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- PDB-5chm: CRYSTAL STRUCTURE OF Fox-4 cephamycinase complexed with ceftazidi... -

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Basic information

Entry
Database: PDB / ID: 5chm
TitleCRYSTAL STRUCTURE OF Fox-4 cephamycinase complexed with ceftazidime BATSI (LP06)
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / 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
ACETATE ION / Chem-CB4 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Toro, R. / Lefurgy, S. / Almo, S.C.
CitationJournal: Biomolecules / Year: 2020
Title: Structures of FOX-4 Cephamycinase in Complex with Transition-State Analog Inhibitors.
Authors: Lefurgy, S.T. / Caselli, E. / Taracila, M.A. / Malashkevich, V.N. / Biju, B. / Papp-Wallace, K.M. / Bonanno, J.B. / Prati, F. / Almo, S.C. / Bonomo, R.A.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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.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.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.value / _pdbx_struct_oper_list.symmetry_operation / _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 1.2Sep 27, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)39,5479
Polymers38,8081
Non-polymers7398
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.803, 57.144, 56.123
Angle α, β, γ (deg.)90.000, 95.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 38807.797 Da / Num. of mol.: 1 / Fragment: UNP residues 24-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fox-4 / Plasmid: pHMTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L387, beta-lactamase

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-CB4 / PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE


Mass: 330.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15BN4O6S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.05M zinc acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 27189 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.39 Å2 / Rmerge(I) obs: 0.094 / Χ2: 0.949 / Net I/av σ(I): 11.995 / Net I/σ(I): 9.7 / Num. measured all: 94986
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.933.20.42213320.92798
1.93-1.973.30.49313300.93198.3
1.97-2.013.40.59513870.98198.9
2.01-2.053.40.38313350.98999
2.05-2.093.40.34313470.95398.6
2.09-2.143.50.29813490.92598.9
2.14-2.193.50.25613590.93999.2
2.19-2.253.40.2113491.00998.9
2.25-2.323.50.213490.92899.3
2.32-2.393.50.18813780.91499.2
2.39-2.483.50.15913720.92599.5
2.48-2.583.60.14113630.91399.6
2.58-2.73.60.12413460.8799
2.7-2.843.60.11613750.92799.5
2.84-3.023.60.10513660.93999.2
3.02-3.253.50.09313670.94699.1
3.25-3.583.50.07913650.9299.1
3.58-4.093.60.06513801.01899.5
4.09-5.163.60.0513860.91899.1
5.16-503.40.04913541.12494.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.72 Å
Translation2.5 Å19.72 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CGS

5cgs


Resolution: 1.9→25.964 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1347 4.99 %
Rwork0.1702 50510 -
obs0.1732 25823 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.52 Å2 / Biso mean: 33.7536 Å2 / Biso min: 11.63 Å2
Refinement stepCycle: final / Resolution: 1.9→25.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 25 230 2944
Biso mean--38.8 36.96 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072788
X-RAY DIFFRACTIONf_angle_d1.0873795
X-RAY DIFFRACTIONf_chiral_restr0.042414
X-RAY DIFFRACTIONf_plane_restr0.005496
X-RAY DIFFRACTIONf_dihedral_angle_d13.5121007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92790.30081430.28552385252890
1.9279-1.9650.37871400.24582662280299
1.965-2.00510.35541590.24572695285499
2.0051-2.04870.30091210.20262652277399
2.0487-2.09630.23781190.20482689280899
2.0963-2.14870.27951360.19962682281899
2.1487-2.20680.28971340.198226732807100
2.2068-2.27170.26381170.20952732284999
2.2717-2.34490.30511200.18582690281099
2.3449-2.42870.22891470.17192657280499
2.4287-2.52590.20531220.164627052827100
2.5259-2.64070.19741290.171227182847100
2.6407-2.77980.26571400.177526592799100
2.7798-2.95370.24071450.185927212866100
2.9537-3.18140.25931370.18152664280199
3.1814-3.50090.26251980.17232610280899
3.5009-4.00590.18051590.14526682827100
4.0059-5.04090.15261610.119626722833100
5.0409-25.96630.18841250.14262576270195
Refinement TLS params.Method: refined / Origin x: 65.4665 Å / Origin y: 10.7516 Å / Origin z: 15.8824 Å
111213212223313233
T0.1388 Å2-0.0151 Å20.0145 Å2-0.1367 Å20.0104 Å2--0.1706 Å2
L1.7203 °2-0.3019 °20.2169 °2-2.0679 °20.4106 °2--2.0953 °2
S-0.0092 Å °0.1056 Å °-0.0653 Å °-0.1405 Å °0.0457 Å °-0.1703 Å °0.1492 Å °0.0894 Å °-0.012 Å °
Refinement TLS groupSelection details: (chain A and resseq 7:361)

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