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- PDB-5cgx: CRYSTAL STRUCTURE OF Fox-4 cephamycinase mutant Y150F complexed w... -

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Basic information

Entry
Database: PDB / ID: 5cgx
TitleCRYSTAL STRUCTURE OF Fox-4 cephamycinase mutant Y150F complexed with cefoxitin
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
Chem-1S7 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.21 Å
AuthorsMalashkevich, V.N. / Toro, R. / Lefurgy, S. / Almo, S.C.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2015
Title: FOX-4 cephamycinase: an analysis of structure and function.
Authors: Lefurgy, S.T. / Malashkevich, V.N. / Aguilan, J.T. / Nieves, E. / Mundorff, E.C. / Biju, B. / Noel, M.A. / Toro, R. / Baiwir, D. / Papp-Wallace, K.M. / Almo, S.C. / Frere, J.M. / Bou, G. / Bonomo, R.A.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)39,5769
Polymers38,7921
Non-polymers7848
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.524, 56.588, 55.485
Angle α, β, γ (deg.)90.000, 99.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase /


Mass: 38791.797 Da / Num. of mol.: 1 / Fragment: UNP residues 24-382 / Mutation: Y150F
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
#2: Chemical ChemComp-1S7 / (2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefoxitin, bound form / Cefoxitin


Mass: 368.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N2O5S2 / Comment: antibiotic*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
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: RAYONIX MX225HE / Detector: CCD / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Number: 355116 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / D res high: 1.21 Å / D res low: 19.676 Å / Num. obs: 96864 / % possible obs: 95.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
3.8319.6810.0330.0333.6
2.713.8310.0370.0373.8
2.212.7110.0570.0573.8
1.912.2110.0810.0813.8
1.711.9110.1050.1053.8
1.561.7110.1390.1393.7
1.451.5610.2180.2183.6
1.351.4510.360.363.6
1.281.3510.5080.5083.6
1.211.2810.7390.7393.6
ReflectionResolution: 1.21→19.676 Å / Num. obs: 96864 / % possible obs: 95.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 11.41 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/av σ(I): 7.16 / Net I/σ(I): 6.4 / Num. measured all: 355116
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueNet I/σ(I) obs% possible all
1.21-1.283.60.739148683136170.7391.692.2
1.28-1.353.60.5081.546623130590.5082.393.2
1.35-1.453.60.362.144640124160.363.294.6
1.45-1.563.60.2183.542478116590.2184.995.5
1.56-1.713.70.1395.340388108700.1396.896.4
1.71-1.913.80.1056.53741799450.1058.697.4
1.91-2.213.80.0817.93330888140.0811197.8
2.21-2.713.80.05711.12844875390.05712.598.4
2.71-3.833.80.03716.32195558430.03713.698.6
3.83-19.6763.60.03318.41117631020.03313.593.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.64 Å
Translation2.5 Å19.64 Å

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Processing

Software
NameVersionClassification
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5CGS

5cgs


Resolution: 1.21→19.643 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 4837 5 %
Rwork0.1808 91993 -
obs0.182 96830 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.92 Å2 / Biso mean: 19.765 Å2 / Biso min: 6.43 Å2
Refinement stepCycle: final / Resolution: 1.21→19.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 45 374 3153
Biso mean--34.03 28.51 -
Num. residues----362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0242904
X-RAY DIFFRACTIONf_angle_d2.3783903
X-RAY DIFFRACTIONf_chiral_restr0.105422
X-RAY DIFFRACTIONf_plane_restr0.012514
X-RAY DIFFRACTIONf_dihedral_angle_d16.4941041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.21-1.22380.36931430.34032945308892
1.2238-1.23810.32821540.3362950310492
1.2381-1.25320.34791560.32052921307792
1.2532-1.26910.32661370.31162991312893
1.2691-1.28580.35321640.29822969313392
1.2858-1.30340.31621680.29822930309893
1.3034-1.3220.27661570.28423016317393
1.322-1.34180.33371560.2713004316094
1.3418-1.36270.29931850.2732953313894
1.3627-1.38510.24711590.2573025318494
1.3851-1.40890.27981550.25452998315395
1.4089-1.43450.25631630.24713058322195
1.4345-1.46210.26731740.23353069324395
1.4621-1.4920.2431570.22443018317595
1.492-1.52440.23741510.22093061321296
1.5244-1.55980.24081290.21253114324396
1.5598-1.59880.23351580.19573094325296
1.5988-1.6420.20491680.19573079324796
1.642-1.69030.20281540.19153108326297
1.6903-1.74490.20161660.18493126329297
1.7449-1.80720.22111560.17893121327797
1.8072-1.87950.20721860.18093121330797
1.8795-1.96490.23681770.18083110328798
1.9649-2.06840.19031430.16263191333498
2.0684-2.19790.19151910.15373134332598
2.1979-2.36730.18631640.15673159332398
2.3673-2.6050.16851620.14313189335199
2.605-2.98090.17351790.14683196337599
2.9809-3.75130.16781650.14023219338499
3.7513-19.64590.15391600.14333124328494
Refinement TLS params.Method: refined / Origin x: 55.1091 Å / Origin y: -0.5705 Å / Origin z: 70.8679 Å
111213212223313233
T0.0848 Å2-0.0072 Å20.0411 Å2-0.0757 Å20.0075 Å2--0.0849 Å2
L0.9206 °20.3345 °20.3352 °2-0.8025 °20.1498 °2--0.5344 °2
S-0.0506 Å °0.0649 Å °0.0539 Å °-0.046 Å °0.0161 Å °0.0058 Å °-0.0367 Å °-0.0007 Å °0.0248 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 407
2X-RAY DIFFRACTION1allA408
3X-RAY DIFFRACTION1allW1 - 442

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