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- PDB-3vff: BlaC E166A CDC-OMe Acyl-Intermediate Complex -

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Basic information

Entry
Database: PDB / ID: 3vff
TitleBlaC E166A CDC-OMe Acyl-Intermediate Complex
ComponentsBeta-lactamase
KeywordsHydrolase/hydrolase inhibitor / beta-lactamase / serine hydrolase / serine esterase / acyl-intermediate / Hydrolase-hydrolase inhibitor complex / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


penicillinase activity / cephalosporinase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / 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
Chem-CD8 / PHOSPHATE ION / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.777 Å
AuthorsMire, J.A. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: BlaC-Specific Fluorogenic Probes for Rapid Tuberculosis Detection
Authors: Xie, H. / Mire, J.A. / Kong, Y. / Chang, M. / Sacchettini, J.C. / Cirillo, J.D. / Rao, J.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,63511
Polymers121,9564
Non-polymers1,6787
Water23413
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8372
Polymers30,4891
Non-polymers3481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9323
Polymers30,4891
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9323
Polymers30,4891
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9323
Polymers30,4891
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.061, 96.603, 108.555
Angle α, β, γ (deg.)90.00, 107.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase / / Penicillinase


Mass: 30489.074 Da / Num. of mol.: 4 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaA, blaC, MT2128, MTCY49.07c, Rv2068c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical
ChemComp-CD8 / (2R)-2-[(1S)-1-(benzoylamino)-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 348.374 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16N2O5S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.28 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91943 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91943 Å / Relative weight: 1
ReflectionResolution: 2.777→50 Å / Num. all: 39953 / Num. obs: 38850 / % possible obs: 99 % / Observed criterion σ(I): 1.35 / Redundancy: 4.1 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.12
Reflection shell
Resolution (Å)Num. unique allDiffraction-ID% possible all
2.777-2.84612133175
2.8461-2.923282611
2.923-3.00928171100
3.009-3.106128311100
3.1061-3.217128651100
3.2171-3.345928431100
3.3459-3.498128161100
3.4981-3.682428471100
3.6824-3.913128401100
3.9131-4.21528561100
4.215-4.63892793198
4.6389-5.30932780197
5.3093-6.68622856199
6.6862-47.16762747194

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GDN

2gdn


Resolution: 2.777→47.161 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7941 / SU ML: 0.41 / σ(F): 0 / σ(I): 0 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 2001 5.15 %random selected 5.15% of reflections
Rwork0.2454 ---
obs0.2462 38850 97.21 %-
all-38850 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.296 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 130.5 Å2 / Biso mean: 72.9417 Å2 / Biso min: 40.47 Å2
Baniso -1Baniso -2Baniso -3
1-16.9949 Å2-0 Å2-14.9167 Å2
2---21.9337 Å20 Å2
3---4.9388 Å2
Refinement stepCycle: LAST / Resolution: 2.777→47.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7285 0 111 13 7409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117549
X-RAY DIFFRACTIONf_angle_d1.27710366
X-RAY DIFFRACTIONf_chiral_restr0.071229
X-RAY DIFFRACTIONf_plane_restr0.0081353
X-RAY DIFFRACTIONf_dihedral_angle_d14.1442533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.777-2.84610.32461240.32842009213375
2.8461-2.9230.35491410.329326852826100
2.923-3.0090.30051430.296626742817100
3.009-3.10610.29751420.274426892831100
3.1061-3.21710.29691510.268427142865100
3.2171-3.34590.30581440.26926992843100
3.3459-3.49810.25581450.243126712816100
3.4981-3.68240.21651420.222527052847100
3.6824-3.91310.23421400.2227002840100
3.9131-4.2150.23331500.212927062856100
4.215-4.63890.23561470.20542646279398
4.6389-5.30930.23351450.23192635278097
5.3093-6.68620.3081440.27682712285699
6.6862-47.16760.25241430.25232604274794

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