HEADER TOXIN 15-APR-19 6RFM TITLE BORDETELLA PERTUSSIS ADENYLATE CYCLASE TOXIN TRANSMEMBRANE SEGMENT TITLE 2 411-490 IN DPC MICELLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL HEMOLYSIN/ADENYLATE CYCLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AC-HLY,ACT,CYCLOLYSIN; COMPND 5 EC: 4.6.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORDETELLA PERTUSSIS; SOURCE 3 ORGANISM_TAXID: 520; SOURCE 4 GENE: CYA, CYAA, BN118_0468; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ADENYLATE CYCLASE, BORDETELLA PERTUSSIS, MEMBRANE PROTEIN, CALCIUM KEYWDS 2 BINDING, TOXIN EXPDTA SOLUTION NMR NUMMDL 50 AUTHOR J.MASIN,L.BUMBA,V.VEVERKA REVDAT 3 14-JUN-23 6RFM 1 JRNL DBREF REVDAT 2 25-NOV-20 6RFM 1 JRNL REVDAT 1 13-MAY-20 6RFM 0 JRNL AUTH A.SUKOVA,L.BUMBA,P.SRB,V.VEVERKA,O.STANEK,J.HOLUBOVA, JRNL AUTH 2 J.CHMELIK,R.FISER,P.SEBO,J.MASIN JRNL TITL NEGATIVE CHARGE OF THE AC-TO-HLY LINKING SEGMENT MODULATES JRNL TITL 2 CALCIUM-DEPENDENT MEMBRANE ACTIVITIES OF BORDETELLA JRNL TITL 3 ADENYLATE CYCLASE TOXIN. JRNL REF BIOCHIM BIOPHYS ACTA V.1862 83310 2020 JRNL REF 2 BIOMEMBR JRNL REFN ESSN 1879-2642 JRNL PMID 32333856 JRNL DOI 10.1016/J.BBAMEM.2020.183310 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA REMARK 3 AUTHORS : YASARA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6RFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101850. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 125 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 450 UM [U-13C; U-15N] CYA411 REMARK 210 -490, 25 MM SODIUM PHOSPHATE, REMARK 210 100 MM SODIUM CHLORIDE, 1 MM REMARK 210 TCEP, 100 MM [U-2H] DPC, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HCCH-TOCSY; 3D 1H-13C REMARK 210 NOESY; 3D 1H-15N 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 : CYANA, SPARKY, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 50 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 7980 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 23 ARG A 443 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 37 ARG A 443 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 50 PRO A 449 C - N - CA ANGL. DEV. = 9.0 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 SER A 414 -162.89 77.82 REMARK 500 1 ALA A 442 160.17 68.73 REMARK 500 1 HIS A 457 -71.58 -105.75 REMARK 500 2 SER A 412 40.11 -73.96 REMARK 500 2 ASP A 446 33.06 -87.82 REMARK 500 3 ALA A 442 29.19 -146.15 REMARK 500 3 ARG A 443 -49.22 -132.57 REMARK 500 3 ASP A 446 83.88 -150.53 REMARK 500 3 ALA A 447 30.76 -141.23 REMARK 500 3 HIS A 457 -76.89 -105.57 REMARK 500 3 ALA A 488 11.72 56.63 REMARK 500 4 ALA A 440 -157.27 48.98 REMARK 500 4 HIS A 457 -76.77 -105.77 REMARK 500 5 SER A 416 32.92 -90.67 REMARK 500 5 LEU A 417 -42.68 64.18 REMARK 500 5 ASP A 446 24.75 -74.73 REMARK 500 5 ALA A 447 43.74 -92.73 REMARK 500 5 ALA A 454 -40.72 -152.21 REMARK 500 5 HIS A 457 -76.79 -105.73 REMARK 500 6 GLN A 444 15.74 -152.82 REMARK 500 6 HIS A 457 -70.12 -104.98 REMARK 500 7 SER A 416 33.74 -89.39 REMARK 500 7 LEU A 417 -42.98 63.49 REMARK 500 7 ASP A 446 53.98 -147.41 REMARK 500 7 HIS A 457 -67.92 -101.11 REMARK 500 8 ASP A 445 -61.47 64.13 REMARK 500 8 ASP A 446 19.26 -160.54 REMARK 500 8 ALA A 447 46.82 -96.56 REMARK 500 8 HIS A 457 -67.93 -92.93 REMARK 500 9 LEU A 417 -46.81 63.73 REMARK 500 9 ALA A 440 -44.57 -146.80 REMARK 500 9 ALA A 442 70.16 52.44 REMARK 500 9 ARG A 443 -148.77 61.06 REMARK 500 9 GLN A 444 26.99 -141.87 REMARK 500 10 SER A 416 32.81 -91.99 REMARK 500 10 LEU A 417 -53.96 63.18 REMARK 500 10 ARG A 443 -162.89 55.99 REMARK 500 10 GLN A 444 41.50 -142.12 REMARK 500 10 ALA A 447 43.42 -98.79 REMARK 500 10 ALA A 454 39.94 -77.04 REMARK 500 10 HIS A 457 -62.47 -105.30 REMARK 500 11 SER A 412 -51.95 -157.32 REMARK 500 11 ALA A 454 -156.09 59.27 REMARK 500 11 ALA A 488 28.38 -78.74 REMARK 500 12 LEU A 417 -46.92 63.90 REMARK 500 12 ALA A 440 -138.55 -127.27 REMARK 500 13 SER A 416 31.16 -82.54 REMARK 500 13 LEU A 417 -47.38 65.36 REMARK 500 13 SER A 452 174.22 68.76 REMARK 500 13 ALA A 456 170.80 69.03 REMARK 500 REMARK 500 THIS ENTRY HAS 255 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34393 RELATED DB: BMRB REMARK 900 BORDETELLA PERTUSSIS ADENYLATE CYCLASE TOXIN TRANSMEMBRANE SEGMENT REMARK 900 411-490 IN DPC MICELLES DBREF 6RFM A 411 490 UNP J7QLC0 CYAA_BORP1 411 490 SEQRES 1 A 80 GLY SER ARG SER PHE SER LEU GLY GLU VAL SER ASP MET SEQRES 2 A 80 ALA ALA VAL GLU ALA ALA GLU LEU GLU MET THR ARG GLN SEQRES 3 A 80 VAL LEU HIS ALA GLY ALA ARG GLN ASP ASP ALA GLU PRO SEQRES 4 A 80 GLY VAL SER GLY ALA SER ALA HIS TRP GLY GLN ARG ALA SEQRES 5 A 80 LEU GLN GLY ALA GLN ALA VAL ALA ALA ALA GLN ARG LEU SEQRES 6 A 80 VAL HIS ALA ILE ALA LEU MET THR GLN PHE GLY ARG ALA SEQRES 7 A 80 GLY SER HELIX 1 AA1 SER A 416 ALA A 440 1 25 HELIX 2 AA2 ARG A 443 ALA A 447 5 5 HELIX 3 AA3 HIS A 457 PHE A 485 1 29 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