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- PDB-3fcz: Adaptive protein evolution grants organismal fitness by improving... -

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Basic information

Entry
Database: PDB / ID: 3fcz
TitleAdaptive protein evolution grants organismal fitness by improving catalysis and flexibility
ComponentsBeta-lactamase 2
KeywordsHYDROLASE / metallo-beta-lactamase / antibiotic resistance / Metal-binding / Zinc
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-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsTomatis, P. / Fabiane, S. / Simona, F. / Carloni, P. / Sutton, B. / Vila, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility.
Authors: Tomatis, P.E. / Fabiane, S.M. / Simona, F. / Carloni, P. / Sutton, B.J. / Vila, A.J.
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: 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

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Assembly

Deposited unit
A: Beta-lactamase 2
B: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0056
Polymers48,7442
Non-polymers2624
Water75742
1
A: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5033
Polymers24,3721
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5033
Polymers24,3721
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.670, 48.810, 77.190
Angle α, β, γ (deg.)90.00, 109.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 32:45 or resseq 47:61 or resseq...
211chain B and (resseq 32:45 or resseq 47:61 or resseq...

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Components

#1: Protein Beta-lactamase 2 / Beta-lactamase II / Penicillinase / Cephalosporinase


Mass: 24371.770 Da / Num. of mol.: 2 / Mutation: N70S, V112A, L250S, G262S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: 569/H/9 / Gene: blm / Production host: Escherichia coli (E. coli) / References: UniProt: P04190, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24% PEG 3350, 0.1M sodium tartrate, 1mM DTT, 1mM zinc acetate, 0.1M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. all: 8961 / Num. obs: 8961 / % possible obs: 73.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2bc2

2bc2


Resolution: 2.804→72.599 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 463 5.18 %random
Rwork0.1938 ---
obs0.197 8944 73.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.768 Å2 / ksol: 0.322 e/Å3
Refinement stepCycle: LAST / Resolution: 2.804→72.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 4 42 3430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.777
X-RAY DIFFRACTIONf_bond_d0.005
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1664X-RAY DIFFRACTIONPOSITIONAL
12B1664X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8040.3449800.2906130934.63
3.2096-4.04370.29111760.2181337287.17
4.0437-72.62350.22422070.1643380096.72
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)
19.3949-1.60011.26573.3014-1.04783.14590.33940.1077-0.454-0.1088-0.359-0.15160.38180.15180.00060.4039-0.0302-0.03320.35920.04090.3560.8522.8202-48.6936
27.96712.52770.94922.66980.28794.05460.0945-0.5728-0.06030.3022-0.0458-0.1698-0.1783-0.186700.42380.0086-0.00320.2539-0.04130.2703-9.8002-3.5284-13.8601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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