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- PDB-5f1f: Crystal structure of CMY-10 adenylylated by acetyl-AMP -

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Basic information

Entry
Database: PDB / ID: 5f1f
TitleCrystal structure of CMY-10 adenylylated by acetyl-AMP
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class C beta lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / nucleotide binding / response to antibiotic / metal ion binding
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
ADENOSINE MONOPHOSPHATE / : / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.548 Å
AuthorsAn, Y.J. / Kim, M.K. / Na, J.H. / Cha, S.S.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2015R 1A2A2A 01004168 Korea, Republic Of
National Research Foundation of KoreaNRF-2015M 1A5A 1037480 Korea, Republic Of
KIOST in-house programsPE99314 Korea, Republic Of
KIOST in-house programsPE99302 Korea, Republic Of
CitationJournal: J.Antimicrob.Chemother. / Year: 2017
Title: Structural and mechanistic insights into the inhibition of class C beta-lactamases through the adenylylation of the nucleophilic serine.
Authors: Kim, M.K. / An, Y.J. / Na, J.H. / Seol, J.H. / Ryu, J.Y. / Lee, J.W. / Kang, L.W. / Chung, K.M. / Lee, J.H. / Moon, J.H. / Lee, J.S. / Cha, S.S.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_symmetry / _struct_conn_type.id
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3258
Polymers39,3031
Non-polymers1,0227
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-29 kcal/mol
Surface area14690 Å2
Unit cell
Length a, b, c (Å)49.874, 59.342, 111.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase /


Mass: 39303.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: blaCMY-10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99QC1, beta-lactamase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5 / Details: Cadmium chloride, Na-Cacodylate, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.548→50 Å / Num. obs: 44969 / % possible obs: 96.4 % / Redundancy: 6 % / Net I/σ(I): 62

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZKJ

1zkj


Resolution: 1.548→38.18 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.54 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1965 2405 5.08 %
Rwork0.1658 --
obs0.1673 44969 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.548→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 0 28 321 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132832
X-RAY DIFFRACTIONf_angle_d1.4533802
X-RAY DIFFRACTIONf_dihedral_angle_d12.6751000
X-RAY DIFFRACTIONf_chiral_restr0.06416
X-RAY DIFFRACTIONf_plane_restr0.008494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5481-1.57970.21241270.16692431X-RAY DIFFRACTION90
1.5797-1.6140.20751430.15752500X-RAY DIFFRACTION92
1.614-1.65160.19761490.14942520X-RAY DIFFRACTION93
1.6516-1.69290.19351390.15492533X-RAY DIFFRACTION94
1.6929-1.73860.21251510.15832566X-RAY DIFFRACTION95
1.7386-1.78980.18011470.1592617X-RAY DIFFRACTION96
1.7898-1.84760.20561350.16252636X-RAY DIFFRACTION97
1.8476-1.91360.20821340.16382642X-RAY DIFFRACTION97
1.9136-1.99020.21281380.16392674X-RAY DIFFRACTION98
1.9902-2.08080.20121270.16042701X-RAY DIFFRACTION98
2.0808-2.19050.20481510.15522682X-RAY DIFFRACTION98
2.1905-2.32770.15931470.15642685X-RAY DIFFRACTION99
2.3277-2.50740.18881460.16432738X-RAY DIFFRACTION99
2.5074-2.75960.19021400.1692748X-RAY DIFFRACTION99
2.7596-3.15880.22751570.18042743X-RAY DIFFRACTION99
3.1588-3.97910.17321370.16452781X-RAY DIFFRACTION98
3.9791-38.19190.20551370.1782773X-RAY DIFFRACTION94

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