HEADER METAL TRANSPORT 21-AUG-19 6SLY TITLE NMR SOLUTION STRUCTURE OF HELICOBACTER PYLORI TONB-CTD (RESIDUES 179- TITLE 2 285) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN TONB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 GENE: EC544_07375; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TONB-DEPENDENT IRON UPTAKE, C-TERMINAL DOMAIN, METAL TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.CIRAGAN,H.A.HEIKKINEN,H.IWAI REVDAT 6 28-FEB-24 6SLY 1 JRNL REVDAT 5 14-JUN-23 6SLY 1 REMARK REVDAT 4 17-FEB-21 6SLY 1 JRNL REVDAT 3 10-FEB-21 6SLY 1 JRNL REVDAT 2 15-APR-20 6SLY 1 JRNL REVDAT 1 25-MAR-20 6SLY 0 JRNL AUTH A.CIRAGAN,S.M.BACKLUND,K.M.MIKULA,H.M.BEYER, JRNL AUTH 2 O.H.SAMULI OLLILA,H.IWAI JRNL TITL NMR STRUCTURE AND DYNAMICS OF TONB INVESTIGATED BY SCAR-LESS JRNL TITL 2 SEGMENTAL ISOTOPIC LABELING USING A SALT-INDUCIBLE SPLIT JRNL TITL 3 INTEIN. JRNL REF FRONT CHEM V. 8 136 2020 JRNL REFN ESSN 2296-2646 JRNL PMID 32266203 JRNL DOI 10.3389/FCHEM.2020.00136 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.A.HEIKKINEN,S.M.BACKLUND,H.IWAI REMARK 1 TITL NMR STRUCTURE DETERMINATIONS OF SMALL PROTEINS USING ONLY REMARK 1 TITL 2 ONE FRACTIONALLY 20% 13 C- AND UNIFORMLY 100% 15 N-LABELED REMARK 1 TITL 3 SAMPLE. REMARK 1 REF MOLECULES V. 26 2021 REMARK 1 REFN ESSN 1420-3049 REMARK 1 PMID 33535444 REMARK 1 DOI 10.3390/MOLECULES26030747 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 14 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6SLY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1292100315. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 TONB, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HN(CA)CO; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-COSY; 3D REMARK 210 H(CC)(CO)NH; 3D (H)CC(CO)NH; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR 2.4.1, CYANA 3.0, TALOS REMARK 210 N, PSVS 1.5 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 2 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 10 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 15 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 17 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 19 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES 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 THR A 183 45.75 -77.28 REMARK 500 2 ALA A 182 40.25 -73.42 REMARK 500 2 ASN A 190 60.12 -117.31 REMARK 500 4 THR A 183 34.25 -66.67 REMARK 500 4 ASN A 190 55.59 -118.44 REMARK 500 4 GLU A 284 77.07 -101.79 REMARK 500 7 GLU A 284 9.01 -151.31 REMARK 500 9 ASN A 190 61.05 -115.89 REMARK 500 10 THR A 183 43.63 -70.85 REMARK 500 11 ASN A 190 65.99 -113.26 REMARK 500 12 THR A 183 -7.82 -58.49 REMARK 500 13 ASP A 233 0.01 -69.36 REMARK 500 15 ASN A 245 38.73 -143.79 REMARK 500 15 GLU A 284 47.12 -158.47 REMARK 500 18 THR A 183 8.22 -64.16 REMARK 500 19 LYS A 283 7.55 -67.27 REMARK 500 20 ASN A 190 52.38 -117.81 REMARK 500 20 ASN A 245 31.11 -146.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 183 SER A 184 1 -148.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34425 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF HELICOBACTER PYLORI TONB-CTD (RESIDUES REMARK 900 179-285) DBREF1 6SLY A 179 285 UNP A0A438WSV6_HELPX DBREF2 6SLY A A0A438WSV6 178 284 SEQRES 1 A 107 SER GLU GLY ALA THR SER GLU ALA GLN ALA TYR ASN PRO SEQRES 2 A 107 GLY VAL SER ASN GLU PHE LEU MET LYS ILE GLN THR ALA SEQRES 3 A 107 ILE SER SER LYS ASN ARG TYR PRO LYS MET ALA GLN ILE SEQRES 4 A 107 ARG GLY ILE GLU GLY GLU VAL LEU VAL SER PHE THR ILE SEQRES 5 A 107 ASN ALA ASP GLY SER VAL THR ASP ILE LYS VAL VAL LYS SEQRES 6 A 107 SER ASN THR THR ASP ILE LEU ASN HIS ALA ALA LEU GLU SEQRES 7 A 107 ALA ILE LYS SER ALA ALA HIS LEU PHE PRO LYS PRO GLU SEQRES 8 A 107 GLU THR VAL HIS LEU LYS ILE PRO ILE ALA TYR SER LEU SEQRES 9 A 107 LYS GLU ASP HELIX 1 AA1 SER A 184 ASN A 190 1 7 HELIX 2 AA2 SER A 194 ASN A 209 1 16 HELIX 3 AA3 PRO A 212 ILE A 217 1 6 HELIX 4 AA4 THR A 247 ALA A 262 1 16 HELIX 5 AA5 HIS A 263 PHE A 265 5 3 SHEET 1 AA1 3 SER A 235 SER A 244 0 SHEET 2 AA1 3 GLY A 222 ASN A 231 -1 N SER A 227 O LYS A 240 SHEET 3 AA1 3 VAL A 272 TYR A 280 -1 O VAL A 272 N ILE A 230 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