PDB Short entry for 6IFM HEADER TOXIN/ANTITOXIN/DNA 20-SEP-18 6IFM TITLE CRYSTAL STRUCTURE OF DNA BOUND VAPBC FROM SALMONELLA TYPHIMURIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA(FMET)-SPECIFIC ENDONUCLEASE VAPC; COMPND 3 CHAIN: A, E, C, G; COMPND 4 SYNONYM: RNASE VAPC,TOXIN VAPC; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ANTITOXIN VAPB; COMPND 9 CHAIN: B, F, H, D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA FORWARD (27-MER); COMPND 13 CHAIN: M; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA BACKWARD (27-MER); COMPND 17 CHAIN: N; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM STR. LT2; SOURCE 4 ORGANISM_TAXID: 99287; SOURCE 5 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 6 GENE: VAPC, STM3033; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 11 TYPHIMURIUM STR. LT2; SOURCE 12 ORGANISM_TAXID: 99287; SOURCE 13 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 14 GENE: VAPB, STM3034; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630 KEYWDS TOXIN-ANTITOXIN, TOXIN-ANTITOXIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.W.PARK,B.J.LEE REVDAT 3 27-MAR-24 6IFM 1 REMARK REVDAT 2 26-FEB-20 6IFM 1 JRNL REVDAT 1 29-JAN-20 6IFM 0 JRNL AUTH D.PARK,H.J.YOON,K.Y.LEE,S.J.PARK,S.H.CHEON,H.H.LEE,S.J.LEE, JRNL AUTH 2 B.J.LEE JRNL TITL CRYSTAL STRUCTURE OF PROTEOLYZED VAPBC AND DNA-BOUND VAPBC JRNL TITL 2 FROM SALMONELLA ENTERICA TYPHIMURIUM LT2 AND VAPC AS A JRNL TITL 3 PUTATIVE CA2+-DEPENDENT RIBONUCLEASE. JRNL REF FASEB J. V. 34 3051 2020 JRNL REFN ESSN 1530-6860 JRNL PMID 31908032 JRNL DOI 10.1096/FJ.201901989R REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 24.590 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 29329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1469 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.8748 - 6.0398 0.95 2807 148 0.1970 0.2174 REMARK 3 2 6.0398 - 4.7953 0.95 2777 146 0.2116 0.2047 REMARK 3 3 4.7953 - 4.1895 0.95 2792 147 0.1920 0.2114 REMARK 3 4 4.1895 - 3.8066 0.95 2813 148 0.2185 0.2389 REMARK 3 5 3.8066 - 3.5339 0.95 2806 148 0.2196 0.2675 REMARK 3 6 3.5339 - 3.3256 0.95 2758 145 0.2304 0.2706 REMARK 3 7 3.3256 - 3.1591 0.95 2802 148 0.2169 0.2650 REMARK 3 8 3.1591 - 3.0216 0.95 2759 145 0.2186 0.2353 REMARK 3 9 3.0216 - 2.9053 0.95 2818 148 0.1943 0.2244 REMARK 3 10 2.9053 - 2.8050 0.93 2723 144 0.2017 0.2782 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 7703 REMARK 3 ANGLE : 1.089 10642 REMARK 3 CHIRALITY : 0.053 1200 REMARK 3 PLANARITY : 0.007 1181 REMARK 3 DIHEDRAL : 15.373 4445 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 6IFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300009093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29329 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 200 AND I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM CITRATE TRIBASIC PH7, REMARK 280 20% W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.81333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 81.62667 REMARK 290 REMARK 290 REMARK: NULL 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: DECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 33370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -147.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, C, G, B, F, H, D, M, N 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 IN SAME ASYMMETRIC UNIT 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 OD1 ASP D 59 O HOH D 101 1.68 REMARK 500 OD2 ASP C 130 O HOH C 201 2.00 REMARK 500 O ILE F 20 NH2 ARG D 38 2.03 REMARK 500 OE2 GLU G 86 O HOH G 201 2.03 REMARK 500 OE1 GLU G 86 O HOH G 202 2.08 REMARK 500 O HOH E 206 O HOH E 225 2.08 REMARK 500 O GLU F 24 N VAL F 26 2.10 REMARK 500 NE2 GLN B 66 O HOH B 101 2.11 REMARK 500 O ARG C 108 O HOH C 202 2.11 REMARK 500 O4 DT M 3 N6 DA N 25 2.11 REMARK 500 OG1 THR F 3 O ARG F 15 2.11 REMARK 500 OG1 THR D 3 O ARG D 15 2.11 REMARK 500 O HIS B 28 O HOH B 102 2.12 REMARK 500 OD1 ASP E 71 O HOH E 201 2.13 REMARK 500 N MET B 1 OE2 GLU H 30 2.15 REMARK 500 N7 DA N 8 O HOH N 101 2.15 REMARK 500 NH1 ARG G 25 O HOH G 203 2.16 REMARK 500 OG1 THR H 3 O ARG H 15 2.17 REMARK 500 O THR E 30 O HOH E 202 2.17 REMARK 500 N7 DA M 17 O HOH M 101 2.18 REMARK 500 O SER H 57 O HOH H 101 2.19 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 VAL F 26 N VAL F 26 CA 0.149 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 LEU A 6 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 CYS E 11 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG C 55 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 GLU F 24 CA - C - N ANGL. DEV. = 14.3 DEGREES REMARK 500 GLU F 24 O - C - N ANGL. DEV. = -13.3 DEGREES REMARK 500 ASP F 25 N - CA - C ANGL. DEV. = 20.7 DEGREES REMARK 500 VAL F 26 N - CA - C ANGL. DEV. = 26.4 DEGREES REMARK 500 DG N 1 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT N 3 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT N 22 O4' - C1' - N1 ANGL. DEV. = 1.9 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 LYS A 18 54.55 33.09 REMARK 500 SER A 31 -5.27 74.97 REMARK 500 LYS A 49 4.74 -67.26 REMARK 500 ALA A 52 61.53 -159.73 REMARK 500 LEU A 67 -166.32 -125.82 REMARK 500 VAL A 113 119.23 -26.07 REMARK 500 LYS E 18 57.69 32.32 REMARK 500 ALA E 52 64.14 -160.85 REMARK 500 TYR E 72 92.51 -65.52 REMARK 500 ASN E 116 64.49 -100.53 REMARK 500 ARG E 122 8.92 -67.70 REMARK 500 LYS C 18 59.99 34.06 REMARK 500 SER C 31 -4.18 76.22 REMARK 500 ALA C 52 62.39 64.69 REMARK 500 ALA C 102 -72.70 -59.19 REMARK 500 SER B 8 78.67 -107.92 REMARK 500 ASN B 9 -35.05 72.94 REMARK 500 ARG B 10 1.97 -162.77 REMARK 500 PRO B 17 150.02 -48.33 REMARK 500 PRO B 23 173.91 -59.89 REMARK 500 ARG B 36 9.74 -69.54 REMARK 500 ALA B 56 -178.19 -65.95 REMARK 500 ARG B 64 -31.74 -132.32 REMARK 500 PRO B 67 86.89 -61.40 REMARK 500 HIS F 2 116.03 -160.47 REMARK 500 SER F 8 -155.28 -91.82 REMARK 500 ASN F 9 81.31 -68.17 REMARK 500 GLU F 24 87.81 61.80 REMARK 500 ASP F 25 -31.10 32.60 REMARK 500 VAL F 26 -156.43 -83.71 REMARK 500 MET F 61 55.89 -140.50 REMARK 500 PRO F 67 -168.10 -64.66 REMARK 500 ASN H 9 -34.49 69.75 REMARK 500 ARG H 10 -45.07 -154.03 REMARK 500 SER H 62 -9.98 -59.71 REMARK 500 PRO H 67 85.86 -65.59 REMARK 500 THR D 3 -167.31 -160.11 REMARK 500 ARG D 10 -9.85 70.79 REMARK 500 GLU D 65 60.94 38.06 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 VAL A 112 VAL A 113 -141.92 REMARK 500 HIS B 28 VAL B 29 -147.19 REMARK 500 ASP F 25 VAL F 26 -106.50 REMARK 500 GLN H 66 PRO H 67 -149.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 6IFM A 1 132 UNP Q8ZM86 VAPC_SALTY 1 132 DBREF 6IFM E 1 132 UNP Q8ZM86 VAPC_SALTY 1 132 DBREF 6IFM C 1 132 UNP Q8ZM86 VAPC_SALTY 1 132 DBREF 6IFM G 1 132 UNP Q8ZM86 VAPC_SALTY 1 132 DBREF 6IFM B 1 68 UNP Q7CPV2 VAPB_SALTY 1 68 DBREF 6IFM F 1 68 UNP Q7CPV2 VAPB_SALTY 1 68 DBREF 6IFM H 1 68 UNP Q7CPV2 VAPB_SALTY 1 68 DBREF 6IFM D 1 68 UNP Q7CPV2 VAPB_SALTY 1 68 DBREF 6IFM M 1 27 PDB 6IFM 6IFM 1 27 DBREF 6IFM N 1 27 PDB 6IFM 6IFM 1 27 SEQRES 1 A 132 MET LEU LYS PHE MET LEU ASP THR ASN THR CYS ILE PHE SEQRES 2 A 132 THR ILE LYS ASN LYS PRO GLU HIS ILE ARG GLU ARG PHE SEQRES 3 A 132 ASN LEU ASN THR SER ARG MET CYS ILE SER SER ILE THR SEQRES 4 A 132 LEU MET GLU LEU ILE TYR GLY ALA GLU LYS SER LEU ALA SEQRES 5 A 132 PRO GLU ARG ASN LEU ALA VAL VAL GLU GLY PHE ILE SER SEQRES 6 A 132 ARG LEU GLU VAL LEU ASP TYR ASP THR GLN ALA ALA ILE SEQRES 7 A 132 HIS THR GLY GLN ILE ARG ALA GLU LEU ALA ARG LYS GLY SEQRES 8 A 132 THR PRO VAL GLY PRO TYR ASP GLN MET ILE ALA GLY HIS SEQRES 9 A 132 ALA GLY SER ARG GLY LEU VAL VAL VAL THR ASN ASN LEU SEQRES 10 A 132 ARG GLU PHE GLU ARG ILE PRO GLY ILE ARG ILE GLU ASP SEQRES 11 A 132 TRP CYS SEQRES 1 E 132 MET LEU LYS PHE MET LEU ASP THR ASN THR CYS ILE PHE SEQRES 2 E 132 THR ILE LYS ASN LYS PRO GLU HIS ILE ARG GLU ARG PHE SEQRES 3 E 132 ASN LEU ASN THR SER ARG MET CYS ILE SER SER ILE THR SEQRES 4 E 132 LEU MET GLU LEU ILE TYR GLY ALA GLU LYS SER LEU ALA SEQRES 5 E 132 PRO GLU ARG ASN LEU ALA VAL VAL GLU GLY PHE ILE SER SEQRES 6 E 132 ARG LEU GLU VAL LEU ASP TYR ASP THR GLN ALA ALA ILE SEQRES 7 E 132 HIS THR GLY GLN ILE ARG ALA GLU LEU ALA ARG LYS GLY SEQRES 8 E 132 THR PRO VAL GLY PRO TYR ASP GLN MET ILE ALA GLY HIS SEQRES 9 E 132 ALA GLY SER ARG GLY LEU VAL VAL VAL THR ASN ASN LEU SEQRES 10 E 132 ARG GLU PHE GLU ARG ILE PRO GLY ILE ARG ILE GLU ASP SEQRES 11 E 132 TRP CYS SEQRES 1 C 132 MET LEU LYS PHE MET LEU ASP THR ASN THR CYS ILE PHE SEQRES 2 C 132 THR ILE LYS ASN LYS PRO GLU HIS ILE ARG GLU ARG PHE SEQRES 3 C 132 ASN LEU ASN THR SER ARG MET CYS ILE SER SER ILE THR SEQRES 4 C 132 LEU MET GLU LEU ILE TYR GLY ALA GLU LYS SER LEU ALA SEQRES 5 C 132 PRO GLU ARG ASN LEU ALA VAL VAL GLU GLY PHE ILE SER SEQRES 6 C 132 ARG LEU GLU VAL LEU ASP TYR ASP THR GLN ALA ALA ILE SEQRES 7 C 132 HIS THR GLY GLN ILE ARG ALA GLU LEU ALA ARG LYS GLY SEQRES 8 C 132 THR PRO VAL GLY PRO TYR ASP GLN MET ILE ALA GLY HIS SEQRES 9 C 132 ALA GLY SER ARG GLY LEU VAL VAL VAL THR ASN ASN LEU SEQRES 10 C 132 ARG GLU PHE GLU ARG ILE PRO GLY ILE ARG ILE GLU ASP SEQRES 11 C 132 TRP CYS SEQRES 1 G 132 MET LEU LYS PHE MET LEU ASP THR ASN THR CYS ILE PHE SEQRES 2 G 132 THR ILE LYS ASN LYS PRO GLU HIS ILE ARG GLU ARG PHE SEQRES 3 G 132 ASN LEU ASN THR SER ARG MET CYS ILE SER SER ILE THR SEQRES 4 G 132 LEU MET GLU LEU ILE TYR GLY ALA GLU LYS SER LEU ALA SEQRES 5 G 132 PRO GLU ARG ASN LEU ALA VAL VAL GLU GLY PHE ILE SER SEQRES 6 G 132 ARG LEU GLU VAL LEU ASP TYR ASP THR GLN ALA ALA ILE SEQRES 7 G 132 HIS THR GLY GLN ILE ARG ALA GLU LEU ALA ARG LYS GLY SEQRES 8 G 132 THR PRO VAL GLY PRO TYR ASP GLN MET ILE ALA GLY HIS SEQRES 9 G 132 ALA GLY SER ARG GLY LEU VAL VAL VAL THR ASN ASN LEU SEQRES 10 G 132 ARG GLU PHE GLU ARG ILE PRO GLY ILE ARG ILE GLU ASP SEQRES 11 G 132 TRP CYS SEQRES 1 B 68 MET HIS THR THR LEU PHE PHE SER ASN ARG THR GLN ALA SEQRES 2 B 68 VAL ARG LEU PRO LYS SER ILE SER PHE PRO GLU ASP VAL SEQRES 3 B 68 LYS HIS VAL GLU ILE ILE ALA VAL GLY ARG SER ARG ILE SEQRES 4 B 68 ILE THR PRO VAL GLY GLU SER TRP ASP SER TRP PHE ASP SEQRES 5 B 68 GLY GLU GLY ALA SER THR ASP PHE MET SER THR ARG GLU SEQRES 6 B 68 GLN PRO ALA SEQRES 1 F 68 MET HIS THR THR LEU PHE PHE SER ASN ARG THR GLN ALA SEQRES 2 F 68 VAL ARG LEU PRO LYS SER ILE SER PHE PRO GLU ASP VAL SEQRES 3 F 68 LYS HIS VAL GLU ILE ILE ALA VAL GLY ARG SER ARG ILE SEQRES 4 F 68 ILE THR PRO VAL GLY GLU SER TRP ASP SER TRP PHE ASP SEQRES 5 F 68 GLY GLU GLY ALA SER THR ASP PHE MET SER THR ARG GLU SEQRES 6 F 68 GLN PRO ALA SEQRES 1 H 68 MET HIS THR THR LEU PHE PHE SER ASN ARG THR GLN ALA SEQRES 2 H 68 VAL ARG LEU PRO LYS SER ILE SER PHE PRO GLU ASP VAL SEQRES 3 H 68 LYS HIS VAL GLU ILE ILE ALA VAL GLY ARG SER ARG ILE SEQRES 4 H 68 ILE THR PRO VAL GLY GLU SER TRP ASP SER TRP PHE ASP SEQRES 5 H 68 GLY GLU GLY ALA SER THR ASP PHE MET SER THR ARG GLU SEQRES 6 H 68 GLN PRO ALA SEQRES 1 D 68 MET HIS THR THR LEU PHE PHE SER ASN ARG THR GLN ALA SEQRES 2 D 68 VAL ARG LEU PRO LYS SER ILE SER PHE PRO GLU ASP VAL SEQRES 3 D 68 LYS HIS VAL GLU ILE ILE ALA VAL GLY ARG SER ARG ILE SEQRES 4 D 68 ILE THR PRO VAL GLY GLU SER TRP ASP SER TRP PHE ASP SEQRES 5 D 68 GLY GLU GLY ALA SER THR ASP PHE MET SER THR ARG GLU SEQRES 6 D 68 GLN PRO ALA SEQRES 1 M 27 DC DC DT DG DT DA DT DA DT DC DT DC DT SEQRES 2 M 27 DT DT DG DA DC DA DT DA DT DA DC DA DT SEQRES 3 M 27 DC SEQRES 1 N 27 DG DA DT DG DT DA DT DA DT DG DT DC DA SEQRES 2 N 27 DA DA DG DA DG DA DT DA DT DA DC DA DG SEQRES 3 N 27 DG FORMUL 11 HOH *149(H2 O) HELIX 1 AA1 ASP A 7 LYS A 18 1 12 HELIX 2 AA2 GLU A 20 ASN A 29 1 10 HELIX 3 AA3 SER A 37 LYS A 49 1 13 HELIX 4 AA4 ALA A 52 SER A 65 1 14 HELIX 5 AA5 ASP A 73 LYS A 90 1 18 HELIX 6 AA6 GLY A 95 ARG A 108 1 14 HELIX 7 AA7 ASN A 116 GLU A 121 1 6 HELIX 8 AA8 ASP E 7 LYS E 18 1 12 HELIX 9 AA9 PRO E 19 ASN E 29 1 11 HELIX 10 AB1 SER E 37 LYS E 49 1 13 HELIX 11 AB2 ALA E 52 ARG E 66 1 15 HELIX 12 AB3 ASP E 73 ARG E 84 1 12 HELIX 13 AB4 ARG E 84 ARG E 89 1 6 HELIX 14 AB5 GLY E 95 SER E 107 1 13 HELIX 15 AB6 ASN E 116 ARG E 122 1 7 HELIX 16 AB7 ASP C 7 LYS C 18 1 12 HELIX 17 AB8 GLU C 20 ASN C 29 1 10 HELIX 18 AB9 SER C 37 SER C 50 1 14 HELIX 19 AC1 ALA C 52 ARG C 66 1 15 HELIX 20 AC2 ASP C 73 GLY C 91 1 19 HELIX 21 AC3 GLY C 95 SER C 107 1 13 HELIX 22 AC4 ASN C 116 GLU C 121 1 6 HELIX 23 AC5 ASP G 7 LYS G 18 1 12 HELIX 24 AC6 PRO G 19 ASN G 29 1 11 HELIX 25 AC7 SER G 37 LYS G 49 1 13 HELIX 26 AC8 ALA G 52 ARG G 66 1 15 HELIX 27 AC9 ASP G 73 LYS G 90 1 18 HELIX 28 AD1 GLY G 95 GLY G 109 1 15 HELIX 29 AD2 TRP B 47 GLY B 53 1 7 HELIX 30 AD3 PRO F 17 SER F 21 5 5 HELIX 31 AD4 TRP F 47 ASP F 52 1 6 HELIX 32 AD5 PRO H 17 SER H 21 5 5 HELIX 33 AD6 SER H 46 ASP H 52 1 7 HELIX 34 AD7 PRO D 17 SER D 21 5 5 HELIX 35 AD8 SER D 46 ASP D 52 1 7 SHEET 1 AA1 3 PHE A 4 LEU A 6 0 SHEET 2 AA1 3 MET A 33 SER A 36 1 O CYS A 34 N LEU A 6 SHEET 3 AA1 3 GLU A 68 LEU A 70 1 O GLU A 68 N ILE A 35 SHEET 1 AA2 5 GLU E 68 LEU E 70 0 SHEET 2 AA2 5 MET E 33 SER E 36 1 N ILE E 35 O LEU E 70 SHEET 3 AA2 5 PHE E 4 LEU E 6 1 N PHE E 4 O CYS E 34 SHEET 4 AA2 5 VAL E 111 VAL E 113 1 O VAL E 113 N MET E 5 SHEET 5 AA2 5 ILE E 128 GLU E 129 1 O GLU E 129 N VAL E 112 SHEET 1 AA3 5 GLU C 68 LEU C 70 0 SHEET 2 AA3 5 MET C 33 SER C 36 1 N ILE C 35 O LEU C 70 SHEET 3 AA3 5 PHE C 4 LEU C 6 1 N LEU C 6 O CYS C 34 SHEET 4 AA3 5 VAL C 111 VAL C 113 1 O VAL C 111 N MET C 5 SHEET 5 AA3 5 ILE C 128 GLU C 129 1 O GLU C 129 N VAL C 112 SHEET 1 AA4 5 GLU G 68 LEU G 70 0 SHEET 2 AA4 5 MET G 33 SER G 36 1 N ILE G 35 O LEU G 70 SHEET 3 AA4 5 PHE G 4 LEU G 6 1 N LEU G 6 O CYS G 34 SHEET 4 AA4 5 VAL G 111 VAL G 113 1 O VAL G 111 N MET G 5 SHEET 5 AA4 5 ILE G 128 GLU G 129 1 O GLU G 129 N VAL G 112 SHEET 1 AA5 9 THR B 3 SER B 8 0 SHEET 2 AA5 9 THR B 11 LEU B 16 -1 O ALA B 13 N PHE B 6 SHEET 3 AA5 9 THR H 11 ARG H 15 -1 O GLN H 12 N LEU B 16 SHEET 4 AA5 9 HIS H 2 SER H 8 -1 N SER H 8 O THR H 11 SHEET 5 AA5 9 VAL B 29 VAL B 34 -1 N VAL B 29 O THR H 3 SHEET 6 AA5 9 SER B 37 PRO B 42 -1 O THR B 41 N GLU B 30 SHEET 7 AA5 9 SER H 37 PRO H 42 -1 O ARG H 38 N ILE B 40 SHEET 8 AA5 9 HIS H 28 VAL H 34 -1 N VAL H 34 O SER H 37 SHEET 9 AA5 9 THR B 3 SER B 8 -1 N THR B 3 O VAL H 29 SHEET 1 AA610 ALA D 33 VAL D 34 0 SHEET 2 AA610 SER D 37 PRO D 42 -1 O SER D 37 N VAL D 34 SHEET 3 AA610 HIS D 28 GLU D 30 -1 N GLU D 30 O THR D 41 SHEET 4 AA610 THR F 3 PHE F 7 -1 N THR F 3 O VAL D 29 SHEET 5 AA610 GLN F 12 LEU F 16 -1 O ALA F 13 N PHE F 6 SHEET 6 AA610 THR D 11 LEU D 16 -1 O GLN D 12 N LEU F 16 SHEET 7 AA610 HIS D 2 SER D 8 -1 N SER D 8 O THR D 11 SHEET 8 AA610 HIS F 28 VAL F 34 -1 N VAL F 29 O THR D 3 SHEET 9 AA610 SER F 37 PRO F 42 -1 O THR F 41 N GLU F 30 SHEET 10 AA610 SER D 37 PRO D 42 -1 O ILE D 40 N ARG F 38 CRYST1 93.677 93.677 122.440 90.00 90.00 120.00 P 31 12 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 0.010675 0.006163 0.000000 0.00000 SCALE2 0.000000 0.012326 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008167 0.00000