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- PDB-8d2z: Crystal Structure of a Metallo-beta-lactamase superfamily protein... -

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Basic information

Entry
Database: PDB / ID: 8d2z
TitleCrystal Structure of a Metallo-beta-lactamase superfamily protein from Burkholderia cenocepacia
ComponentsMetallo-beta-lactamase superfamily protein
KeywordsHYDROLASE / SSGCID / Burkholderia cenocepacia / metallo-beta-lactamase superfamily protein / 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 / OXAMIC ACID / Metallo-beta-lactamase superfamily protein
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of a Metallo-beta-lactamase superfamily protein from Burkholderia cenocepacia
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase superfamily protein
B: Metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,09510
Polymers72,4792
Non-polymers6168
Water8,899494
1
A: Metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5836
Polymers36,2391
Non-polymers3445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5124
Polymers36,2391
Non-polymers2733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.160, 89.390, 121.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase superfamily protein


Mass: 36239.277 Da / Num. of mol.: 2 / Fragment: BuceA.12746.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAM1430 / Plasmid: BuceA.12746.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4EIY5

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Non-polymers , 6 types, 502 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MolecularDimensions/Calibre Morpheus screen, condition G12: 12.5% (V/V) PEG 1000, 12.5% (w/V) PEG 3350, 12.5% (V/V) MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, ...Details: MolecularDimensions/Calibre Morpheus screen, condition G12: 12.5% (V/V) PEG 1000, 12.5% (w/V) PEG 3350, 12.5% (V/V) MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate: 100mM bicine/ trizma base pH 8.5: BuceA.12746.a.B1.PS02032 at 40mg/ml: tray: 321581 g12: cryo: direct: puck kuz4-9.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 3, 2022 / 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: 1.85→50 Å / Num. obs: 54854 / % possible obs: 99.9 % / Redundancy: 6.854 % / Biso Wilson estimate: 35.182 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.056 / Χ2: 0.948 / Net I/σ(I): 20.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.94.2820.646239880.7330.73999.3
1.9-1.955.2360.4793.1639000.8820.53499.9
1.95-2.016.6210.3854.6437820.9360.417100
2.01-2.077.3880.3046.3137020.9670.327100
2.07-2.147.3970.2398.0236030.980.257100
2.14-2.217.4030.18810.2634530.9860.202100
2.21-2.297.3840.14113.5233520.9920.151100
2.29-2.397.3790.11915.6332110.9950.128100
2.39-2.497.3680.118.3731120.9960.108100
2.49-2.627.3610.08621.0329680.9970.093100
2.62-2.767.3210.07224.9428480.9970.078100
2.76-2.937.2960.05929.5326930.9980.064100
2.93-3.137.2650.04835.4625210.9990.052100
3.13-3.387.1680.0440.623640.9990.043100
3.38-3.77.1110.03446.4221810.9990.037100
3.7-4.147.0490.03149.7319950.9990.034100
4.14-4.787.0220.02752.5317580.9990.029100
4.78-5.856.9320.02652.54153010.028100
5.85-8.276.8150.02652.1111960.9990.028100
8.27-506.0830.02353.016970.9990.02598.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model obtained from the Moonbear server

Resolution: 1.85→35.44 Å / SU ML: 0.1676 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2082 3.8 %0
Rwork0.1513 52760 --
obs0.1525 54842 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 32 494 5204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844917
X-RAY DIFFRACTIONf_angle_d0.94956705
X-RAY DIFFRACTIONf_chiral_restr0.0576758
X-RAY DIFFRACTIONf_plane_restr0.0079864
X-RAY DIFFRACTIONf_dihedral_angle_d11.96651774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.24251330.20823429X-RAY DIFFRACTION99.22
1.89-1.940.22151360.19343499X-RAY DIFFRACTION99.89
1.94-1.990.23141400.18913440X-RAY DIFFRACTION100
1.99-2.050.23051460.16773468X-RAY DIFFRACTION100
2.05-2.120.17091340.16043478X-RAY DIFFRACTION99.97
2.12-2.190.20781370.15393499X-RAY DIFFRACTION100
2.19-2.280.18991340.15373476X-RAY DIFFRACTION99.97
2.28-2.380.2111350.15923500X-RAY DIFFRACTION99.97
2.39-2.510.19181540.16143484X-RAY DIFFRACTION100
2.51-2.670.21661450.16893510X-RAY DIFFRACTION100
2.67-2.870.20551270.16323528X-RAY DIFFRACTION100
2.87-3.160.19361390.15953541X-RAY DIFFRACTION100
3.16-3.620.15821360.13613562X-RAY DIFFRACTION100
3.62-4.560.16571350.1273598X-RAY DIFFRACTION100
4.56-35.440.15131510.1453748X-RAY DIFFRACTION99.9
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)
12.25342539475-0.6037226671-0.9713518650331.42642984159-1.148989370943.56861917326-0.04164037680970.174369705315-0.0883665800871-0.25686407884-0.0613779997141-0.03608941940680.1522187305880.07785520416750.1066576850130.223009725973-0.02906702384760.03099942502090.197382784561-0.04722784001560.21106343754438.333890931321.999143392926.8189807643
22.779524241820.934562343978-0.5684570530872.144371279780.1066132888281.86419335987-0.0938773406287-0.156630290335-0.386049193955-0.01516956131160.0021686578964-0.024086370130.1986478963020.07768271890420.09111346692310.1392742122550.007230919774990.007789823319270.1777400238230.02743917890310.17977384814733.556982999718.240255963639.727188308
34.19099918391.7179145697-0.02536425272921.59383935834-0.1053888580660.652501279889-0.09237493033930.1646111788550.17373544177-0.1405822085890.09405505590120.201804401518-0.0841055016267-0.131730717744-0.0005132376665550.215207014964-0.00240457617073-0.008466815091150.193549568512-0.01653083625230.19705044572818.05116534327.593551697129.7693114145
41.86372294763-0.3749018577-0.3544169053422.21766940701-2.107753879274.38329132779-0.0182084556579-0.125951722569-0.0817415636936-0.1116600249980.07831476982180.1840719038580.487623180112-0.119685295081-0.09453523355550.196747122149-0.053855750116-0.01815321360060.226253037659-0.02308951111230.21072890393311.578794569113.116887687935.7594440049
52.824590494470.737218400323-1.693038337852.063095731131.111231586024.34272769639-0.06293301819490.112221875939-0.0110770867975-0.381970931267-0.05298920829090.5635478792470.0751765411421-0.4919469983810.07082324543850.178881140494-0.0191730812037-0.08436778625080.223906015762-0.01379793541830.2964990279593.20212765515-11.55120436134.41522627966
61.49065481063-0.452821605416-0.1457426828263.914745808230.4663314904741.81300997098-0.0273862522337-0.02753512352740.0851802041527-0.0372489280671-0.003099930722450.412556488003-0.145518235223-0.1889238380670.01917261121610.162770056270.0249817576313-0.009135593603190.1885423722290.01624703126910.156411637868.50009176701-0.35589936817414.0387130579
70.8929990785180.305291624738-0.1536915302573.117178435030.0723272070691.0427021328-0.0555570318170.1025646234830.0350903623872-0.1896020461740.02426146414720.0185220030429-0.1061515615730.1179341106120.02803423017850.188578098947-0.0211037273454-0.01751137846130.211153563415-0.006596654668370.13952081371319.03463420560.384001774039-1.36255601639
81.27448034978-0.54948860929-0.4948088541151.401106179410.05189237518034.68916496680.05128653040940.05832225048410.284301683285-0.1650441271020.01385485551340.0793469544697-0.840987708104-0.245110041145-0.05845893668090.410377424747-0.0262100225951-0.02155833567550.241129239590.01355209544790.2640698268814.759226441919.73878949160.295338132774
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 85 )AA14 - 851 - 72
22chain 'A' and (resid 86 through 152 )AA86 - 15273 - 139
33chain 'A' and (resid 153 through 275 )AA153 - 275140 - 262
44chain 'A' and (resid 276 through 319 )AA276 - 319263 - 306
55chain 'B' and (resid 15 through 76 )BG15 - 761 - 62
66chain 'B' and (resid 77 through 152 )BG77 - 15263 - 138
77chain 'B' and (resid 153 through 255 )BG153 - 255139 - 241
88chain 'B' and (resid 256 through 318 )BG256 - 318242 - 304

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