HEADER ANTITOXIN 26-MAR-14 2MN2 TITLE 3D STRUCTURE OF YMOB, A MODULATOR OF BIOFILM FORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: YMOB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: YBAJ; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA ENTEROCOLITICA; SOURCE 3 ORGANISM_TAXID: 630; SOURCE 4 STRAIN: W22711; SOURCE 5 GENE: YBAJ, YEW_DG13760, YMOB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHAT2 KEYWDS FOUR HELIX BUNDLE, BURIED CYSTEINE, ANTITOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR O.MARIMON,T.N.CORDEIRO,I.AMATA,M.PONS REVDAT 3 14-JUN-23 2MN2 1 REMARK SEQADV REVDAT 2 21-DEC-16 2MN2 1 JRNL REVDAT 1 01-APR-15 2MN2 0 JRNL AUTH O.MARIMON,J.M.TEIXEIRA,T.N.CORDEIRO,V.W.SOO,T.L.WOOD, JRNL AUTH 2 M.MAYZEL,I.AMATA,J.GARCIA,A.MORERA,M.GAY,M.VILASECA, JRNL AUTH 3 V.Y.OREKHOV,T.K.WOOD,M.PONS JRNL TITL AN OXYGEN-SENSITIVE TOXIN-ANTITOXIN SYSTEM. JRNL REF NAT COMMUN V. 7 13634 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27929062 JRNL DOI 10.1038/NCOMMS13634 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.0 AND 3.0, CNS 1.2.1, CYANA REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000103811. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM YMOB-C117S, 20 MM SODIUM REMARK 210 PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 1 MM TCEP, 0.2 MM EDTA, REMARK 210 0.1% SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O; 1 MM [U-100% 15N] YMOB- REMARK 210 C117S, 20 MM SODIUM PHOSPHATE, REMARK 210 150 MM SODIUM CHLORIDE, 1 MM REMARK 210 TCEP, 0.2 MM EDTA, 0.1% SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 13C; U-100% 15N] YMOB-C117S, REMARK 210 20 MM SODIUM PHOSPHATE, 150 MM REMARK 210 SODIUM CHLORIDE, 1 MM TCEP, 0.2 REMARK 210 MM EDTA, 0.1% SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O; 1 MM [U-100% 13C; U- REMARK 210 100% 15N] YMOB-C117S, 20 MM REMARK 210 SODIUM PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 1 MM TCEP, 0.2 MM EDTA, REMARK 210 0.1% SODIUM AZIDE, 100% D2O; 1 REMARK 210 MM [U-10% 13C; U-100% 15N] YMOB- REMARK 210 C117S, 20 MM SODIUM PHOSPHATE, REMARK 210 150 MM SODIUM CHLORIDE, 1 MM REMARK 210 TCEP, 0.2 MM EDTA, 0.1% SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HN(CO)CA; 3D CBCA(CO)NH; 2D 1H- REMARK 210 13C HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC CONSTANT TIME; 3D REMARK 210 HBHA(CO)NH; 3D HNCACB; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 1D 1H WATERGATE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ 3.2, NMRPIPE, MDDNMR, REMARK 210 NMRDRAW, NMRVIEW, CARA 1.9.0 REMARK 210 BETA 3, UNIO'10 VERSION 2.0.2, REMARK 210 TALOS +, CYANA 2.1, PROCHECKNMR, REMARK 210 MOLMOL, PYMOL REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 SER A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE A 58 H PHE A 62 1.53 REMARK 500 O LYS A 15 H GLU A 19 1.58 REMARK 500 O GLN A 13 H LEU A 17 1.58 REMARK 500 O GLY A 25 H LEU A 29 1.58 REMARK 500 OG1 THR A 83 HE1 TRP A 100 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 GLU A 3 40.59 -90.77 REMARK 500 1 TRP A 36 -77.64 -119.98 REMARK 500 1 GLU A 114 -90.68 -83.18 REMARK 500 1 LYS A 121 -84.69 -64.72 REMARK 500 2 TYR A 4 -103.04 -85.54 REMARK 500 2 GLU A 114 -76.41 -89.54 REMARK 500 3 TRP A 36 -62.48 -107.46 REMARK 500 3 GLU A 114 -146.63 -94.52 REMARK 500 4 ASP A 2 -68.53 71.54 REMARK 500 4 TRP A 36 -82.04 -142.41 REMARK 500 4 ASP A 69 37.70 -98.48 REMARK 500 4 GLU A 114 -70.11 -33.88 REMARK 500 5 GLU A 3 67.14 -113.44 REMARK 500 5 ASP A 39 105.20 -53.46 REMARK 500 5 GLU A 114 -79.31 -59.51 REMARK 500 5 MET A 120 77.04 -103.30 REMARK 500 6 GLU A 3 -72.48 -145.20 REMARK 500 6 TRP A 36 -45.69 71.07 REMARK 500 6 TYR A 66 76.59 -112.33 REMARK 500 6 GLU A 114 -82.74 -72.64 REMARK 500 6 LYS A 121 -81.89 -75.50 REMARK 500 7 ASP A 2 -62.54 -147.25 REMARK 500 7 SER A 5 -72.19 -143.06 REMARK 500 7 GLU A 114 -139.80 -103.59 REMARK 500 8 ASP A 2 -166.89 -176.82 REMARK 500 8 TYR A 4 -41.73 -130.90 REMARK 500 8 PRO A 6 87.00 -50.11 REMARK 500 8 GLU A 114 -77.54 -64.53 REMARK 500 10 ASP A 2 105.25 57.88 REMARK 500 10 GLU A 3 129.13 67.51 REMARK 500 10 SER A 5 79.28 -113.65 REMARK 500 10 PRO A 6 104.64 -55.31 REMARK 500 10 ASP A 31 60.51 -103.44 REMARK 500 10 TRP A 36 -61.67 -102.79 REMARK 500 10 GLU A 114 -91.32 -89.51 REMARK 500 11 TRP A 36 -75.36 -112.75 REMARK 500 11 PRO A 67 -9.05 -59.18 REMARK 500 11 GLU A 114 -83.03 -94.97 REMARK 500 11 LYS A 121 -62.52 46.69 REMARK 500 12 PRO A 6 111.72 -39.36 REMARK 500 12 TYR A 90 -60.03 -29.96 REMARK 500 12 ASP A 94 -179.21 55.78 REMARK 500 12 GLU A 114 -151.81 -124.51 REMARK 500 13 GLU A 3 -70.53 -143.14 REMARK 500 13 ASP A 31 -106.25 -78.27 REMARK 500 13 GLU A 114 -99.91 -70.45 REMARK 500 14 GLU A 3 -72.76 -48.35 REMARK 500 14 TYR A 4 -73.16 -85.12 REMARK 500 14 PRO A 6 97.15 -69.08 REMARK 500 14 TRP A 36 -64.89 -170.92 REMARK 500 REMARK 500 THIS ENTRY HAS 71 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19876 RELATED DB: BMRB DBREF 2MN2 A 1 122 UNP F4MY12 F4MY12_YEREN 1 122 SEQADV 2MN2 MET A -10 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 SER A -9 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 HIS A -8 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 HIS A -7 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 HIS A -6 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 HIS A -5 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 HIS A -4 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 HIS A -3 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 SER A -2 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 MET A -1 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 GLY A 0 UNP F4MY12 EXPRESSION TAG SEQADV 2MN2 SER A 117 UNP F4MY12 CYS 117 ENGINEERED MUTATION SEQRES 1 A 133 MET SER HIS HIS HIS HIS HIS HIS SER MET GLY MET ASP SEQRES 2 A 133 GLU TYR SER PRO LYS ARG HIS ASP VAL ALA GLN LEU LYS SEQRES 3 A 133 PHE LEU CYS GLU SER LEU TYR ASP GLU GLY ILE ALA THR SEQRES 4 A 133 LEU GLY ASP SER HIS HIS GLY TRP VAL ASN ASP PRO THR SEQRES 5 A 133 SER ALA VAL ASN LEU GLN LEU ASN ASP LEU ILE GLU HIS SEQRES 6 A 133 ILE ALA SER PHE VAL MET SER PHE LYS ILE LYS TYR PRO SEQRES 7 A 133 ASP ASP GLY ASP LEU SER GLU LEU VAL GLU GLU TYR LEU SEQRES 8 A 133 ASP ASP THR TYR THR LEU PHE SER SER TYR GLY ILE ASN SEQRES 9 A 133 ASP PRO GLU LEU GLN ARG TRP GLN LYS THR LYS GLU ARG SEQRES 10 A 133 LEU PHE ARG LEU PHE SER GLY GLU TYR ILE SER THR LEU SEQRES 11 A 133 MET LYS THR HELIX 1 1 PRO A 6 ASP A 31 1 26 HELIX 2 2 SER A 42 TYR A 66 1 25 HELIX 3 3 ASP A 69 SER A 88 1 20 HELIX 4 4 ASN A 93 SER A 112 1 20 HELIX 5 5 TYR A 115 MET A 120 1 6 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1