760.05590.0222-0.0780.22310.0457-0.02930.2625-0.0075-0.00690.1107-0.00210.19425.36-23.5776.9747
124.2242-0.547-1.33916.05360.4746.325-0.0024-0.03420.07010.0743-0.0222-0.3367-0.00880.5626-0.01450.14560.0116-0.03950.14330.01940.201720.1671-14.60336.95
134.9519-1.2336-1.1182.2076-0.23420.88790.12370.23010.1694-0.1571-0.0118-0.1134-0.3646-0.0065-0.12720.2664-0.0282-0.01190.1707-0.02040.22995.998330.01837.0844
141.80650.0684-0.32292.41470.1831.4434-0.0180.01140.0321-0.150.0275-0.3334-0.11090.235-0.00120.1144-0.02870.00940.16540.00990.182717.883313.44430.5785
153.41050.2423-3.13582.6058-0.33478.76980.0530.27510.0396-0.39690.1161-0.3144-0.1785-0.036-0.15490.29330.00230.01540.24540.00220.2208-9.379414.9876-21.9675
161.0009-0.2536-0.21670.95030.1221.11930.0090.0107-0.0274-0.0667-0.04010.0676-0.0818-0.05820.00920.1178-0.0068-0.01580.11930.00080.1457-0.038914.28824.7081
174.1702-1.0166-0.38654.0412-0.48336.79020.0526-0.0520.2967-0.2330.05180.0383-0.6954-0.454-0.08640.21780.0268-0.02120.2191-0.0260.1693-17.291618.2556-10.3215
184.5733-1.57411.96762.3492-0.88063.75090.09110.314-0.2085-0.86040.05780.26670.5253-0.1348-0.23170.4331-0.0382-0.06630.2154-0.00820.3037-28.0884-15.148440.7059
192.2574-0.01170.35282.0935-0.51821.56470.09580.1478-0.0376-0.5150.15650.476-0.0321-0.6333-0.12540.28080.0681-0.13370.42040.04490.2604-38.01012.283233.4258
202.7146-0.8357-1.67370.24970.57441.23410.12620.40490.0223-0.2458-0.08050.0177-0.3253-0.2992-0.05620.35640.03130.00670.3030.010.2244-13.73435.868521.3108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 182 through 300 )C182 - 300
2X-RAY DIFFRACTION2chain 'C' and (resid 301 through 356 )C301 - 356
3X-RAY DIFFRACTION3chain 'D' and (resid -4 through 133 )D-4 - 133
4X-RAY DIFFRACTION4chain 'D' and (resid 134 through 164 )D134 - 164
5X-RAY DIFFRACTION5chain 'D' and (resid 165 through 356 )D165 - 356
6X-RAY DIFFRACTION6chain 'A' and (resid -6 through 35 )A-6 - 35
7X-RAY DIFFRACTION7chain 'A' and (resid 36 through 133 )A36 - 133
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 164 )A134 - 164
9X-RAY DIFFRACTION9chain 'A' and (resid 165 through 194 )A165 - 194
10X-RAY DIFFRACTION10chain 'A' and (resid 195 through 257 )A195 - 257
11X-RAY DIFFRACTION11chain 'A' and (resid 258 through 322 )A258 - 322
12X-RAY DIFFRACTION12chain 'A' and (resid 323 through 356 )A323 - 356
13X-RAY DIFFRACTION13chain 'B' and (resid -2 through 22 )B-2 - 22
14X-RAY DIFFRACTION14chain 'B' and (resid 23 through 134 )B23 - 134
15X-RAY DIFFRACTION15chain 'B' and (resid 135 through 164 )B135 - 164
16X-RAY DIFFRACTION16chain 'B' and (resid 165 through 300 )B165 - 300
17X-RAY DIFFRACTION17chain 'B' and (resid 301 through 356 )B301 - 356
18X-RAY DIFFRACTION18chain 'C' and (resid -2 through 22 )C-2 - 22
19X-RAY DIFFRACTION19chain 'C' and (resid 23 through 132 )C23 - 132
20X-RAY DIFFRACTION20chain 'C' and (resid 133 through 181 )C133 - 181

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