HEADER RNA BINDING PROTEIN/RNA 02-DEC-18 6IV9 TITLE THE CAS13D BINARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAS13D; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CRRNA (50-MER); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED RUMINOCOCCUS SP; SOURCE 3 ORGANISM_TAXID: 165186; SOURCE 4 GENE: SAMEA3545300_02264; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: UNCULTURED RUMINOCOCCUS SP.; SOURCE 9 ORGANISM_TAXID: 165186; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRISPR, CAS13D, CRRNA, BINARY COMPLEX, RNA BINDING PROTEIN-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHANG,Y.M.YE,W.W.YE,S.Y.OUYANG REVDAT 3 22-NOV-23 6IV9 1 LINK REVDAT 2 26-JUN-19 6IV9 1 JRNL REVDAT 1 19-JUN-19 6IV9 0 JRNL AUTH B.ZHANG,Y.YE,W.YE,V.PERCULIJA,H.JIANG,Y.CHEN,Y.LI,J.CHEN, JRNL AUTH 2 J.LIN,S.WANG,Q.CHEN,Y.S.HAN,S.OUYANG JRNL TITL TWO HEPN DOMAINS DICTATE CRISPR RNA MATURATION AND TARGET JRNL TITL 2 CLEAVAGE IN CAS13D. JRNL REF NAT COMMUN V. 10 2544 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31186424 JRNL DOI 10.1038/S41467-019-10507-3 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 115013 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6055 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8436 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 414 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7106 REMARK 3 NUCLEIC ACID ATOMS : 1054 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 475 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.41000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -1.73000 REMARK 3 B12 (A**2) : 0.00000 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): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.369 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8419 ; 0.015 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 7186 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11542 ; 1.735 ; 1.596 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16908 ; 1.170 ; 1.741 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 879 ; 5.828 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 401 ;35.343 ;23.042 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1435 ;16.840 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;20.005 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1135 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8627 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1604 ; 0.002 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6IV9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1300009991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 121127 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 100.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 14.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6IV8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (8% (V/V) TACSIMATE (PH 7.0), 17% REMARK 280 (W/V) POLYETHYLENE GLYCOL 3350), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 36.11200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.64150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.24050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.64150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.11200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.24050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 LYS A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 MET A 7 REMARK 465 LYS A 8 REMARK 465 PRO A 9 REMARK 465 ARG A 10 REMARK 465 GLU A 11 REMARK 465 LEU A 12 REMARK 465 ARG A 13 REMARK 465 GLU A 14 REMARK 465 ALA A 15 REMARK 465 GLN A 16 REMARK 465 LYS A 17 REMARK 465 LYS A 18 REMARK 465 ALA A 19 REMARK 465 ARG A 20 REMARK 465 GLN A 21 REMARK 465 LEU A 22 REMARK 465 LYS A 23 REMARK 465 ALA A 24 REMARK 465 ALA A 25 REMARK 465 GLU A 26 REMARK 465 ILE A 27 REMARK 465 ASN A 28 REMARK 465 ASN A 29 REMARK 465 ASN A 30 REMARK 465 ALA A 31 REMARK 465 ALA A 32 REMARK 465 PRO A 33 REMARK 465 ALA A 34 REMARK 465 ILE A 35 REMARK 465 ALA A 36 REMARK 465 ALA A 37 REMARK 465 MET A 38 REMARK 465 PRO A 39 REMARK 465 ALA A 40 REMARK 465 ALA A 41 REMARK 465 GLU A 42 REMARK 465 VAL A 43 REMARK 465 ILE A 44 REMARK 465 ALA A 45 REMARK 465 PRO A 46 REMARK 465 VAL A 47 REMARK 465 ALA A 48 REMARK 465 LEU A 923 REMARK 465 GLU A 924 REMARK 465 HIS A 925 REMARK 465 HIS A 926 REMARK 465 HIS A 927 REMARK 465 HIS A 928 REMARK 465 HIS A 929 REMARK 465 HIS A 930 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 GLN A 557 N GLN A 557 CA 0.129 REMARK 500 A B -29 O3' C B -28 P -0.081 REMARK 500 C B -14 P C B -14 OP1 -0.126 REMARK 500 C B -14 P C B -14 OP2 -0.133 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 ASP A 207 CB - CA - C ANGL. DEV. = 12.5 DEGREES REMARK 500 U B -24 O5' - P - OP2 ANGL. DEV. = -6.0 DEGREES REMARK 500 U B 1 O5' - P - OP2 ANGL. DEV. = -6.1 DEGREES REMARK 500 A B 14 O5' - P - OP1 ANGL. DEV. = 7.3 DEGREES REMARK 500 C B 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 C B 17 O5' - P - OP2 ANGL. DEV. = -5.7 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 ASP A 165 53.92 -95.23 REMARK 500 TYR A 206 -57.42 -135.96 REMARK 500 PHE A 209 -76.11 -90.74 REMARK 500 ARG A 417 -58.95 -124.59 REMARK 500 CYS A 544 58.46 -147.98 REMARK 500 ALA A 639 -155.91 -133.25 REMARK 500 GLU A 871 89.33 -61.91 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 ARG A 158 0.26 SIDE CHAIN REMARK 500 ARG A 268 0.18 SIDE CHAIN REMARK 500 ARG A 390 0.09 SIDE CHAIN REMARK 500 ARG A 428 0.10 SIDE CHAIN REMARK 500 ARG A 601 0.08 SIDE CHAIN REMARK 500 ARG A 668 0.14 SIDE CHAIN REMARK 500 ARG A 719 0.22 SIDE CHAIN REMARK 500 ARG A 789 0.27 SIDE CHAIN REMARK 500 ARG A 820 0.12 SIDE CHAIN REMARK 500 ARG A 833 0.11 SIDE CHAIN REMARK 500 ARG A 843 0.09 SIDE CHAIN REMARK 500 ARG A 863 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 137 O REMARK 620 2 GLU A 140 O 103.2 REMARK 620 3 HOH A1294 O 92.0 85.5 REMARK 620 4 HOH A1357 O 87.9 77.8 162.9 REMARK 620 5 HOH A1395 O 85.2 171.5 93.3 103.8 REMARK 620 6 HOH A1402 O 173.6 82.3 91.6 90.3 89.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1203 O REMARK 620 2 HOH A1272 O 77.8 REMARK 620 3 C B -7 OP1 158.8 81.3 REMARK 620 4 HOH B 205 O 90.3 80.4 89.9 REMARK 620 5 HOH B 221 O 78.4 80.9 94.6 159.9 REMARK 620 6 HOH B 308 O 102.2 178.8 98.6 100.8 97.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 101 DBREF1 6IV9 A 1 922 UNP A0A1C5SD84_9FIRM DBREF2 6IV9 A A0A1C5SD84 1 922 DBREF 6IV9 B -30 20 PDB 6IV9 6IV9 -30 20 SEQADV 6IV9 ALA A 288 UNP A0A1C5SD8 ARG 288 ENGINEERED MUTATION SEQADV 6IV9 ALA A 823 UNP A0A1C5SD8 ARG 823 ENGINEERED MUTATION SEQADV 6IV9 LEU A 923 UNP A0A1C5SD8 EXPRESSION TAG SEQADV 6IV9 GLU A 924 UNP A0A1C5SD8 EXPRESSION TAG SEQADV 6IV9 HIS A 925 UNP A0A1C5SD8 EXPRESSION TAG SEQADV 6IV9 HIS A 926 UNP A0A1C5SD8 EXPRESSION TAG SEQADV 6IV9 HIS A 927 UNP A0A1C5SD8 EXPRESSION TAG SEQADV 6IV9 HIS A 928 UNP A0A1C5SD8 EXPRESSION TAG SEQADV 6IV9 HIS A 929 UNP A0A1C5SD8 EXPRESSION TAG SEQADV 6IV9 HIS A 930 UNP A0A1C5SD8 EXPRESSION TAG SEQRES 1 A 930 MET ALA LYS LYS ASN LYS MET LYS PRO ARG GLU LEU ARG SEQRES 2 A 930 GLU ALA GLN LYS LYS ALA ARG GLN LEU LYS ALA ALA GLU SEQRES 3 A 930 ILE ASN ASN ASN ALA ALA PRO ALA ILE ALA ALA MET PRO SEQRES 4 A 930 ALA ALA GLU VAL ILE ALA PRO VAL ALA GLU LYS LYS LYS SEQRES 5 A 930 SER SER VAL LYS ALA ALA GLY MET LYS SER ILE LEU VAL SEQRES 6 A 930 SER GLU ASN LYS MET TYR ILE THR SER PHE GLY LYS GLY SEQRES 7 A 930 ASN SER ALA VAL LEU GLU TYR GLU VAL ASP ASN ASN ASP SEQRES 8 A 930 TYR ASN LYS THR GLN LEU SER SER LYS ASP ASN SER ASN SEQRES 9 A 930 ILE GLU LEU GLY ASP VAL ASN GLU VAL ASN ILE THR PHE SEQRES 10 A 930 SER SER LYS HIS GLY PHE GLY SER GLY VAL GLU ILE ASN SEQRES 11 A 930 THR SER ASN PRO THR HIS ARG SER GLY GLU SER SER PRO SEQRES 12 A 930 VAL ARG GLY ASP MET LEU GLY LEU LYS SER GLU LEU GLU SEQRES 13 A 930 LYS ARG PHE PHE GLY LYS THR PHE ASP ASP ASN ILE HIS SEQRES 14 A 930 ILE GLN LEU ILE TYR ASN ILE LEU ASP ILE GLU LYS ILE SEQRES 15 A 930 LEU ALA VAL TYR VAL THR ASN ILE VAL TYR ALA LEU ASN SEQRES 16 A 930 ASN MET LEU GLY ILE LYS ASP SER GLU SER TYR ASP ASP SEQRES 17 A 930 PHE MET GLY TYR LEU SER ALA ARG ASN THR TYR GLU VAL SEQRES 18 A 930 PHE THR HIS PRO ASP LYS SER ASN LEU SER ASP LYS VAL SEQRES 19 A 930 LYS GLY ASN ILE LYS LYS SER LEU SER LYS PHE ASN ASP SEQRES 20 A 930 LEU LEU LYS THR LYS ARG LEU GLY TYR PHE GLY LEU GLU SEQRES 21 A 930 GLU PRO LYS THR LYS ASP THR ARG ALA SER GLU ALA TYR SEQRES 22 A 930 LYS LYS ARG VAL TYR HIS MET LEU ALA ILE VAL GLY GLN SEQRES 23 A 930 ILE ALA GLN CYS VAL PHE HIS ASP LYS SER GLY ALA LYS SEQRES 24 A 930 ARG PHE ASP LEU TYR SER PHE ILE ASN ASN ILE ASP PRO SEQRES 25 A 930 GLU TYR ARG ASP THR LEU ASP TYR LEU VAL GLU GLU ARG SEQRES 26 A 930 LEU LYS SER ILE ASN LYS ASP PHE ILE GLU GLY ASN LYS SEQRES 27 A 930 VAL ASN ILE SER LEU LEU ILE ASP MET MET LYS GLY TYR SEQRES 28 A 930 GLU ALA ASP ASP ILE ILE ARG LEU TYR TYR ASP PHE ILE SEQRES 29 A 930 VAL LEU LYS SER GLN LYS ASN LEU GLY PHE SER ILE LYS SEQRES 30 A 930 LYS LEU ARG GLU LYS MET LEU GLU GLU TYR GLY PHE ARG SEQRES 31 A 930 PHE LYS ASP LYS GLN TYR ASP SER VAL ARG SER LYS MET SEQRES 32 A 930 TYR LYS LEU MET ASP PHE LEU LEU PHE CYS ASN TYR TYR SEQRES 33 A 930 ARG ASN ASP VAL ALA ALA GLY GLU ALA LEU VAL ARG LYS SEQRES 34 A 930 LEU ARG PHE SER MET THR ASP ASP GLU LYS GLU GLY ILE SEQRES 35 A 930 TYR ALA ASP GLU ALA ALA LYS LEU TRP GLY LYS PHE ARG SEQRES 36 A 930 ASN ASP PHE GLU ASN ILE ALA ASP HIS MET ASN GLY ASP SEQRES 37 A 930 VAL ILE LYS GLU LEU GLY LYS ALA ASP MET ASP PHE ASP SEQRES 38 A 930 GLU LYS ILE LEU ASP SER GLU LYS LYS ASN ALA SER ASP SEQRES 39 A 930 LEU LEU TYR PHE SER LYS MET ILE TYR MET LEU THR TYR SEQRES 40 A 930 PHE LEU ASP GLY LYS GLU ILE ASN ASP LEU LEU THR THR SEQRES 41 A 930 LEU ILE SER LYS PHE ASP ASN ILE LYS GLU PHE LEU LYS SEQRES 42 A 930 ILE MET LYS SER SER ALA VAL ASP VAL GLU CYS GLU LEU SEQRES 43 A 930 THR ALA GLY TYR LYS LEU PHE ASN ASP SER GLN ARG ILE SEQRES 44 A 930 THR ASN GLU LEU PHE ILE VAL LYS ASN ILE ALA SER MET SEQRES 45 A 930 ARG LYS PRO ALA ALA SER ALA LYS LEU THR MET PHE ARG SEQRES 46 A 930 ASP ALA LEU THR ILE LEU GLY ILE ASP ASP ASN ILE THR SEQRES 47 A 930 ASP ASP ARG ILE SER GLU ILE LEU LYS LEU LYS GLU LYS SEQRES 48 A 930 GLY LYS GLY ILE HIS GLY LEU ARG ASN PHE ILE THR ASN SEQRES 49 A 930 ASN VAL ILE GLU SER SER ARG PHE VAL TYR LEU ILE LYS SEQRES 50 A 930 TYR ALA ASN ALA GLN LYS ILE ARG GLU VAL ALA LYS ASN SEQRES 51 A 930 GLU LYS VAL VAL MET PHE VAL LEU GLY GLY ILE PRO ASP SEQRES 52 A 930 THR GLN ILE GLU ARG TYR TYR LYS SER CYS VAL GLU PHE SEQRES 53 A 930 PRO ASP MET ASN SER SER LEU GLU ALA LYS ARG SER GLU SEQRES 54 A 930 LEU ALA ARG MET ILE LYS ASN ILE SER PHE ASP ASP PHE SEQRES 55 A 930 LYS ASN VAL LYS GLN GLN ALA LYS GLY ARG GLU ASN VAL SEQRES 56 A 930 ALA LYS GLU ARG ALA LYS ALA VAL ILE GLY LEU TYR LEU SEQRES 57 A 930 THR VAL MET TYR LEU LEU VAL LYS ASN LEU VAL ASN VAL SEQRES 58 A 930 ASN ALA ARG TYR VAL ILE ALA ILE HIS CYS LEU GLU ARG SEQRES 59 A 930 ASP PHE GLY LEU TYR LYS GLU ILE ILE PRO GLU LEU ALA SEQRES 60 A 930 SER LYS ASN LEU LYS ASN ASP TYR ARG ILE LEU SER GLN SEQRES 61 A 930 THR LEU CYS GLU LEU CYS ASP ASP ARG ASN GLU SER SER SEQRES 62 A 930 ASN LEU PHE LEU LYS LYS ASN LYS ARG LEU ARG LYS CYS SEQRES 63 A 930 VAL GLU VAL ASP ILE ASN ASN ALA ASP SER SER MET THR SEQRES 64 A 930 ARG LYS TYR ALA ASN CYS ILE ALA HIS LEU THR VAL VAL SEQRES 65 A 930 ARG GLU LEU LYS GLU TYR ILE GLY ASP ILE ARG THR VAL SEQRES 66 A 930 ASP SER TYR PHE SER ILE TYR HIS TYR VAL MET GLN ARG SEQRES 67 A 930 CYS ILE THR LYS ARG GLY ASP ASP THR LYS GLN GLU GLU SEQRES 68 A 930 LYS ILE LYS TYR GLU ASP ASP LEU LEU LYS ASN HIS GLY SEQRES 69 A 930 TYR THR LYS ASP PHE VAL LYS ALA LEU ASN SER PRO PHE SEQRES 70 A 930 GLY TYR ASN ILE PRO ARG PHE LYS ASN LEU SER ILE GLU SEQRES 71 A 930 GLN LEU PHE ASP ARG ASN GLU TYR LEU THR GLU LYS LEU SEQRES 72 A 930 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 50 C A C U G G U G C A A A U SEQRES 2 B 50 U U G C A C U A G U C U A SEQRES 3 B 50 A A A C U C C U C G A U U SEQRES 4 B 50 A C A U A C A C A A A HET MG A1001 1 HET MG B 101 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *475(H2 O) HELIX 1 AA1 SER A 53 GLY A 59 1 7 HELIX 2 AA2 GLY A 122 VAL A 127 5 6 HELIX 3 AA3 LEU A 151 GLY A 161 1 11 HELIX 4 AA4 ASN A 167 LEU A 198 1 32 HELIX 5 AA5 PHE A 209 LEU A 213 5 5 HELIX 6 AA6 THR A 218 HIS A 224 1 7 HELIX 7 AA7 SER A 231 LYS A 252 1 22 HELIX 8 AA8 ARG A 253 GLY A 258 5 6 HELIX 9 AA9 ASP A 266 PHE A 292 1 27 HELIX 10 AB1 SER A 305 ILE A 310 1 6 HELIX 11 AB2 ASP A 311 LYS A 331 1 21 HELIX 12 AB3 ASP A 332 ASN A 337 1 6 HELIX 13 AB4 ASN A 337 MET A 348 1 12 HELIX 14 AB5 GLU A 352 LEU A 366 1 15 HELIX 15 AB6 LYS A 367 LEU A 372 5 6 HELIX 16 AB7 SER A 375 TYR A 387 1 13 HELIX 17 AB8 GLY A 388 SER A 398 5 11 HELIX 18 AB9 VAL A 399 ARG A 417 1 19 HELIX 19 AC1 ASP A 419 SER A 433 1 15 HELIX 20 AC2 THR A 435 MET A 465 1 31 HELIX 21 AC3 ASN A 466 ALA A 476 1 11 HELIX 22 AC4 ASP A 481 ASP A 486 5 6 HELIX 23 AC5 ASN A 491 LEU A 495 5 5 HELIX 24 AC6 LEU A 496 THR A 506 1 11 HELIX 25 AC7 TYR A 507 LEU A 509 5 3 HELIX 26 AC8 ASP A 510 LYS A 536 1 27 HELIX 27 AC9 THR A 547 ASN A 554 5 8 HELIX 28 AD1 ASP A 555 SER A 571 1 17 HELIX 29 AD2 LYS A 580 GLY A 592 1 13 HELIX 30 AD3 THR A 598 LYS A 607 1 10 HELIX 31 AD4 HIS A 616 VAL A 626 1 11 HELIX 32 AD5 SER A 629 ALA A 639 1 11 HELIX 33 AD6 ASN A 640 ALA A 648 1 9 HELIX 34 AD7 ASN A 650 ILE A 661 1 12 HELIX 35 AD8 PRO A 662 VAL A 674 1 13 HELIX 36 AD9 SER A 682 ILE A 697 1 16 HELIX 37 AE1 SER A 698 LYS A 703 5 6 HELIX 38 AE2 ARG A 712 GLU A 761 1 50 HELIX 39 AE3 ILE A 762 ALA A 767 5 6 HELIX 40 AE4 ASN A 770 TYR A 775 5 6 HELIX 41 AE5 ARG A 776 ARG A 789 1 14 HELIX 42 AE6 ASN A 794 ASN A 800 1 7 HELIX 43 AE7 ASN A 800 ALA A 814 1 15 HELIX 44 AE8 ASP A 815 HIS A 828 1 14 HELIX 45 AE9 LEU A 829 GLU A 834 1 6 HELIX 46 AF1 GLU A 834 ILE A 839 1 6 HELIX 47 AF2 GLY A 840 ILE A 842 5 3 HELIX 48 AF3 SER A 847 LYS A 862 1 16 HELIX 49 AF4 TYR A 875 HIS A 883 1 9 HELIX 50 AF5 THR A 886 ASN A 894 1 9 HELIX 51 AF6 SER A 895 GLY A 898 5 4 HELIX 52 AF7 ASN A 900 ILE A 909 1 10 HELIX 53 AF8 ILE A 909 ASP A 914 1 6 SHEET 1 AA1 4 MET A 60 VAL A 65 0 SHEET 2 AA1 4 LYS A 69 PHE A 75 -1 O TYR A 71 N LEU A 64 SHEET 3 AA1 4 ALA A 81 ASP A 88 -1 O GLU A 84 N ILE A 72 SHEET 4 AA1 4 LYS A 94 GLN A 96 -1 O THR A 95 N GLU A 86 SHEET 1 AA2 3 ILE A 105 VAL A 110 0 SHEET 2 AA2 3 ASN A 114 SER A 119 -1 O THR A 116 N GLY A 108 SHEET 3 AA2 3 ILE A 129 SER A 132 -1 O ILE A 129 N PHE A 117 LINK O ARG A 137 MG MG A1001 1555 1555 2.37 LINK O GLU A 140 MG MG A1001 1555 1555 2.25 LINK MG MG A1001 O HOH A1294 1555 1555 2.44 LINK MG MG A1001 O HOH A1357 1555 1555 2.44 LINK MG MG A1001 O HOH A1395 1555 1555 2.31 LINK MG MG A1001 O HOH A1402 1555 1555 2.44 LINK O HOH A1203 MG MG B 101 1555 1555 2.33 LINK O HOH A1272 MG MG B 101 1555 1555 2.48 LINK OP1 C B -7 MG MG B 101 1555 1555 2.05 LINK MG MG B 101 O HOH B 205 1555 1555 2.11 LINK MG MG B 101 O HOH B 221 1555 1555 2.25 LINK MG MG B 101 O HOH B 308 1555 1555 2.59 SITE 1 AC1 6 ARG A 137 GLU A 140 HOH A1294 HOH A1357 SITE 2 AC1 6 HOH A1395 HOH A1402 SITE 1 AC2 6 HOH A1203 HOH A1272 C B -7 HOH B 205 SITE 2 AC2 6 HOH B 221 HOH B 308 CRYST1 72.224 136.481 147.283 90.00 90.00 90.00 P 21 21 21 4 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 0.013846 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006790 0.00000