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- PDB-6v4w: The crystal structure of a beta-lactamase from Chitinophaga pinen... -

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Basic information

Entry
Database: PDB / ID: 6v4w
TitleThe crystal structure of a beta-lactamase from Chitinophaga pinensis DSM 2588
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class A beta-lactamase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
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
ACETATE ION / FORMIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesChitinophaga pinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsTan, K. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
CitationJournal: To Be Published
Title: The crystal structure of a beta-lactamase from Chitinophaga pinensis DSM 2588
Authors: Tan, K. / Welk, L. / Endres, M. / Joachimiak, A.
History
DepositionDec 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,80715
Polymers61,1052
Non-polymers70213
Water9,710539
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8127
Polymers30,5531
Non-polymers2606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9958
Polymers30,5531
Non-polymers4427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.702, 76.313, 89.376
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

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 30552.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga pinensis (strain ATCC 43595 / DSM 2588 / NCIB 11800 / UQM 2034) (bacteria)
Strain: ATCC 43595 / DSM 2588 / NCIB 11800 / UQM 2034 / Gene: Cpin_1435 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: C7PRN9, beta-lactamase

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Non-polymers , 5 types, 552 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium Chloride, 0.1 M MES:NaOH, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 7, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 127393 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 15.83 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.067 / Rrim(I) all: 0.121 / Χ2: 3.11 / Net I/σ(I): 23.1
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6253 / CC1/2: 0.457 / Rpim(I) all: 0.563 / Rrim(I) all: 0.961 / Χ2: 3.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G58

5g58


Resolution: 1.29→38.48 Å / SU ML: 0.1379 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6195
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 6346 5 %random
Rwork0.1606 ---
obs0.1619 127043 97.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.15 Å2
Refinement stepCycle: LAST / Resolution: 1.29→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 35 539 4736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054359
X-RAY DIFFRACTIONf_angle_d0.84715919
X-RAY DIFFRACTIONf_chiral_restr0.0746688
X-RAY DIFFRACTIONf_plane_restr0.0044761
X-RAY DIFFRACTIONf_dihedral_angle_d16.44761603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.30.31851850.27873557X-RAY DIFFRACTION86.78
1.3-1.320.29711940.26193851X-RAY DIFFRACTION94.18
1.32-1.340.25912230.25343902X-RAY DIFFRACTION96.76
1.34-1.350.2882080.23724099X-RAY DIFFRACTION99.31
1.35-1.370.28211770.23534088X-RAY DIFFRACTION99.46
1.37-1.390.25452110.22814062X-RAY DIFFRACTION99.51
1.39-1.410.26612430.22724063X-RAY DIFFRACTION99.29
1.41-1.430.26032090.21294067X-RAY DIFFRACTION99.19
1.43-1.450.2472430.19394004X-RAY DIFFRACTION98.58
1.45-1.480.22692040.17984005X-RAY DIFFRACTION98.32
1.48-1.50.20452050.16344064X-RAY DIFFRACTION98.45
1.5-1.530.17841950.15863973X-RAY DIFFRACTION96.71
1.53-1.560.19872040.15573980X-RAY DIFFRACTION96.74
1.56-1.590.21262090.15034097X-RAY DIFFRACTION99.58
1.59-1.630.18472290.14784075X-RAY DIFFRACTION99.38
1.63-1.660.19332090.1384064X-RAY DIFFRACTION99.16
1.66-1.70.16672040.13534095X-RAY DIFFRACTION99.26
1.7-1.750.172290.13424096X-RAY DIFFRACTION99.29
1.75-1.80.18122230.1444033X-RAY DIFFRACTION98.79
1.8-1.860.18362090.14754070X-RAY DIFFRACTION98.07
1.86-1.930.18332030.14283948X-RAY DIFFRACTION95.84
1.93-20.17732080.14174107X-RAY DIFFRACTION99.2
2-2.10.17742170.1434121X-RAY DIFFRACTION99.45
2.1-2.210.16312320.14474093X-RAY DIFFRACTION99.2
2.21-2.340.17571880.14934105X-RAY DIFFRACTION98.08
2.34-2.520.16552100.15994103X-RAY DIFFRACTION98.52
2.52-2.780.18922280.17083992X-RAY DIFFRACTION95.65
2.78-3.180.192240.1694046X-RAY DIFFRACTION96.15
3.18-4.010.17662190.15283945X-RAY DIFFRACTION93.18
4.01-38.480.1682040.16123992X-RAY DIFFRACTION90.31

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