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- PDB-5u8o: Crystal Structure of Beta-lactamase domain protein, from Burkhold... -

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Basic information

Entry
Database: PDB / ID: 5u8o
TitleCrystal Structure of Beta-lactamase domain protein, from Burkholderia multivorans
ComponentsZn-dependent hydrolase
KeywordsHYDROLASE / Structural Genomics / 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 / hydrolase activity / Winged helix-like DNA-binding domain superfamily / metal ion binding / Zn-dependent hydrolase
Function and homology information
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Beta-lactamase domain protein, from Burkholderia multivorans
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Delker, S.L. / Conrady, D.G. / Lorimer, D. / Edwards, T.E.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 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 / 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_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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.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_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: Zn-dependent hydrolase
B: Zn-dependent hydrolase
C: Zn-dependent hydrolase
D: Zn-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,34218
Polymers164,7434
Non-polymers59914
Water6,251347
1
A: Zn-dependent hydrolase
B: Zn-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,70910
Polymers82,3722
Non-polymers3378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-186 kcal/mol
Surface area27190 Å2
MethodPISA
2
C: Zn-dependent hydrolase
D: Zn-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6338
Polymers82,3722
Non-polymers2626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-165 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.520, 106.830, 144.330
Angle α, β, γ (deg.)90.000, 91.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid -1 and (name N or name...
21(chain B and ((resid -1 and (name N or name...
31(chain C and ((resid -1 and (name N or name...
41(chain D and (resid -1 through 54 or (resid 55...

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
11HISHISHISHIS(chain A and ((resid -1 and (name N or name...AA-17
12HISHISALAALA(chain A and ((resid -1 and (name N or name...AA-2 - 3586 - 366
13HISHISALAALA(chain A and ((resid -1 and (name N or name...AA-2 - 3586 - 366
14HISHISALAALA(chain A and ((resid -1 and (name N or name...AA-2 - 3586 - 366
15HISHISALAALA(chain A and ((resid -1 and (name N or name...AA-2 - 3586 - 366
21HISHISHISHIS(chain B and ((resid -1 and (name N or name...BB-17
22HISHISZNZN(chain B and ((resid -1 and (name N or name...BB - J-3 - 4025
23HISHISZNZN(chain B and ((resid -1 and (name N or name...BB - J-3 - 4025
24HISHISZNZN(chain B and ((resid -1 and (name N or name...BB - J-3 - 4025
25HISHISZNZN(chain B and ((resid -1 and (name N or name...BB - J-3 - 4025
31HISHISHISHIS(chain C and ((resid -1 and (name N or name...CC-17
32HISHISZNZN(chain C and ((resid -1 and (name N or name...CC - N-2 - 4026
33HISHISZNZN(chain C and ((resid -1 and (name N or name...CC - N-2 - 4026
34HISHISZNZN(chain C and ((resid -1 and (name N or name...CC - N-2 - 4026
35HISHISZNZN(chain C and ((resid -1 and (name N or name...CC - N-2 - 4026
41HISHISGLYGLY(chain D and (resid -1 through 54 or (resid 55...DD-1 - 547 - 62
42GLNGLNALAALA(chain D and (resid -1 through 54 or (resid 55...DD55 - 5663 - 64
43HISHISZNZN(chain D and (resid -1 through 54 or (resid 55...DD - Q-1 - 4027
44HISHISZNZN(chain D and (resid -1 through 54 or (resid 55...DD - Q-1 - 4027
45HISHISZNZN(chain D and (resid -1 through 54 or (resid 55...DD - Q-1 - 4027
46HISHISZNZN(chain D and (resid -1 through 54 or (resid 55...DD - Q-1 - 4027

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Zn-dependent hydrolase / BumuA.15997.a.B1


Mass: 41185.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: BMULJ_02874 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3KRR5

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Non-polymers , 5 types, 361 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MCSG1: 0.2 M Calcium Chloride 0.1 M Tris: HCl, pH 8.5 25 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 7, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.4→48.098 Å / Num. obs: 53172 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 5.38 % / Biso Wilson estimate: 37.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.079 / Χ2: 0.974 / Net I/σ(I): 17.83 / Num. measured all: 286070 / Scaling rejects: 26
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.4-2.465.4630.53630.902198
2.46-2.535.4550.4863.40.91197.5
2.53-2.65.4520.4183.990.922198.3
2.6-2.685.4370.3125.220.957197.7
2.68-2.775.4260.2646.110.967198.5
2.77-2.875.4210.2157.410.983198
2.87-2.985.4050.1659.680.987198.4
2.98-3.15.4120.14211.440.99198.5
3.1-3.245.390.10814.410.994198.3
3.24-3.395.3940.07918.60.997198.7
3.39-3.585.3540.0623.130.998198.9
3.58-3.795.3610.05227.050.998198.7
3.79-4.065.370.03933.160.999198.9
4.06-4.385.340.03438.290.999199.2
4.38-4.85.3310.0341.660.999199.1
4.8-5.375.3240.0340.760.999199.3
5.37-6.25.3010.03238.750.999199.3
6.2-7.595.2250.02842.270.999198.8
7.59-10.735.1110.02448.920.999199.3
10.73-48.0984.5370.02244.380.999196.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I0P

5i0p


Resolution: 2.4→48.098 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.05
RfactorNum. reflection% reflection
Rfree0.2215 1974 3.72 %
Rwork0.163 --
obs0.1652 53071 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.35 Å2 / Biso mean: 47.0852 Å2 / Biso min: 0.34 Å2
Refinement stepCycle: final / Resolution: 2.4→48.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10896 0 14 349 11259
Biso mean--52.16 39.75 -
Num. residues----1415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711229
X-RAY DIFFRACTIONf_angle_d0.91615318
X-RAY DIFFRACTIONf_chiral_restr0.0561685
X-RAY DIFFRACTIONf_plane_restr0.0062008
X-RAY DIFFRACTIONf_dihedral_angle_d16.0746581
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6094X-RAY DIFFRACTION7.746TORSIONAL
12B6094X-RAY DIFFRACTION7.746TORSIONAL
13C6094X-RAY DIFFRACTION7.746TORSIONAL
14D6094X-RAY DIFFRACTION7.746TORSIONAL
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 (%)
2.4001-2.46010.27611280.20823606373498
2.4601-2.52660.28181710.21273611378297
2.5266-2.6010.27531420.2093582372498
2.601-2.68490.27391280.19713660378898
2.6849-2.78090.26041120.19063619373198
2.7809-2.89220.24931520.19083641379398
2.8922-3.02380.28551470.17493661380898
3.0238-3.18320.22611380.17963604374299
3.1832-3.38260.2491320.17513672380498
3.3826-3.64370.20441410.15983662380399
3.6437-4.01020.21341720.14613666383899
4.0102-4.59010.18871520.12983688384099
4.5901-5.78150.18861380.13953722386099
5.7815-48.10730.1831210.15643703382497
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)
13.70210.1149-0.54791.80820.86132.7540.0401-0.28210.26410.22730.1493-0.1957-0.14910.2167-0.14870.2143-0.0003-0.03930.216-0.0370.23328.99192.78858.4724
22.004-0.7464-0.48741.95540.06563.08920.18390.10330.2713-0.1302-0.0182-0.0827-0.5194-0.1617-0.10640.23120.0038-0.00060.1913-0.01490.2593-0.45936.1392-5.5591
35.0865-0.2716-0.51273.8025-2.14794.50390.73060.26381.1323-0.7855-0.2056-0.2494-1.5096-0.2028-0.33860.87370.17560.21480.40970.08950.5568-3.763821.4449-18.4586
41.30540.8217-0.20723.26080.40012.28530.14580.3128-0.0105-0.4843-0.0469-0.3517-0.41990.2042-0.08780.39190.04810.07660.37230.01180.2614.5256-4.3724-35.5924
51.7395-1.14080.92152.6604-2.51532.5844-0.1150.7630.5426-0.3227-0.2732-0.4938-0.45840.70940.30220.4604-0.1666-0.03530.5645-0.02370.585932.1856-9.9965-14.2808
61.137-0.6045-0.31371.835-0.23761.66080.11210.2071-0.1322-0.2188-0.01440.1043-0.0625-0.1175-0.1090.1570.0029-0.01150.2336-0.03880.21818.8174-14.8033-23.7511
76.26030.7927-1.37294.0417-0.05124.1247-0.23120.08480.0553-0.0740.1317-0.42120.16030.21110.12270.13690.0001-0.05340.1617-0.01040.315224.8241-24.1045-9.9656
83.45210.1344-1.13352.1780.25073.7266-0.0012-0.5410.17180.29620.0874-0.212-0.1890.6155-0.08220.27780.0067-0.02050.45440.020.2793-12.53224.0789-63.318
92.3793-0.5028-0.57262.3117-0.14712.94480.0734-0.06630.2035-0.04390.07760.0018-0.3026-0.0515-0.10510.2254-0.01520.01030.25080.02590.2317-21.56677.8719-77.3735
103.7840.1013-0.16214.3354-1.42244.81670.40480.2461.1272-0.3222-0.0676-0.0443-0.9648-0.3007-0.26950.52940.10510.1390.38980.1330.5212-25.655923.4451-90.6123
112.77420.3351-0.37743.41080.14932.1251-0.12480.67-0.3419-0.85820.0574-0.16710.2422-0.04630.02360.5437-0.0950.08460.4536-0.05740.3108-7.9718-0.6924-108.2034
120.9204-0.50270.85781.498-2.68334.8393-0.05120.51570.39250.0279-0.598-0.7436-1.03530.88420.60420.5169-0.1340.05880.59040.02950.69110.9397-7.661-86.5426
131.6929-0.6337-0.37141.8941-0.96051.4572-0.20530.2959-0.5401-0.30420.15120.23860.3702-0.13960.02510.438-0.11450.09580.3434-0.07110.4111-12.9994-12.1867-96.2558
145.70430.5426-1.2663.51760.46074.2027-0.4871-0.0433-0.3944-0.10220.1071-0.31340.5520.24280.36430.3450.04390.15430.25260.03960.61692.9413-21.9-82.5442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 134 )A-2 - 134
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 300 )A135 - 300
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 358 )A301 - 358
4X-RAY DIFFRACTION4chain 'B' and (resid -3 through 133 )B-3 - 133
5X-RAY DIFFRACTION5chain 'B' and (resid 134 through 172 )B134 - 172
6X-RAY DIFFRACTION6chain 'B' and (resid 173 through 300 )B173 - 300
7X-RAY DIFFRACTION7chain 'B' and (resid 301 through 359 )B301 - 359
8X-RAY DIFFRACTION8chain 'C' and (resid -2 through 132 )C-2 - 132
9X-RAY DIFFRACTION9chain 'C' and (resid 133 through 300 )C133 - 300
10X-RAY DIFFRACTION10chain 'C' and (resid 301 through 358 )C301 - 358
11X-RAY DIFFRACTION11chain 'D' and (resid -1 through 133 )D-1 - 133
12X-RAY DIFFRACTION12chain 'D' and (resid 134 through 172 )D134 - 172
13X-RAY DIFFRACTION13chain 'D' and (resid 173 through 300 )D173 - 300
14X-RAY DIFFRACTION14chain 'D' and (resid 301 through 359 )D301 - 359

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