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- PDB-1qow: Mersacidin from Bacillus -

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Basic information

Entry
Database: PDB / ID: 1qow
TitleMersacidin from Bacillus
ComponentsMERSACIDIN
KeywordsANTIBIOTIC / LANTIBIOTIC / METHICILLIN RESISTANCE / THIOESTER / TYPE B LANTIBIOTIC / LANTHIONINE
Function / homologyType 2 lantibiotic, leader peptide domain / killing of cells of another organism / defense response to bacterium / signaling receptor binding / Mersacidin / METHANOL / Lantibiotic mersacidin
Function and homology information
Biological speciesBACILLUS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / HALF-BAKED / Resolution: 1.06 Å
AuthorsSchneider, T.R. / Kaercher, J. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Ab initio structure determination of the lantibiotic mersacidin.
Authors: Schneider, T.R. / Karcher, J. / Pohl, E. / Lubini, P. / Sheldrick, G.M.
History
DepositionNov 19, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Jul 27, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Refinement description
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4Apr 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Jul 24, 2019Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method
Revision 1.7Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf
Revision 2.0May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MERSACIDIN
B: MERSACIDIN
C: MERSACIDIN
D: MERSACIDIN
E: MERSACIDIN
F: MERSACIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,29415
Polymers11,0066
Non-polymers2889
Water1,02757
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-70.4 kcal/mol
Surface area6040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.090, 46.090, 31.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein/peptide
MERSACIDIN


Type: Oligopeptide / Class: Antibiotic / Mass: 1834.256 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: MERSACIDIN IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AA AND THE FORMATION OF THIOETHER BONDS ...Details: MERSACIDIN IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AA AND THE FORMATION OF THIOETHER BONDS WITH CYSTEINE. THE CARBOXY-TERMINAL BETA-METHYLLANTHIONINE UNDERGOES DECARBOXYLATION. THIOETHER BONDS WITH CYSTEINE RESULT IN FOUR RINGS. THIS IS FOLLOWED BY MEMBRANE TRANSLOCATION AND CLEAVAGE OF THE MODIFIED PRECURSOR.
Source: (natural) BACILLUS SP. (bacteria) / Strain: HIL Y-85, 54728 / References: UniProt: P43683, Mersacidin
#2: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMERSACIDIN IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE ...MERSACIDIN IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS ARE CHARACTERIZED BY LANTHIONINE AND/OR METHYLLANTHIONINE NONPROTEINOGENIC AMINO ACIDS. HERE, MERSACIDIN IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: MERSACIDIN CHAIN: A, B, C, D, E, F COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 20 DESCRIPTION: MERSACIDIN IS A TETRACYCLIC PEPTIDE. THIOETHER BONDS WITH CYSTEINE RESULT IN FOUR RINGS. CROSSLINK 1-4 BETA-METHYLLANTHIONINE (CYS-DBB) CROSSLINK 4-12 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 13-18 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 15-20 S-(2-AMINOVINYL)-3-METHYL-D- CYSTEINE (DBB-TEE)

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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: 1.73 Å3/Da / Density % sol: 28.84 %
Crystal growTemperature: 294 K / Method: evaporation / pH: 7
Details: LYOPHILIZED MERSACIDIN WAS DISSOLVED TO SATURATION IN METHANOL. CRYSTALS GREW AT ROOM TEMPERATURE BY SLOW EVAPORATION OF METHANOL FROM A 1:1 MIXTURE OF THE SATURATED SOLUTION WITH BENZENE ...Details: LYOPHILIZED MERSACIDIN WAS DISSOLVED TO SATURATION IN METHANOL. CRYSTALS GREW AT ROOM TEMPERATURE BY SLOW EVAPORATION OF METHANOL FROM A 1:1 MIXTURE OF THE SATURATED SOLUTION WITH BENZENE AND REACHED A MAXIMUM SIZE OF 0.3 X 0.3 X 0.3 MM IN 10 DAYS., pH 7.00
Crystal grow
*PLUS
Method: slow evaporation
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %satmethanol11
250 %satbenzene11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.865
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.865 Å / Relative weight: 1
ReflectionResolution: 1.06→39.9 Å / Num. obs: 33469 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.9
Reflection shellResolution: 1.06→1.08 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3 / % possible all: 99.6
Reflection
*PLUS
Num. all: 33485 / Num. measured all: 164063
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: HALF-BAKED / Resolution: 1.06→40 Å / Num. parameters: 7438 / Num. restraintsaints: 10782 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: SIMILARITY RESTRAINTS FOR NON-STANDARD RESIDUES AS IMPLEMENTED IN SHELXL97
Stereochemistry target values: ENGH AND HUBER
Details: MEROHEDRAL TWINNING: THE CRYSTAL WAS MEROHEDRALLY TWINNED. THE EFFECT OF MEROHEDRAL WAS TAKEN INTO ACCOUNT EMPLOYING THE METHOD OF PRATT ET AL., J.CHEM.SOC.(A)(1971)2146-2151 AND JAMESON ET ...Details: MEROHEDRAL TWINNING: THE CRYSTAL WAS MEROHEDRALLY TWINNED. THE EFFECT OF MEROHEDRAL WAS TAKEN INTO ACCOUNT EMPLOYING THE METHOD OF PRATT ET AL., J.CHEM.SOC.(A)(1971)2146-2151 AND JAMESON ET AL., ACTA CRYST.B54 (1982)443-449 AS IMPLEMENTED IN SHELXL-97 USING THE TWIN MATRIX: (0 1 0 1 0 0 0 0 -1). THE SIX MOLECULES IN THE ASYMMETRIC UNIT ARE ARRANGED WITH APPROXIMATE 32 (D3) POINT GROUP SYMMETRY AND CAN BE DESCRIBED AS A DIMER OF TRIMERS. THE TWO FOLD AXIS RUNS ALONG THE SHORT DIAGONAL OF THE A*B* PLANE.
RfactorNum. reflection% reflectionSelection details
all0.1414 33449 --
obs0.1414 -99.9 %-
Rfree---RANDOM
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 719 / Occupancy sum non hydrogen: 826
Refinement stepCycle: LAST / Resolution: 1.06→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 0 18 57 825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0.017
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.068
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / Rfactor obs: 0.134 / Rfactor Rwork: 0.1414
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.027

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