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- PDB-2hdr: AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid -

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Basic information

Entry
Database: PDB / ID: 2hdr
TitleAmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / AmpC fragment-based drug design beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-AMINO-3-HYDROXYBENZOIC ACID / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBabaoglu, K. / Shoichet, B.K.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: Deconstructing fragment-based inhibitor discovery
Authors: Babaoglu, K. / Shoichet, B.K.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,56818
Polymers79,1762
Non-polymers2,39216
Water5,603311
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,90810
Polymers39,5881
Non-polymers1,3209
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6608
Polymers39,5881
Non-polymers1,0727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.239, 77.340, 99.010
Angle α, β, γ (deg.)90.00, 118.44, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a monomer

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ampC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-4A3 / 4-AMINO-3-HYDROXYBENZOIC ACID


Mass: 153.135 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C7H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.8M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 3.1 % / Av σ(I) over netI: 8.1 / Number: 121501 / Rmerge(I) obs: 0.076 / Χ2: 0.79 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 38774 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745093.110.0341.0123.3
3.764.7496.210.0340.8383.3
3.293.7697.310.050.8883.3
2.993.299810.0820.8113.2
2.772.9998.410.1270.8093.2
2.612.7798.610.1870.7333.2
2.482.6198.810.2420.7013.2
2.372.4898.910.3130.6963.1
2.282.3798.610.380.6992.9
2.22.289710.4160.7012.5
ReflectionResolution: 2.2→50 Å / Num. all: 38774 / Num. obs: 38774 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.076 / Χ2: 0.794 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.416 / Num. unique all: 3829 / Χ2: 0.701 / % possible all: 97

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.553 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1941 5 %RANDOM
Rwork0.197 ---
obs0.197 38763 97.45 %-
all-38763 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.54 Å2
2--0.06 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5557 0 170 311 6038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225848
X-RAY DIFFRACTIONr_bond_other_d0.0010.023843
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9758003
X-RAY DIFFRACTIONr_angle_other_deg0.81139341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19724.793242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16815870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8561521
X-RAY DIFFRACTIONr_chiral_restr0.0570.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021204
X-RAY DIFFRACTIONr_nbd_refined0.1820.21137
X-RAY DIFFRACTIONr_nbd_other0.1730.23952
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22831
X-RAY DIFFRACTIONr_nbtor_other0.0810.22761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2311
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.213
X-RAY DIFFRACTIONr_mcbond_it0.7091.54553
X-RAY DIFFRACTIONr_mcbond_other0.0921.51423
X-RAY DIFFRACTIONr_mcangle_it0.79325714
X-RAY DIFFRACTIONr_scbond_it1.14733036
X-RAY DIFFRACTIONr_scangle_it1.7524.52289
LS refinement shellResolution: 2.2→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 150 -
Rwork0.228 2637 -
obs-2787 95.94 %

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