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- PDB-3q6v: Crystal Structure of Serratia fonticola Sfh-I: glycerol complex -

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Basic information

Entry
Database: PDB / ID: 3q6v
TitleCrystal Structure of Serratia fonticola Sfh-I: glycerol complex
ComponentsBeta-lactamase
KeywordsHYDROLASE / METALLOENZYME / ALPHA-BETA / METALLO-BETA-LACTAMASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia fonticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsFonseca, F. / Saavedra, M.J. / Correia, A. / Spencer, J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structure of Serratia fonticola Sfh-I: activation of the nucleophile in mono-zinc metallo-beta-lactamases.
Authors: Fonseca, F. / Bromley, E.H. / Saavedra, M.J. / Correia, A. / Spencer, J.
History
DepositionJan 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / reflns / reflns_shell / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,9056
Polymers52,5902
Non-polymers3154
Water7,674426
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4523
Polymers26,2951
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4523
Polymers26,2951
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.830, 87.280, 72.570
Angle α, β, γ (deg.)90.000, 90.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase /


Mass: 26294.844 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 3-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia fonticola (bacteria) / Strain: UTAD54 / Gene: blaSfh-I, sfhI / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9RMI1, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNON-SEQUENTIAL RESIDUE NUMBERING IS USED IN THIS ENTRY. IT IS THE STANDARD NUMBERING SCHEME FOR ...NON-SEQUENTIAL RESIDUE NUMBERING IS USED IN THIS ENTRY. IT IS THE STANDARD NUMBERING SCHEME FOR METALLO-BETA-LACTAMASES.

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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: 1.99 Å3/Da / Density % sol: 38.08 % / Mosaicity: 0.59 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium acetate, 27% w/v PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2009 / Details: mirrors
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.37→72.562 Å / Num. all: 84788 / Num. obs: 84788 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.37→1.45 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.3 / Num. unique all: 12336 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→26.23 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2013 / WRfactor Rwork: 0.1699 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8872 / SU B: 2.185 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0733 / SU Rfree: 0.0634 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 4241 5 %RANDOM
Rwork0.1628 ---
obs0.1644 84755 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 143.28 Å2 / Biso mean: 16.5653 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.47 Å2
2---0.22 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.37→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 14 426 4054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224008
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9615498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78925.351185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67715694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5711514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213124
X-RAY DIFFRACTIONr_mcbond_it1.0491.52454
X-RAY DIFFRACTIONr_mcangle_it1.64624033
X-RAY DIFFRACTIONr_scbond_it2.34931554
X-RAY DIFFRACTIONr_scangle_it3.494.51457
X-RAY DIFFRACTIONr_rigid_bond_restr1.28734008
X-RAY DIFFRACTIONr_sphericity_free6.053428
X-RAY DIFFRACTIONr_sphericity_bonded5.60233890
LS refinement shellResolution: 1.374→1.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 306 -
Rwork0.265 5932 -
all-6238 -
obs--99.95 %

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