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- PDB-8u00: Crystal structure of metallo-beta-lactamase superfamily protein f... -

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Basic information

Entry
Database: PDB / ID: 8u00
TitleCrystal structure of metallo-beta-lactamase superfamily protein from Caulobacter vibrioides
ComponentsMetallo-beta-lactamase superfamily protein
KeywordsHYDROLASE / metallo-beta-lacatamase / antibiotic-resistance / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologyMetallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / NICKEL (II) ION / Metallo-beta-lactamase superfamily protein
Function and homology information
Biological speciesCaulobacter vibrioides CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of metallo-beta-lactamase superfamily protein from Caulobacter vibrioides
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A.
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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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)59,21419
Polymers58,2982
Non-polymers91617
Water2,144119
1
A: Metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,65310
Polymers29,1491
Non-polymers5049
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5619
Polymers29,1491
Non-polymers4128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.341, 85.341, 78.844
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase superfamily protein


Mass: 29148.979 Da / Num. of mol.: 2 / Mutation: deletion 1-21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides CB15 (bacteria) / Gene: CC_2139 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9A6F5

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Non-polymers , 7 types, 136 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, 18 % w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 47880 / % possible obs: 98.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 38.24 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Net I/σ(I): 34.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2008 / CC1/2: 0.861 / Rpim(I) all: 0.208 / Rrim(I) all: 0.681 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→24.1 Å / SU ML: 0.2437 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.9124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 2357 4.95 %
Rwork0.1885 45278 -
obs0.1903 47635 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 28 119 3833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673881
X-RAY DIFFRACTIONf_angle_d0.79265290
X-RAY DIFFRACTIONf_chiral_restr0.05606
X-RAY DIFFRACTIONf_plane_restr0.0074690
X-RAY DIFFRACTIONf_dihedral_angle_d13.19371401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.31181180.33152344X-RAY DIFFRACTION86.45
1.89-1.930.31141520.29832540X-RAY DIFFRACTION94.96
1.93-1.970.30071590.29092604X-RAY DIFFRACTION98.36
1.97-2.020.28591630.24762648X-RAY DIFFRACTION99.43
2.02-2.080.30851450.24982663X-RAY DIFFRACTION99.19
2.08-2.140.32861170.23042684X-RAY DIFFRACTION99.47
2.14-2.210.25421100.22392708X-RAY DIFFRACTION99.72
2.21-2.290.26821230.21082724X-RAY DIFFRACTION100
2.29-2.380.25021450.20592671X-RAY DIFFRACTION99.33
2.38-2.490.25231150.21552729X-RAY DIFFRACTION99.93
2.49-2.620.25181320.21572695X-RAY DIFFRACTION99.93
2.62-2.780.24151360.21832674X-RAY DIFFRACTION99.86
2.78-30.27841630.22692X-RAY DIFFRACTION99.93
3-3.30.23811880.21392669X-RAY DIFFRACTION99.97
3.3-3.770.23091250.18342710X-RAY DIFFRACTION100
3.77-4.740.1661250.15282758X-RAY DIFFRACTION100
4.75-24.10.17141410.14652765X-RAY DIFFRACTION99.59
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)
13.10372194058-0.683647708377-0.6578256928753.377223426911.12048201524.38443959268-0.0681634118105-0.05558898034960.247903814590.5156728258630.164085528932-0.207177941038-0.1882965240520.0909575279332-0.07344228721710.4822791148130.0597280941082-0.02130977989030.203131663743-0.02151008652370.34670617183325.5119206793-6.1636170173-1.7008129301
22.383475871020.7883906569830.2054208065153.573030465070.03142754949695.25986461304-0.231516671253-0.4186183706420.06648458473420.7508399109140.284665202656-0.3428475297710.4644865887740.283736000161-0.02838686763450.7072489261470.189613403062-0.05601745491110.347704551158-0.009560270850830.38341265988728.8150736325-19.00437100373.79081474923
31.53486351406-1.605288402140.2548605844245.020408905272.114304984331.95799283472-0.257677803911-0.087780984546-0.1522803053780.3633527531120.2387459101720.349679127650.45116586421-0.2000703698540.02888253177950.6010896940290.01025928484740.09357139742290.2695143702660.08114222994310.37661024849219.8573825252-24.7421273301-4.03597676394
43.378732743480.151007165597-0.0964800283083.3602219381-0.8055010274367.576833364390.1215555026490.527036842053-0.2346985975320.371787134441-0.185809550355-0.04608741300520.0948777109375-0.06605703275010.05506461530970.3427158708940.06433177583660.03512034748470.4501325565350.003510659557270.43026678891933.8812940578-24.698207412244.7081803717
53.28667167552-0.601637933921-0.4520352518522.165334974441.254253658873.362685294380.2265399789470.6244476944540.225581295734-0.23695588912-0.138521404076-0.296255151748-0.07951927740960.283553634439-0.09173453674650.2411180421140.0635868428040.04571608113660.5444662896880.03855928692750.39322398687538.0941074018-16.682570132737.5144787387
63.896196109030.733929935713.308584822822.35826745447-0.4630821298584.462867087030.3578353302380.4313381113821.60540425778-0.2008933661380.02298248183170.209828986888-1.29890169102-0.3855964992780.04342325349670.5357587583630.2014462161580.1618187109570.6155183147160.2129781727160.85112231583228.8520541985-3.3673055588636.6314604061
73.299349943390.618264659374-0.9688847632222.11948965797-0.7377946353355.879516756840.2051968238360.5747113050350.119671905481-0.381690838441-0.2792610740270.0474053402570.0955542179435-0.1643922173610.1196499848990.3150801511650.16939247052-0.02530639556110.7260117616150.002852764926140.36327419810523.4001849908-15.671695403433.7335768263
84.38802570069-1.36319871602-1.516517294711.82912206907-0.04621040947372.157348079320.2453904792280.308254960528-0.312496427503-0.115136067648-0.224339966860.07349556737180.167316006061-0.297134827274-0.009214932040990.2794205614210.00697976718414-0.0663413452610.612466925109-0.07806536975940.38853115162517.8984251827-22.813815504541.5957562264
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 147 )AA19 - 1471 - 104
22chain 'A' and (resid 148 through 204 )AA148 - 204105 - 161
33chain 'A' and (resid 205 through 285 )AA205 - 285162 - 242
44chain 'B' and (resid 19 through 40 )BC19 - 401 - 22
55chain 'B' and (resid 41 through 112 )BC41 - 11223 - 94
66chain 'B' and (resid 113 through 155 )BC113 - 15595 - 112
77chain 'B' and (resid 156 through 204 )BC156 - 204113 - 161
88chain 'B' and (resid 205 through 285 )BC205 - 285162 - 242

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