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- PDB-9c3d: Crystal structure of metallo-beta-lactamase superfamily protein C... -

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Basic information

Entry
Database: PDB / ID: 9c3d
TitleCrystal structure of metallo-beta-lactamase superfamily protein CcrA-like_MBL-B1 from Dyadobacter fermentans
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / metallo-beta-lacatamase / CcrA-like_MBL / antibiotic-resistance / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesDyadobacter fermentans DSM 18053 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKim, Y. / Maltseva, N. / Welk, L. / 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 CcrA-like_MBL-B1 from Dyadobacter fermentans
Authors: Kim, Y. / Maltseva, N. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: 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 type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0233
Polymers24,8921
Non-polymers1312
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-77 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.176, 62.256, 72.387
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

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Metallo-beta-lactamase type II


Mass: 24892.285 Da / Num. of mol.: 1 / Fragment: UNP residues 20-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dyadobacter fermentans DSM 18053 (bacteria)
Gene: Dfer_1371 / Plasmid: pMGCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: C6W709, beta-lactamase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 18637 / % possible obs: 98.3 % / Redundancy: 11.9 % / Biso Wilson estimate: 29.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.035 / Rrim(I) all: 0.124 / Net I/σ(I): 26
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.159 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 827 / CC1/2: 0.6 / Rpim(I) all: 0.387 / Rrim(I) all: 1.227 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.2 Å / SU ML: 0.2618 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 952 5.12 %
Rwork0.1877 17626 -
obs0.1889 18578 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.99 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 2 130 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651810
X-RAY DIFFRACTIONf_angle_d0.87432456
X-RAY DIFFRACTIONf_chiral_restr0.0604273
X-RAY DIFFRACTIONf_plane_restr0.0063318
X-RAY DIFFRACTIONf_dihedral_angle_d12.2944655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.940.34641180.29392297X-RAY DIFFRACTION90.48
1.94-2.060.29031290.23322475X-RAY DIFFRACTION98.04
2.06-2.220.25231500.19932515X-RAY DIFFRACTION99.7
2.22-2.450.27331400.19692522X-RAY DIFFRACTION99.78
2.45-2.80.211270.19172558X-RAY DIFFRACTION99.15
2.8-3.530.24051380.19752576X-RAY DIFFRACTION99.67
3.53-47.20.161500.16092683X-RAY DIFFRACTION98.99
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)
15.60586525346-1.17284677490.9901239898165.04290338095-0.3713341679226.97562542201-0.119441214277-0.481095443994-0.3395480856670.532876443532-0.005961642126630.279270101360.4107637759870.04609864748310.1024623552420.3204034531990.03414897895260.08786579523180.195844468234-0.01658681164070.25206287129-13.6767141388-6.07648361245-4.7404451406
21.67317830343-0.767624254607-0.6247395863233.79636457661.368877401732.04704681174-0.01262371762250.077308929839-0.121883737052-0.165862022696-0.009629600069830.008673008299680.106416803570.05595908853860.01711558787830.216520741770.0128359262781-0.006782619090290.2559433912520.0009787510624470.19577517119-9.489690835913.98538842076-10.9431802234
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 76 )20 - 761 - 57
22chain 'A' and (resid 77 through 243 )77 - 24358 - 224

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