HEADER PROTEIN BINDING 26-JUN-19 6S3W TITLE SOLUTION NMR STRUCTURE OF TOLAIII BOUND TO A PEPTIDE DERIVED FROM THE TITLE 2 N-TERMINUS OF TOLB COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLBP; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PEPTIDE SEQUENCE REPRESENTS RESIDUES 22 TO 34 OF THE COMPND 6 TOLB SEQUENCE. THIS IS THE REGION OF TOLB THAT BINDS TO TOLAIII.; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CELL ENVELOPE INTEGRITY/TRANSLOCATION PROTEIN TOLA; COMPND 9 CHAIN: A; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: THIS IS THE 3RD DOMAIN OF THE TOLA PROTEIN. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 8 ORGANISM_TAXID: 287; SOURCE 9 GENE: EFK27_03855; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOLA, TOLB, PAL, BACTERIAL OUTER MEMBRANE, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.KLEANTHOUS,C.REDFIELD,K.RAJASEKAR,P.HOLMES REVDAT 2 14-JUN-23 6S3W 1 REMARK REVDAT 1 25-MAR-20 6S3W 0 JRNL AUTH J.SZCZEPANIAK,P.HOLMES,K.RAJASEKAR,R.KAMINSKA,F.SAMSUDIN, JRNL AUTH 2 P.G.INNS,P.RASSAM,S.KHALID,S.M.MURRAY,C.REDFIELD, JRNL AUTH 3 C.KLEANTHOUS JRNL TITL THE LIPOPROTEIN PAL STABILISES THE BACTERIAL OUTER MEMBRANE JRNL TITL 2 DURING CONSTRICTION BY A MOBILISATION-AND-CAPTURE MECHANISM. JRNL REF NAT COMMUN V. 11 1305 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32161270 JRNL DOI 10.1038/S41467-020-15083-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, CNS 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 8 ROUNDS OF ITERATIVE STRUCTURE REMARK 3 CALCULATION USING ARIA PROTOCOL REMARK 4 REMARK 4 6S3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1292103038. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 140 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-98% 15N] TOLAIII, 3 MM REMARK 210 TOLBP, 20 MM SODIUM PHOSPHATE, REMARK 210 60 MM SODIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 0.6 MM [U-98% 13C; U-98% REMARK 210 15N] TOLAIII, 3 MM TOLBP, 20 MM REMARK 210 SODIUM PHOSPHATE, 60 MM SODIUM REMARK 210 CHLORIDE, 95% H2O/5% D2O; 1.1 MM REMARK 210 TOLAIII, 0.2 MM [U-98% 13C; U-98% REMARK 210 15N] TOLBP, 20 MM SODIUM REMARK 210 PHOSPHATE, 60 MM SODIUM CHLORIDE, REMARK 210 95% H2O/5% D2O; 0.6 MM [U-98% REMARK 210 13C; U-98% 15N] TOLAIII, 3 MM REMARK 210 TOLBP, 20 MM SODIUM PHOSPHATE, REMARK 210 60 MM SODIUM CHLORIDE, 100% D2O; REMARK 210 0.6 MM [U-98% 15N] TOLAIII, 3 MM REMARK 210 TOLBP, 20 MM SODIUM PHOSPHATE, REMARK 210 60 MM SODIUM CHLORIDE, 5 % C12E6/ REMARK 210 N-HEXANOL, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D CBCANH; 3D REMARK 210 CBCA(CO)NH; 3D H(CCO)NH; 3D C(CO) REMARK 210 NH; 3D HBHA(CO)NH; 2D 1H-15N REMARK 210 HSQC; 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY; 2D 1H-13C HSQC; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 2D HNCO; 2D REMARK 210 HBHA(CO)NH; 2D HNCA; 2D CBCA(CO) REMARK 210 NH; 2D HN(CA)CO; 2D 1H-13C NOESY REMARK 210 ALIPHATIC; 2D 1H-15N NOESY; 3D REMARK 210 HCCH-TOCSY; 2D 1H-15N IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II; CUSTOM; HOME-BUILD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; HOME-BUILT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CCPNMR ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 3 PHE A 329 CE1 PHE A 329 CZ 0.117 REMARK 500 3 TYR A 333 CZ TYR A 333 CE2 0.080 REMARK 500 4 TYR A 333 CE1 TYR A 333 CZ -0.080 REMARK 500 4 TYR A 333 CZ TYR A 333 CE2 0.122 REMARK 500 6 TYR A 333 CE1 TYR A 333 CZ -0.113 REMARK 500 6 TYR A 333 CZ TYR A 333 CE2 0.117 REMARK 500 7 TYR A 333 CE1 TYR A 333 CZ -0.082 REMARK 500 7 TYR A 333 CZ TYR A 333 CE2 0.103 REMARK 500 8 PHE A 329 CE1 PHE A 329 CZ 0.119 REMARK 500 11 TYR A 333 CE1 TYR A 333 CZ -0.088 REMARK 500 11 TYR A 333 CZ TYR A 333 CE2 0.111 REMARK 500 12 TYR A 333 CE1 TYR A 333 CZ -0.087 REMARK 500 12 TYR A 333 CZ TYR A 333 CE2 0.118 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 ARG B 12 -166.32 -77.24 REMARK 500 1 ARG A 226 -78.91 66.78 REMARK 500 1 ALA A 227 19.32 -147.00 REMARK 500 1 GLU A 230 -156.47 -168.53 REMARK 500 1 THR A 236 -153.36 -146.49 REMARK 500 1 SER A 248 -73.81 -96.08 REMARK 500 1 VAL A 250 -147.47 -149.09 REMARK 500 1 THR A 251 73.87 53.66 REMARK 500 1 ASN A 274 32.68 -74.43 REMARK 500 1 PRO A 286 4.25 -59.74 REMARK 500 1 ALA A 293 125.64 -173.80 REMARK 500 1 PRO A 319 -71.36 -54.58 REMARK 500 1 PRO A 342 169.02 -28.94 REMARK 500 2 ASP B 2 105.71 70.45 REMARK 500 2 ASP B 11 47.60 -72.16 REMARK 500 2 ALA A 229 71.87 44.84 REMARK 500 2 LEU A 232 74.45 59.27 REMARK 500 2 GLN A 239 -63.49 -131.52 REMARK 500 2 SER A 248 79.20 50.73 REMARK 500 2 GLU A 249 -93.62 -127.20 REMARK 500 2 VAL A 250 -179.65 56.79 REMARK 500 2 PRO A 270 -7.86 -52.87 REMARK 500 2 PRO A 286 -3.68 -58.73 REMARK 500 2 ALA A 293 132.42 -175.96 REMARK 500 2 LEU A 332 -61.16 -100.44 REMARK 500 2 PRO A 342 155.90 -28.20 REMARK 500 2 ASP A 344 75.86 60.59 REMARK 500 2 LEU A 345 -73.39 -80.63 REMARK 500 2 SER A 346 -41.26 177.77 REMARK 500 3 SER B 8 -174.15 -68.86 REMARK 500 3 ASP B 11 23.05 -168.70 REMARK 500 3 ARG A 226 -37.98 -152.54 REMARK 500 3 THR A 235 -172.68 55.45 REMARK 500 3 ARG A 238 97.88 66.13 REMARK 500 3 GLN A 239 175.67 75.25 REMARK 500 3 SER A 248 82.45 -172.51 REMARK 500 3 GLU A 249 -135.68 -83.59 REMARK 500 3 SER A 253 14.74 58.70 REMARK 500 3 PRO A 286 -5.20 -53.47 REMARK 500 3 ALA A 293 132.66 -172.59 REMARK 500 3 PRO A 342 171.76 -31.72 REMARK 500 3 ASP A 344 73.23 52.30 REMARK 500 3 LEU A 345 -93.76 -79.11 REMARK 500 3 SER A 346 -44.02 -169.52 REMARK 500 4 ASP B 2 125.75 69.75 REMARK 500 4 ASP B 11 1.50 -69.60 REMARK 500 4 ARG B 12 173.32 -57.07 REMARK 500 4 MET A 225 35.43 -163.30 REMARK 500 4 LEU A 231 76.38 -101.86 REMARK 500 4 SER A 233 -70.91 -104.06 REMARK 500 REMARK 500 THIS ENTRY HAS 311 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 TYR A 333 0.07 SIDE CHAIN REMARK 500 4 TYR A 333 0.10 SIDE CHAIN REMARK 500 6 TYR A 333 0.06 SIDE CHAIN REMARK 500 7 PHE A 304 0.07 SIDE CHAIN REMARK 500 7 TYR A 333 0.08 SIDE CHAIN REMARK 500 10 ARG A 336 0.16 SIDE CHAIN REMARK 500 11 TYR A 333 0.08 SIDE CHAIN REMARK 500 12 TYR A 333 0.09 SIDE CHAIN REMARK 500 14 TYR A 333 0.06 SIDE CHAIN REMARK 500 17 TYR A 333 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27397 RELATED DB: BMRB DBREF 6S3W B 1 13 PDB 6S3W 6S3W 1 13 DBREF1 6S3W A 226 347 UNP A0A454LZ61_PSEAI DBREF2 6S3W A A0A454LZ61 226 347 SEQADV 6S3W HIS A 224 UNP A0A454LZ6 EXPRESSION TAG SEQADV 6S3W MET A 225 UNP A0A454LZ6 EXPRESSION TAG SEQRES 1 B 13 ALA ASP PRO LEU VAL ILE SER SER GLY ASN ASP ARG ALA SEQRES 1 A 124 HIS MET ARG ALA LEU ALA GLU LEU LEU SER ASP THR THR SEQRES 2 A 124 GLU ARG GLN GLN ALA LEU ALA ASP GLU VAL GLY SER GLU SEQRES 3 A 124 VAL THR GLY SER LEU ASP ASP LEU ILE VAL ASN LEU VAL SEQRES 4 A 124 SER GLN GLN TRP ARG ARG PRO PRO SER ALA ARG ASN GLY SEQRES 5 A 124 MET SER VAL GLU VAL LEU ILE GLU MET LEU PRO ASP GLY SEQRES 6 A 124 THR ILE THR ASN ALA SER VAL SER ARG SER SER GLY ASP SEQRES 7 A 124 LYS PRO PHE ASP SER SER ALA VAL ALA ALA VAL ARG ASN SEQRES 8 A 124 VAL GLY ARG ILE PRO GLU MET GLN GLN LEU PRO ARG ALA SEQRES 9 A 124 THR PHE ASP SER LEU TYR ARG GLN ARG ARG ILE ILE PHE SEQRES 10 A 124 LYS PRO GLU ASP LEU SER LEU HELIX 1 AA1 SER A 253 TRP A 266 1 14 HELIX 2 AA2 ASP A 301 GLY A 316 1 16 HELIX 3 AA3 PRO A 319 LEU A 324 5 6 HELIX 4 AA4 PRO A 325 TYR A 333 1 9 SHEET 1 AA1 4 LEU B 4 ILE B 6 0 SHEET 2 AA1 4 ARG A 337 PHE A 340 1 O ILE A 339 N ILE B 6 SHEET 3 AA1 4 VAL A 278 MET A 284 -1 N VAL A 278 O PHE A 340 SHEET 4 AA1 4 ILE A 290 ARG A 297 -1 O ASN A 292 N GLU A 283 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