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- PDB-2z2p: Crystal Structure of catalytically inactive H270A virginiamycin B... -

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Basic information

Entry
Database: PDB / ID: 2z2p
TitleCrystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin
Components
  • Quinupristin
  • Virginiamycin B lyase
KeywordsLYASE/ANTIBIOTIC / QUINUPRISTIN / DALFOPRISTIN / STREPTOGRAMIN / SYNERCID / LYASE-ANTIBIOTIC COMPLEX / ANTIBIOTIC RESISTANCE / ANTIBIOTIC / VIRGINIAMYCIN B LYASE / VIRGINIAMYCIN B HYDROLASE
Function / homology
Function and homology information


carbon-oxygen lyase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / antibiotic catabolic process / response to antibiotic / magnesium ion binding
Similarity search - Function
Streptogramin lyase / : / Virginiamycin B lyase family / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Quinupristin / Chem-DOL / Virginiamycin B lyase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
STREPTOMYCES GRAMINOFACIEN (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKorczynska, M. / Berghuis, A.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structural Basis for Streptogramin B Resistance in Staphylococcus Aureus by Virginiamycin B Lyase
Authors: Korczynska, M. / Mukhtar, T.A. / Wright, G.D. / Berghuis, A.M.
History
DepositionMay 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Apr 22, 2015Group: Database references
Revision 1.6Nov 1, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.method_details
Revision 2.0Jul 12, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / database_PDB_caveat / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _pdbx_entry_details.sequence_details / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_asym_id / _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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_site.pdbx_num_residues
Revision 2.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 10, 2024Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virginiamycin B lyase
B: Virginiamycin B lyase
C: Quinupristin
D: Quinupristin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,59610
Polymers68,1174
Non-polymers1,4796
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.999, 93.700, 95.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 2 / Auth seq-ID: 2 - 294 / Label seq-ID: 2 - 294

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Virginiamycin B lyase / Streptogramin B lyase


Mass: 33034.242 Da / Num. of mol.: 2 / Mutation: H270A
Source method: isolated from a genetically manipulated source
Details: 1. SEQUENCE FOR RESIDUES 211 AND 212 WAS DERIVED FROM THE ORIGINAL GENE. 2. RESIDUES 51 TO 56 [PLPTPD] WERE REPLACED TO DISRUPT CRYSTAL PACKING INTERACTIONS BY A CORRESPONDING LOOP, RESIDUES 135-140 [ELPNKG].
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: BM30002, PIP524 / Gene: vgb, vgh / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: P17978, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Protein/peptide Quinupristin


Type: Oligopeptide / Class: Antibiotic / Mass: 1024.236 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: QUINUPRISTIN IS A CYLIC HEPTAPEPTIDE. THE RING GENERATED BY LINKING RESIDUE 2 SIDE-CHAIN IS AND MAIN-CHAIN RESIDUE 7.
Source: (synth.) STREPTOMYCES GRAMINOFACIEN (bacteria) / References: Quinupristin
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DOL / 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE / DALFOPRISTIN


Mass: 690.847 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H50N4O9S
Compound detailsQUINUPRISTIN IS A STREPTOGRAMIN ANTIBIOTIC. HERE, QUINUPRISTIN IS REPRESENTED BY SEQUENCE (SEQRES).

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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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growpH: 7.5
Details: 100MM MES BUFFER (PH 6.5), 20%(W/V) PEG 10000, PROTEIN SOLUTION SUPPLEMENTED WITH 3MM MGCL2, 3MM DALFOPRISTIN, 1MM QUINUPRISTIN, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14813 / % possible obs: 91.1 % / Redundancy: 4.1 % / Rsym value: 0.136 / Net I/σ(I): 6
Reflection shellResolution: 2.8→2.99 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.31 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z2N

2z2n


Resolution: 2.8→36.18 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.858 / SU B: 38.266 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.578 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1587 10.7 %RANDOM
Rwork0.262 ---
obs0.268 13189 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 120 0 4782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5122.0096692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8745588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51825.644202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14915788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8641516
X-RAY DIFFRACTIONr_chiral_restr0.4960.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023734
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.22373
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23353
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3730.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4590.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5481.52995
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75224720
X-RAY DIFFRACTIONr_scbond_it0.54132245
X-RAY DIFFRACTIONr_scangle_it0.9724.51972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1176tight positional0.050.05
1098medium positional0.510.5
1176tight thermal0.30.5
1098medium thermal0.372
LS refinement shellResolution: 2.8→2.95 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.424 244 -
Rwork0.302 1935 -
obs--94.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5101-0.29360.34190.90840.31641.18790.0113-0.0147-0.07810.012-0.0447-0.04260.0275-0.07950.0335-0.0665-0.01690.0093-0.0355-0.0005-0.0219-1.215714.3421-23.4271
20.61380.3674-0.27480.76230.11630.95560.03620.01090.0267-0.0212-0.0372-0.0605-0.0009-0.07470.001-0.05750.0161-0.0121-0.02990.011-0.0058-36.749720.7055-24.1827
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 294
2X-RAY DIFFRACTION2B2 - 294

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