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- PDB-2zj9: X-ray crystal structure of AmpC beta-Lactamase (AmpC(D)) from an ... -

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Basic information

Entry
Database: PDB / ID: 2zj9
TitleX-ray crystal structure of AmpC beta-Lactamase (AmpC(D)) from an Escherichia coli with a Tripeptide Deletion (Gly286 Ser287 Asp288) on the H10 Helix
ComponentsAmpC
KeywordsHYDROLASE / lactamase / Tripeptide Deletion
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYamaguchi, Y. / Sato, G. / Yamagata, Y. / Wachino, J. / Arakawa, Y. / Kurosaki, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of AmpC beta-lactamase (AmpCD) from an Escherichia coli clinical isolate with a tripeptide deletion (Gly286-Ser287-Asp288) in the H10 helix
Authors: Yamaguchi, Y. / Sato, G. / Yamagata, Y. / Doi, Y. / Wachino, J. / Arakawa, Y. / Matsuda, K. / Kurosaki, H.
History
DepositionFeb 29, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_conn.ptnr2_label_seq_id / _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: AmpC
B: AmpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0226
Polymers78,8562
Non-polymers1664
Water11,007611
1
A: AmpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5113
Polymers39,4281
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AmpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5113
Polymers39,4281
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.065, 47.381, 81.461
Angle α, β, γ (deg.)82.62, 80.91, 65.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AmpC / AmpC-EC5 / AmpC-EC30 / Class C beta-lactamase AmpC(D)


Mass: 39427.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HKY28 / Plasmid: pBCKS+ / Production host: Escherichia coli (E. coli) / Strain (production host): CS14-2
References: UniProt: Q5EET9, UniProt: Q76DI4*PLUS, beta-lactamase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 214TH RESIDUE IS ARG ACCORDING TO DOI ET AL. [ANTIMICROB AGENTS CHEMOTHER. 48, 2652-2658(2004)]

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10mM Hepes, 20% PEG 4000, 5% iso-propanol, 0.05M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11.07158
SYNCHROTRONPhoton Factory AR-NW12A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 14, 2006
ADSC QUANTUM 2102CCDDec 10, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.071581
211
ReflectionResolution: 1.7→50 Å / Num. obs: 65343 / Redundancy: 2.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.1 / Num. measured all: 141726
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BLS

2bls


Resolution: 1.7→39.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.139 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20557 3287 5 %RANDOM
Rwork0.16314 ---
obs0.16527 62030 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.863 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 2 619 6417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226003
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9498252
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57724.695262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.565151003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7331527
X-RAY DIFFRACTIONr_chiral_restr0.1150.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024627
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.22903
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24135
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2521
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2150.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1350.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.761.53670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37225984
X-RAY DIFFRACTIONr_scbond_it2.37832492
X-RAY DIFFRACTIONr_scangle_it3.8494.52226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 206 -
Rwork0.228 3855 -
obs--79.42 %

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