HEADER TOXIN 02-AUG-23 8KA2 TITLE CRYSTAL STRUCTURE OF THE RID-DEPENDENT TRANSFORMING NADASE DOMAIN TITLE 2 (RDTND)/CALMODULIN-BINDING DOMAIN OF RHO INACTIVATION DOMAIN (RID- TITLE 3 CBD) FROM VIBRIO VULNIFICUS CAVEAT 8KA2 MSE A 2020 HAS WRONG CHIRALITY AT ATOM CA MSE A 2124 HAS CAVEAT 2 8KA2 WRONG CHIRALITY AT ATOM CA MSE B 2020 HAS WRONG CHIRALITY CAVEAT 3 8KA2 AT ATOM CA MSE B 2124 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RDTND-RID CBD; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MARTX TOXIN DUF1-RIDCBD REGION; COMPND 5 SYNONYM: MARTX; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: NCBI ACCESSION ID: WP_015728045.1; ADDITIONAL N- COMPND 9 TERMINUS RESIDUES (GAM) FROM EXPRESSION VECTOR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_COMMON: DUF1-RIDCBD; SOURCE 4 ORGANISM_TAXID: 672; SOURCE 5 GENE: CRN52_02910; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MARTX TOXIN, RDTND-RID, NADASE, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LEE,S.CHOI,J.HWANG,M.H.KIM REVDAT 3 13-NOV-24 8KA2 1 REMARK REVDAT 2 07-AUG-24 8KA2 1 JRNL REVDAT 1 10-JUL-24 8KA2 0 JRNL AUTH S.CHOI,Y.LEE,S.PARK,S.Y.JANG,J.PARK,D.W.OH,S.M.KIM,T.H.KIM, JRNL AUTH 2 G.S.LEE,C.CHO,B.S.KIM,D.LEE,E.H.KIM,H.K.CHEONG,J.H.MOON, JRNL AUTH 3 J.J.SONG,J.HWANG,M.H.KIM JRNL TITL DISSEMINATION OF PATHOGENIC BACTERIA IS REINFORCED BY A JRNL TITL 2 MARTX TOXIN EFFECTOR DUET. JRNL REF NAT COMMUN V. 15 6218 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39043696 JRNL DOI 10.1038/S41467-024-50650-0 REMARK 2 REMARK 2 RESOLUTION. 3.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 3 NUMBER OF REFLECTIONS : 15125 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.288 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.322 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 830 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 6.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 3 REMARK 3 BIN FREE R VALUE : 0.1860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5848 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -1.19000 REMARK 3 B12 (A**2) : 0.18000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.735 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.814 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.764 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5963 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5412 ; 0.035 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8067 ; 1.312 ; 1.638 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12555 ; 2.328 ; 1.584 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 722 ; 6.991 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 357 ;35.601 ;23.249 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 997 ;23.171 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;25.585 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 747 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6742 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1279 ; 0.012 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2909 ; 3.622 ; 5.808 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2908 ; 3.616 ; 5.808 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3624 ; 6.279 ; 8.698 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3625 ; 6.279 ; 8.698 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3054 ; 2.868 ; 5.956 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3055 ; 2.868 ; 5.956 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4444 ; 5.102 ; 8.843 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7266 ;10.794 ;68.993 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7267 ;10.793 ;68.999 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8KA2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300039722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17817 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.380 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% (W/V) PEG 3350 AND 4% (V/V) REMARK 280 TACSIMATE (PH 6.0), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 1956 REMARK 465 ALA A 1957 REMARK 465 MSE A 1958 REMARK 465 GLY A 1959 REMARK 465 GLU A 1960 REMARK 465 ALA A 1961 REMARK 465 SER A 1962 REMARK 465 HIS A 1963 REMARK 465 ASP A 1964 REMARK 465 SER A 1965 REMARK 465 ALA A 1966 REMARK 465 GLU A 1967 REMARK 465 VAL A 1990 REMARK 465 ALA A 1991 REMARK 465 THR A 1992 REMARK 465 ASP A 1993 REMARK 465 LYS A 1994 REMARK 465 TYR A 1995 REMARK 465 VAL A 1996 REMARK 465 PRO A 1997 REMARK 465 VAL A 1998 REMARK 465 PRO A 1999 REMARK 465 GLY A 2000 REMARK 465 PHE A 2001 REMARK 465 GLU A 2002 REMARK 465 ARG A 2003 REMARK 465 VAL A 2004 REMARK 465 ASP A 2005 REMARK 465 VAL A 2006 REMARK 465 TYR A 2372 REMARK 465 ASN A 2373 REMARK 465 THR A 2374 REMARK 465 GLY B 1956 REMARK 465 ALA B 1957 REMARK 465 MSE B 1958 REMARK 465 GLY B 1959 REMARK 465 GLU B 1960 REMARK 465 ALA B 1961 REMARK 465 SER B 1962 REMARK 465 HIS B 1963 REMARK 465 ASP B 1964 REMARK 465 SER B 1965 REMARK 465 ALA B 1966 REMARK 465 GLU B 1967 REMARK 465 ASP B 1987 REMARK 465 ASN B 1988 REMARK 465 ASP B 1989 REMARK 465 VAL B 1990 REMARK 465 ALA B 1991 REMARK 465 THR B 1992 REMARK 465 ASP B 1993 REMARK 465 LYS B 1994 REMARK 465 TYR B 1995 REMARK 465 VAL B 1996 REMARK 465 PRO B 1997 REMARK 465 VAL B 1998 REMARK 465 PRO B 1999 REMARK 465 GLY B 2000 REMARK 465 PHE B 2001 REMARK 465 GLU B 2002 REMARK 465 ARG B 2003 REMARK 465 VAL B 2004 REMARK 465 ASP B 2005 REMARK 465 VAL B 2006 REMARK 465 ASP B 2007 REMARK 465 THR B 2099 REMARK 465 ASP B 2100 REMARK 465 GLY B 2101 REMARK 465 LYS B 2102 REMARK 465 LYS B 2103 REMARK 465 VAL B 2176 REMARK 465 ARG B 2177 REMARK 465 LEU B 2178 REMARK 465 ALA B 2230 REMARK 465 VAL B 2231 REMARK 465 LYS B 2232 REMARK 465 VAL B 2233 REMARK 465 ARG B 2234 REMARK 465 PHE B 2235 REMARK 465 ASP B 2236 REMARK 465 ALA B 2237 REMARK 465 LEU B 2238 REMARK 465 SER B 2239 REMARK 465 HIS B 2240 REMARK 465 GLU B 2241 REMARK 465 ARG B 2242 REMARK 465 GLN B 2243 REMARK 465 ALA B 2244 REMARK 465 GLU B 2245 REMARK 465 LEU B 2246 REMARK 465 LEU B 2247 REMARK 465 ALA B 2248 REMARK 465 ASP B 2249 REMARK 465 ASN B 2250 REMARK 465 PRO B 2251 REMARK 465 ASP B 2252 REMARK 465 GLY B 2253 REMARK 465 TYR B 2254 REMARK 465 LYS B 2255 REMARK 465 ALA B 2256 REMARK 465 ASP B 2257 REMARK 465 THR B 2258 REMARK 465 LEU B 2259 REMARK 465 VAL B 2260 REMARK 465 GLU B 2261 REMARK 465 LEU B 2262 REMARK 465 TYR B 2372 REMARK 465 ASN B 2373 REMARK 465 THR B 2374 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 HIS A2073 -118.64 58.65 REMARK 500 ALA A2074 -138.87 52.66 REMARK 500 ALA A2136 -130.83 59.70 REMARK 500 ALA A2164 -55.94 72.55 REMARK 500 GLN A2165 -5.39 80.59 REMARK 500 GLU A2173 -71.11 -85.69 REMARK 500 LYS A2213 -116.95 43.12 REMARK 500 ALA A2227 -121.77 50.57 REMARK 500 SER A2309 65.48 -157.69 REMARK 500 ASN A2333 -95.53 -116.16 REMARK 500 HIS A2354 -66.43 -109.62 REMARK 500 HIS A2355 -114.47 49.40 REMARK 500 GLN A2364 2.44 -67.42 REMARK 500 SER B2009 -37.18 -140.12 REMARK 500 ASP B2010 -47.29 69.40 REMARK 500 TRP B2082 69.50 -156.57 REMARK 500 ALA B2136 -58.84 72.77 REMARK 500 GLU B2173 -84.09 -116.54 REMARK 500 VAL B2185 -71.18 -124.28 REMARK 500 LEU B2266 -10.22 72.04 REMARK 500 LYS B2308 72.27 -158.58 REMARK 500 ASN B2349 -9.76 75.74 REMARK 500 GLU B2366 -62.86 -137.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE A2081 -12.10 REMARK 500 TRP A2370 -10.59 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8KA2 A 1959 2374 UNP MARTX_VIBVL DBREF2 8KA2 A A0A2S3R7M0 1959 2374 DBREF1 8KA2 B 1959 2374 UNP MARTX_VIBVL DBREF2 8KA2 B A0A2S3R7M0 1959 2374 SEQADV 8KA2 GLY A 1956 UNP A0A2S3R7M CLONING ARTIFACT SEQADV 8KA2 ALA A 1957 UNP A0A2S3R7M CLONING ARTIFACT SEQADV 8KA2 MSE A 1958 UNP A0A2S3R7M CLONING ARTIFACT SEQADV 8KA2 GLY B 1956 UNP A0A2S3R7M CLONING ARTIFACT SEQADV 8KA2 ALA B 1957 UNP A0A2S3R7M CLONING ARTIFACT SEQADV 8KA2 MSE B 1958 UNP A0A2S3R7M CLONING ARTIFACT SEQRES 1 A 419 GLY ALA MSE GLY GLU ALA SER HIS ASP SER ALA GLU SER SEQRES 2 A 419 LEU VAL ALA ALA ARG ALA GLU LYS VAL ALA ASN LEU TYR SEQRES 3 A 419 ARG TRP LEU ASP THR ASP ASN ASP VAL ALA THR ASP LYS SEQRES 4 A 419 TYR VAL PRO VAL PRO GLY PHE GLU ARG VAL ASP VAL ASP SEQRES 5 A 419 VAL SER ASP GLU VAL LYS GLN ARG MSE ILE GLN SER MSE SEQRES 6 A 419 SER GLY TYR ILE GLU HIS THR ASP ASN GLN VAL PRO LYS SEQRES 7 A 419 ASP GLN ALA GLU ALA LEU ALA THR LEU PHE VAL GLU SER SEQRES 8 A 419 THR LEU ASP TYR ASP TRP ASP LYS ARG VAL GLU PHE LEU SEQRES 9 A 419 THR LYS LEU GLU SER TYR GLY TYR SER PHE GLU ALA PRO SEQRES 10 A 419 HIS ALA GLU LYS SER ILE VAL SER PHE TRP SER GLY LYS SEQRES 11 A 419 ASN PHE LYS GLN TYR ARG ASP ILE LEU ASP ASN ALA GLN SEQRES 12 A 419 THR ASP GLY LYS LYS VAL VAL TYR ASP ILE ASP VAL LYS SEQRES 13 A 419 GLY ASN ALA PHE ALA ILE ASP LEU ASN LYS HIS LEU MSE SEQRES 14 A 419 ARG TRP GLY GLY LEU PHE LEU ASP PRO ASP ASN ALA GLU SEQRES 15 A 419 GLN ASN GLN LEU LYS SER SER ILE ASP ALA ALA THR PHE SEQRES 16 A 419 SER ASN THR GLY PHE TRP SER SER VAL TYR ALA THR GLY SEQRES 17 A 419 ALA GLN ASN ASP VAL TYR VAL ILE ALA GLU GLY GLY VAL SEQRES 18 A 419 ARG LEU GLY ASN TYR PHE TRP ASN VAL GLU LEU PRO ALA SEQRES 19 A 419 LEU ARG GLN LEU GLN ARG GLU GLY LEU VAL GLY GLU ILE SEQRES 20 A 419 ARG LEU LEU ASP LYS PRO VAL SER GLU TYR LYS ASP LEU SEQRES 21 A 419 PRO ALA ASP GLN ILE GLY ARG ARG LEU THR ASP ALA GLY SEQRES 22 A 419 VAL ALA VAL LYS VAL ARG PHE ASP ALA LEU SER HIS GLU SEQRES 23 A 419 ARG GLN ALA GLU LEU LEU ALA ASP ASN PRO ASP GLY TYR SEQRES 24 A 419 LYS ALA ASP THR LEU VAL GLU LEU ASP VAL LYS LEU SER SEQRES 25 A 419 ALA ILE ASP SER MSE LEU ARG GLU SER LEU PRO PHE TYR SEQRES 26 A 419 SER LEU ARG THR GLU ARG ASN LEU LEU VAL GLN GLU GLY SEQRES 27 A 419 GLU GLU GLY PHE GLU VAL ARG SER TRP PRO GLY ILE ASP SEQRES 28 A 419 GLY LYS SER LYS THR ILE LEU LEU ASP ASN PRO GLU ASP SEQRES 29 A 419 ALA ALA GLN GLN LYS SER ILE GLU ARG PHE ILE LEU ALA SEQRES 30 A 419 ASN PHE ASP ASN PHE GLU GLN MSE PRO ASP GLU LEU PHE SEQRES 31 A 419 LEU VAL ASP ASN LYS VAL LEU SER HIS HIS ASP GLY ARG SEQRES 32 A 419 THR ARG ILE ILE ALA GLN LYS GLU ASP GLY ALA TRP THR SEQRES 33 A 419 TYR ASN THR SEQRES 1 B 419 GLY ALA MSE GLY GLU ALA SER HIS ASP SER ALA GLU SER SEQRES 2 B 419 LEU VAL ALA ALA ARG ALA GLU LYS VAL ALA ASN LEU TYR SEQRES 3 B 419 ARG TRP LEU ASP THR ASP ASN ASP VAL ALA THR ASP LYS SEQRES 4 B 419 TYR VAL PRO VAL PRO GLY PHE GLU ARG VAL ASP VAL ASP SEQRES 5 B 419 VAL SER ASP GLU VAL LYS GLN ARG MSE ILE GLN SER MSE SEQRES 6 B 419 SER GLY TYR ILE GLU HIS THR ASP ASN GLN VAL PRO LYS SEQRES 7 B 419 ASP GLN ALA GLU ALA LEU ALA THR LEU PHE VAL GLU SER SEQRES 8 B 419 THR LEU ASP TYR ASP TRP ASP LYS ARG VAL GLU PHE LEU SEQRES 9 B 419 THR LYS LEU GLU SER TYR GLY TYR SER PHE GLU ALA PRO SEQRES 10 B 419 HIS ALA GLU LYS SER ILE VAL SER PHE TRP SER GLY LYS SEQRES 11 B 419 ASN PHE LYS GLN TYR ARG ASP ILE LEU ASP ASN ALA GLN SEQRES 12 B 419 THR ASP GLY LYS LYS VAL VAL TYR ASP ILE ASP VAL LYS SEQRES 13 B 419 GLY ASN ALA PHE ALA ILE ASP LEU ASN LYS HIS LEU MSE SEQRES 14 B 419 ARG TRP GLY GLY LEU PHE LEU ASP PRO ASP ASN ALA GLU SEQRES 15 B 419 GLN ASN GLN LEU LYS SER SER ILE ASP ALA ALA THR PHE SEQRES 16 B 419 SER ASN THR GLY PHE TRP SER SER VAL TYR ALA THR GLY SEQRES 17 B 419 ALA GLN ASN ASP VAL TYR VAL ILE ALA GLU GLY GLY VAL SEQRES 18 B 419 ARG LEU GLY ASN TYR PHE TRP ASN VAL GLU LEU PRO ALA SEQRES 19 B 419 LEU ARG GLN LEU GLN ARG GLU GLY LEU VAL GLY GLU ILE SEQRES 20 B 419 ARG LEU LEU ASP LYS PRO VAL SER GLU TYR LYS ASP LEU SEQRES 21 B 419 PRO ALA ASP GLN ILE GLY ARG ARG LEU THR ASP ALA GLY SEQRES 22 B 419 VAL ALA VAL LYS VAL ARG PHE ASP ALA LEU SER HIS GLU SEQRES 23 B 419 ARG GLN ALA GLU LEU LEU ALA ASP ASN PRO ASP GLY TYR SEQRES 24 B 419 LYS ALA ASP THR LEU VAL GLU LEU ASP VAL LYS LEU SER SEQRES 25 B 419 ALA ILE ASP SER MSE LEU ARG GLU SER LEU PRO PHE TYR SEQRES 26 B 419 SER LEU ARG THR GLU ARG ASN LEU LEU VAL GLN GLU GLY SEQRES 27 B 419 GLU GLU GLY PHE GLU VAL ARG SER TRP PRO GLY ILE ASP SEQRES 28 B 419 GLY LYS SER LYS THR ILE LEU LEU ASP ASN PRO GLU ASP SEQRES 29 B 419 ALA ALA GLN GLN LYS SER ILE GLU ARG PHE ILE LEU ALA SEQRES 30 B 419 ASN PHE ASP ASN PHE GLU GLN MSE PRO ASP GLU LEU PHE SEQRES 31 B 419 LEU VAL ASP ASN LYS VAL LEU SER HIS HIS ASP GLY ARG SEQRES 32 B 419 THR ARG ILE ILE ALA GLN LYS GLU ASP GLY ALA TRP THR SEQRES 33 B 419 TYR ASN THR MODRES 8KA2 MSE A 2016 MET MODIFIED RESIDUE MODRES 8KA2 MSE A 2020 MET MODIFIED RESIDUE MODRES 8KA2 MSE A 2124 MET MODIFIED RESIDUE MODRES 8KA2 MSE A 2272 MET MODIFIED RESIDUE MODRES 8KA2 MSE A 2340 MET MODIFIED RESIDUE MODRES 8KA2 MSE B 2016 MET MODIFIED RESIDUE MODRES 8KA2 MSE B 2020 MET MODIFIED RESIDUE MODRES 8KA2 MSE B 2124 MET MODIFIED RESIDUE MODRES 8KA2 MSE B 2272 MET MODIFIED RESIDUE MODRES 8KA2 MSE B 2340 MET MODIFIED RESIDUE HET MSE A2016 8 HET MSE A2020 8 HET MSE A2124 8 HET MSE A2272 8 HET MSE A2340 8 HET MSE B2016 8 HET MSE B2020 8 HET MSE B2124 8 HET MSE B2272 8 HET MSE B2340 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 10(C5 H11 N O2 SE) HELIX 1 AA1 SER A 1968 THR A 1986 1 19 HELIX 2 AA2 ASP A 1987 ASP A 1989 5 3 HELIX 3 AA3 ASP A 2010 HIS A 2026 1 17 HELIX 4 AA4 THR A 2041 ASP A 2049 1 9 HELIX 5 AA5 TRP A 2052 LEU A 2062 1 11 HELIX 6 AA6 PHE A 2087 GLN A 2098 1 12 HELIX 7 AA7 TYR A 2106 VAL A 2110 5 5 HELIX 8 AA8 GLY A 2112 GLY A 2128 1 17 HELIX 9 AA9 GLN A 2138 GLY A 2163 1 26 HELIX 10 AB1 ASN A 2180 VAL A 2185 1 6 HELIX 11 AB2 VAL A 2185 GLU A 2196 1 12 HELIX 12 AB3 PRO A 2208 TYR A 2212 5 5 HELIX 13 AB4 PRO A 2216 ILE A 2220 5 5 HELIX 14 AB5 ASP A 2236 LEU A 2238 5 3 HELIX 15 AB6 HIS A 2240 ASP A 2249 1 10 HELIX 16 AB7 LEU A 2266 MSE A 2272 1 7 HELIX 17 AB8 PHE A 2279 ARG A 2286 1 8 HELIX 18 AB9 ASP A 2319 ASN A 2333 1 15 HELIX 19 AC1 LEU B 1969 LEU B 1984 1 16 HELIX 20 AC2 VAL B 2012 GLU B 2025 1 14 HELIX 21 AC3 ALA B 2036 ASP B 2049 1 14 HELIX 22 AC4 ASP B 2051 SER B 2064 1 14 HELIX 23 AC5 LYS B 2088 GLN B 2098 1 11 HELIX 24 AC6 TYR B 2106 ASP B 2109 5 4 HELIX 25 AC7 VAL B 2110 PHE B 2130 1 21 HELIX 26 AC8 ASP B 2132 ALA B 2136 5 5 HELIX 27 AC9 GLU B 2137 ALA B 2164 1 28 HELIX 28 AD1 ASN B 2180 VAL B 2185 1 6 HELIX 29 AD2 VAL B 2185 GLU B 2196 1 12 HELIX 30 AD3 LEU B 2266 LEU B 2277 1 12 HELIX 31 AD4 PHE B 2279 ARG B 2286 1 8 HELIX 32 AD5 ASP B 2319 PHE B 2334 1 16 SHEET 1 AA1 3 TYR A2169 ILE A2171 0 SHEET 2 AA1 3 ARG A2203 LEU A2205 1 O LEU A2205 N VAL A2170 SHEET 3 AA1 3 ARG A2222 ARG A2223 -1 O ARG A2222 N LEU A2204 SHEET 1 AA2 2 GLY A2228 ARG A2234 0 SHEET 2 AA2 2 LEU A2259 LYS A2265 -1 O VAL A2264 N VAL A2229 SHEET 1 AA3 5 LEU A2288 LEU A2289 0 SHEET 2 AA3 5 PHE A2297 SER A2301 -1 O ARG A2300 N LEU A2289 SHEET 3 AA3 5 LYS A2310 LEU A2314 -1 O LYS A2310 N VAL A2299 SHEET 4 AA3 5 GLU A2343 VAL A2347 1 O LEU A2344 N LEU A2313 SHEET 5 AA3 5 LYS A2350 LEU A2352 -1 O LEU A2352 N PHE A2345 SHEET 1 AA4 5 LEU B2288 GLU B2292 0 SHEET 2 AA4 5 PHE B2297 SER B2301 -1 O ARG B2300 N LEU B2289 SHEET 3 AA4 5 LYS B2310 LEU B2314 -1 O LYS B2310 N VAL B2299 SHEET 4 AA4 5 GLU B2343 VAL B2347 1 O LEU B2344 N THR B2311 SHEET 5 AA4 5 LYS B2350 SER B2353 -1 O LYS B2350 N VAL B2347 LINK C ARG A2015 N MSE A2016 1555 1555 1.35 LINK C MSE A2016 N ILE A2017 1555 1555 1.33 LINK C SER A2019 N MSE A2020 1555 1555 1.34 LINK C MSE A2020 N SER A2021 1555 1555 1.34 LINK C LEU A2123 N MSE A2124 1555 1555 1.34 LINK C MSE A2124 N ARG A2125 1555 1555 1.34 LINK C SER A2271 N MSE A2272 1555 1555 1.34 LINK C MSE A2272 N LEU A2273 1555 1555 1.32 LINK C GLN A2339 N MSE A2340 1555 1555 1.35 LINK C MSE A2340 N PRO A2341 1555 1555 1.37 LINK C ARG B2015 N MSE B2016 1555 1555 1.33 LINK C MSE B2016 N ILE B2017 1555 1555 1.33 LINK C SER B2019 N MSE B2020 1555 1555 1.34 LINK C MSE B2020 N SER B2021 1555 1555 1.34 LINK C LEU B2123 N MSE B2124 1555 1555 1.34 LINK C MSE B2124 N ARG B2125 1555 1555 1.34 LINK C SER B2271 N MSE B2272 1555 1555 1.34 LINK C MSE B2272 N LEU B2273 1555 1555 1.34 LINK C GLN B2339 N MSE B2340 1555 1555 1.34 LINK C MSE B2340 N PRO B2341 1555 1555 1.35 CRYST1 207.726 207.726 54.647 90.00 90.00 120.00 P 6 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 0.004814 0.002779 0.000000 0.00000 SCALE2 0.000000 0.005559 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018299 0.00000