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- PDB-4eqi: Crystal structure of serratia fonticola carbapenemase SFC-1 -

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Basic information

Entry
Database: PDB / ID: 4eqi
TitleCrystal structure of serratia fonticola carbapenemase SFC-1
ComponentsCarbapenem-hydrolizing beta-lactamase SFC-1
KeywordsHYDROLASE / BETA-LACTAMASE / CARBAPENEMASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia fonticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsFonseca, F. / Spencer, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: The basis for carbapenem hydrolysis by class A beta-lactamases: a combined investigation using crystallography and simulations.
Authors: Fonseca, F. / Chudyk, E.I. / van der Kamp, M.W. / Correia, A. / Mulholland, A.J. / Spencer, J.
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 13, 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_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Carbapenem-hydrolizing beta-lactamase SFC-1
B: Carbapenem-hydrolizing beta-lactamase SFC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,37628
Polymers61,6222
Non-polymers75426
Water12,791710
1
A: Carbapenem-hydrolizing beta-lactamase SFC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,12613
Polymers30,8111
Non-polymers31512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbapenem-hydrolizing beta-lactamase SFC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,25015
Polymers30,8111
Non-polymers43914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-173 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.330, 85.430, 70.280
Angle α, β, γ (deg.)90.00, 103.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbapenem-hydrolizing beta-lactamase SFC-1


Mass: 30810.775 Da / Num. of mol.: 2 / Fragment: UNP residues 27-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia fonticola (bacteria) / Strain: UTAD54 / Gene: BLASFC-1, SFC-1 / Plasmid: pET26-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6JP75, beta-lactamase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE TWO SEQADV RECORDS RELATED TO RESIDUES 255 AND 270 REPRESENT DISCREPANCIES BETWEEN THE ...THE TWO SEQADV RECORDS RELATED TO RESIDUES 255 AND 270 REPRESENT DISCREPANCIES BETWEEN THE PREVIOUSLY DEPOSITED SEQUENCE (UNP Q6JP75) AND THE EXPRESSION CLONE, ARISING EITHER FROM PCR ERRORS OR MISTAKES IN THE ORIGINAL SEQUENCE

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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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na acetate, PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2008
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. all: 99798 / Num. obs: 99419 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.234
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.38-1.433.30.5682.03199.4
1.43-1.493.50.4352.88199.7
1.49-1.553.60.3333.99199.4
1.55-1.643.60.2545.28199.1
1.64-1.743.60.1946.35199.5
1.74-1.873.60.1447.43199.8
1.87-2.063.70.09212.81100
2.06-2.363.70.05820.991100
2.36-2.973.80.0431.571100
2.97-503.80.02346.03199.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OV5

2ov5


Resolution: 1.38→17.85 Å / Num. parameters: 46426 / Num. restraintsaints: 58396 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 1.11%
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4966 5 %RANDOM
Rwork0.14 ---
obs0.141 93687 99.5 %-
all-99390 --
Refine analyzeNum. disordered residues: 65 / Occupancy sum hydrogen: 3948 / Occupancy sum non hydrogen: 4913.4
Refinement stepCycle: LAST / Resolution: 1.38→17.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 38 710 4928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.019
X-RAY DIFFRACTIONs_approx_iso_adps0.046

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