HEADER RNA BINDING PROTEIN 16-SEP-20 7D2L TITLE CRYSTAL STRUCTURE OF THE CAS12I1 R-LOOP COMPLEX BEFORE TARGET DNA TITLE 2 CLEAVAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 12I1-D647A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (43-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (30-MER); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (26-MER); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACHNOSPIRACEAE BACTERIUM ND2006; SOURCE 3 ORGANISM_TAXID: 1410628; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: LACHNOSPIRACEAE BACTERIUM ND2006; SOURCE 8 ORGANISM_TAXID: 1410628; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: LACHNOSPIRACEAE BACTERIUM ND2006; SOURCE 13 ORGANISM_TAXID: 1410628; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: LACHNOSPIRACEAE BACTERIUM ND2006; SOURCE 18 ORGANISM_TAXID: 1410628; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS THE RNP COMPLEX 1, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHANG,D.Y.LUO,Y.LI,S.Y.OUYANG REVDAT 4 03-APR-24 7D2L 1 REMARK REVDAT 3 30-JUN-21 7D2L 1 SOURCE REVDAT 2 23-JUN-21 7D2L 1 JRNL REVDAT 1 19-MAY-21 7D2L 0 JRNL AUTH B.ZHANG,D.LUO,Y.LI,V.PERCULIJA,J.CHEN,J.LIN,Y.YE,S.OUYANG JRNL TITL MECHANISTIC INSIGHTS INTO THE R-LOOP FORMATION AND CLEAVAGE JRNL TITL 2 IN CRISPR-CAS12I1. JRNL REF NAT COMMUN V. 12 3476 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34108490 JRNL DOI 10.1038/S41467-021-23876-5 REMARK 2 REMARK 2 RESOLUTION. 2.75 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 48018 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2477 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3467 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3650 REMARK 3 BIN FREE R VALUE SET COUNT : 181 REMARK 3 BIN FREE R VALUE : 0.4290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8684 REMARK 3 NUCLEIC ACID ATOMS : 2060 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.06000 REMARK 3 B22 (A**2) : 1.22000 REMARK 3 B33 (A**2) : -2.28000 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): 0.282 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.350 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.000 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.003 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7D2L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018642. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-19 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50543 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 59.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.76100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX 1.13-2998 REMARK 200 STARTING MODEL: THE SELENOMETHIONINE (SEMET)-LABELED COMPLEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE (PH5.5), PEG3350 REMARK 280 (18%), 0.1M SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 104.75850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 104.75850 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 1.000000 0.000000 0.000000 64.59600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.32200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 64.59600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.32200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 104.75850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 64.59600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.32200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 104.75850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 64.59600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.32200 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 60280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SER A 2 REMARK 465 ASN A 3 REMARK 465 LYS A 4 REMARK 465 GLU A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 826 REMARK 465 ASN A 827 REMARK 465 SER A 828 REMARK 465 LYS A 829 REMARK 465 SER A 830 REMARK 465 ASP A 831 REMARK 465 VAL A 832 REMARK 465 LYS A 833 REMARK 465 LYS A 1092 REMARK 465 LYS A 1093 REMARK 465 LEU A 1094 REMARK 465 GLU A 1095 REMARK 465 HIS A 1096 REMARK 465 HIS A 1097 REMARK 465 HIS A 1098 REMARK 465 HIS A 1099 REMARK 465 HIS A 1100 REMARK 465 HIS A 1101 REMARK 465 DG C -9 REMARK 465 DG C -8 REMARK 465 DG C -7 REMARK 465 DG C -6 REMARK 465 DG C -5 REMARK 465 DA C -4 REMARK 465 DG C -3 REMARK 465 DC C -2 REMARK 465 DT C -1 REMARK 465 DT C 0 REMARK 465 DT D 13 REMARK 465 DA D 14 REMARK 465 DA D 15 REMARK 465 DC D 30 REMARK 465 DA D 31 REMARK 465 DA D 32 REMARK 465 DG D 33 REMARK 465 DC D 34 REMARK 465 DT D 35 REMARK 465 DC D 36 REMARK 465 DC D 37 REMARK 465 DC D 38 REMARK 465 DC D 39 REMARK 465 DC D 40 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 LYS A 342 CG CD CE NZ REMARK 470 LYS A 386 CG CD CE NZ REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 ARG A 691 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 844 CG CD CE NZ REMARK 470 LYS A1011 CG CD CE NZ 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 G B 7 O3' U B 8 P -0.089 REMARK 500 U B 8 O3' G B 9 P -0.072 REMARK 500 G B 9 O3' C B 10 P -0.077 REMARK 500 C B 10 O3' C B 11 P -0.076 REMARK 500 C B 11 O3' C B 12 P -0.074 REMARK 500 A B 13 O3' U B 14 P -0.075 REMARK 500 U B 14 O3' C B 15 P -0.078 REMARK 500 G B 19 O3' G B 20 P -0.080 REMARK 500 U B 26 O3' U B 27 P -0.080 REMARK 500 U B 27 O3' A B 28 P -0.081 REMARK 500 A B 28 O3' A B 29 P -0.073 REMARK 500 A B 29 O3' G B 30 P -0.086 REMARK 500 G B 30 O3' G B 31 P -0.092 REMARK 500 DC C 14 O3' DC C 15 P -0.073 REMARK 500 DT C 16 O3' DT C 17 P -0.087 REMARK 500 DA C 18 O3' DA C 19 P -0.094 REMARK 500 DA C 19 O3' DT C 20 P -0.086 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 ARG A 22 -152.48 -126.18 REMARK 500 LYS A 66 -129.13 50.43 REMARK 500 GLU A 370 -128.79 53.35 REMARK 500 ARG A 439 41.96 -100.18 REMARK 500 VAL A 540 -67.46 -135.63 REMARK 500 ASP A 673 3.49 85.03 REMARK 500 ARG A 787 -84.85 -111.53 REMARK 500 LYS A 824 -73.09 -47.58 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 12 0.10 SIDE CHAIN REMARK 500 ARG A 26 0.22 SIDE CHAIN REMARK 500 ARG A 57 0.17 SIDE CHAIN REMARK 500 ARG A 137 0.12 SIDE CHAIN REMARK 500 ARG A 146 0.13 SIDE CHAIN REMARK 500 ARG A 225 0.10 SIDE CHAIN REMARK 500 ARG A 228 0.07 SIDE CHAIN REMARK 500 ARG A 233 0.09 SIDE CHAIN REMARK 500 ARG A 272 0.17 SIDE CHAIN REMARK 500 ARG A 402 0.28 SIDE CHAIN REMARK 500 ARG A 434 0.15 SIDE CHAIN REMARK 500 ARG A 439 0.12 SIDE CHAIN REMARK 500 ARG A 503 0.09 SIDE CHAIN REMARK 500 ARG A 523 0.23 SIDE CHAIN REMARK 500 ARG A 535 0.17 SIDE CHAIN REMARK 500 ARG A 556 0.10 SIDE CHAIN REMARK 500 ARG A 558 0.17 SIDE CHAIN REMARK 500 ARG A 579 0.22 SIDE CHAIN REMARK 500 ARG A 586 0.21 SIDE CHAIN REMARK 500 ARG A 591 0.12 SIDE CHAIN REMARK 500 ARG A 652 0.19 SIDE CHAIN REMARK 500 ARG A 715 0.26 SIDE CHAIN REMARK 500 ARG A 716 0.29 SIDE CHAIN REMARK 500 ARG A 723 0.09 SIDE CHAIN REMARK 500 ARG A 769 0.13 SIDE CHAIN REMARK 500 ARG A 860 0.12 SIDE CHAIN REMARK 500 ARG A 918 0.12 SIDE CHAIN REMARK 500 ARG A 962 0.26 SIDE CHAIN REMARK 500 ARG A 965 0.09 SIDE CHAIN REMARK 500 ARG A 976 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 7D2L A 1 1101 PDB 7D2L 7D2L 1 1101 DBREF 7D2L B 1 43 PDB 7D2L 7D2L 1 43 DBREF 7D2L C -9 30 PDB 7D2L 7D2L -9 30 DBREF 7D2L D 1 40 PDB 7D2L 7D2L 1 40 SEQRES 1 A 1101 MET SER ASN LYS GLU LYS ASN ALA SER GLU THR ARG LYS SEQRES 2 A 1101 ALA TYR THR THR LYS MET ILE PRO ARG SER HIS ASP ARG SEQRES 3 A 1101 MET LYS LEU LEU GLY ASN PHE MET ASP TYR LEU MET ASP SEQRES 4 A 1101 GLY THR PRO ILE PHE PHE GLU LEU TRP ASN GLN PHE GLY SEQRES 5 A 1101 GLY GLY ILE ASP ARG ASP ILE ILE SER GLY THR ALA ASN SEQRES 6 A 1101 LYS ASP LYS ILE SER ASP ASP LEU LEU LEU ALA VAL ASN SEQRES 7 A 1101 TRP PHE LYS VAL MET PRO ILE ASN SER LYS PRO GLN GLY SEQRES 8 A 1101 VAL SER PRO SER ASN LEU ALA ASN LEU PHE GLN GLN TYR SEQRES 9 A 1101 SER GLY SER GLU PRO ASP ILE GLN ALA GLN GLU TYR PHE SEQRES 10 A 1101 ALA SER ASN PHE ASP THR GLU LYS HIS GLN TRP LYS ASP SEQRES 11 A 1101 MET ARG VAL GLU TYR GLU ARG LEU LEU ALA GLU LEU GLN SEQRES 12 A 1101 LEU SER ARG SER ASP MET HIS HIS ASP LEU LYS LEU MET SEQRES 13 A 1101 TYR LYS GLU LYS CYS ILE GLY LEU SER LEU SER THR ALA SEQRES 14 A 1101 HIS TYR ILE THR SER VAL MET PHE GLY THR GLY ALA LYS SEQRES 15 A 1101 ASN ASN ARG GLN THR LYS HIS GLN PHE TYR SER LYS VAL SEQRES 16 A 1101 ILE GLN LEU LEU GLU GLU SER THR GLN ILE ASN SER VAL SEQRES 17 A 1101 GLU GLN LEU ALA SER ILE ILE LEU LYS ALA GLY ASP CYS SEQRES 18 A 1101 ASP SER TYR ARG LYS LEU ARG ILE ARG CYS SER ARG LYS SEQRES 19 A 1101 GLY ALA THR PRO SER ILE LEU LYS ILE VAL GLN ASP TYR SEQRES 20 A 1101 GLU LEU GLY THR ASN HIS ASP ASP GLU VAL ASN VAL PRO SEQRES 21 A 1101 SER LEU ILE ALA ASN LEU LYS GLU LYS LEU GLY ARG PHE SEQRES 22 A 1101 GLU TYR GLU CYS GLU TRP LYS CYS MET GLU LYS ILE LYS SEQRES 23 A 1101 ALA PHE LEU ALA SER LYS VAL GLY PRO TYR TYR LEU GLY SEQRES 24 A 1101 SER TYR SER ALA MET LEU GLU ASN ALA LEU SER PRO ILE SEQRES 25 A 1101 LYS GLY MET THR THR LYS ASN CYS LYS PHE VAL LEU LYS SEQRES 26 A 1101 GLN ILE ASP ALA LYS ASN ASP ILE LYS TYR GLU ASN GLU SEQRES 27 A 1101 PRO PHE GLY LYS ILE VAL GLU GLY PHE PHE ASP SER PRO SEQRES 28 A 1101 TYR PHE GLU SER ASP THR ASN VAL LYS TRP VAL LEU HIS SEQRES 29 A 1101 PRO HIS HIS ILE GLY GLU SER ASN ILE LYS THR LEU TRP SEQRES 30 A 1101 GLU ASP LEU ASN ALA ILE HIS SER LYS TYR GLU GLU ASP SEQRES 31 A 1101 ILE ALA SER LEU SER GLU ASP LYS LYS GLU LYS ARG ILE SEQRES 32 A 1101 LYS VAL TYR GLN GLY ASP VAL CYS GLN THR ILE ASN THR SEQRES 33 A 1101 TYR CYS GLU GLU VAL GLY LYS GLU ALA LYS THR PRO LEU SEQRES 34 A 1101 VAL GLN LEU LEU ARG TYR LEU TYR SER ARG LYS ASP ASP SEQRES 35 A 1101 ILE ALA VAL ASP LYS ILE ILE ASP GLY ILE THR PHE LEU SEQRES 36 A 1101 SER LYS LYS HIS LYS VAL GLU LYS GLN LYS ILE ASN PRO SEQRES 37 A 1101 VAL ILE GLN LYS TYR PRO SER PHE ASN PHE GLY ASN ASN SEQRES 38 A 1101 SER LYS LEU LEU GLY LYS ILE ILE SER PRO LYS ASP LYS SEQRES 39 A 1101 LEU LYS HIS ASN LEU LYS CYS ASN ARG ASN GLN VAL ASP SEQRES 40 A 1101 ASN TYR ILE TRP ILE GLU ILE LYS VAL LEU ASN THR LYS SEQRES 41 A 1101 THR MET ARG TRP GLU LYS HIS HIS TYR ALA LEU SER SER SEQRES 42 A 1101 THR ARG PHE LEU GLU GLU VAL TYR TYR PRO ALA THR SER SEQRES 43 A 1101 GLU ASN PRO PRO ASP ALA LEU ALA ALA ARG PHE ARG THR SEQRES 44 A 1101 LYS THR ASN GLY TYR GLU GLY LYS PRO ALA LEU SER ALA SEQRES 45 A 1101 GLU GLN ILE GLU GLN ILE ARG SER ALA PRO VAL GLY LEU SEQRES 46 A 1101 ARG LYS VAL LYS LYS ARG GLN MET ARG LEU GLU ALA ALA SEQRES 47 A 1101 ARG GLN GLN ASN LEU LEU PRO ARG TYR THR TRP GLY LYS SEQRES 48 A 1101 ASP PHE ASN ILE ASN ILE CYS LYS ARG GLY ASN ASN PHE SEQRES 49 A 1101 GLU VAL THR LEU ALA THR LYS VAL LYS LYS LYS LYS GLU SEQRES 50 A 1101 LYS ASN TYR LYS VAL VAL LEU GLY TYR ALA ALA ASN ILE SEQRES 51 A 1101 VAL ARG LYS ASN THR TYR ALA ALA ILE GLU ALA HIS ALA SEQRES 52 A 1101 ASN GLY ASP GLY VAL ILE ASP TYR ASN ASP LEU PRO VAL SEQRES 53 A 1101 LYS PRO ILE GLU SER GLY PHE VAL THR VAL GLU SER GLN SEQRES 54 A 1101 VAL ARG ASP LYS SER TYR ASP GLN LEU SER TYR ASN GLY SEQRES 55 A 1101 VAL LYS LEU LEU TYR CYS LYS PRO HIS VAL GLU SER ARG SEQRES 56 A 1101 ARG SER PHE LEU GLU LYS TYR ARG ASN GLY THR MET LYS SEQRES 57 A 1101 ASP ASN ARG GLY ASN ASN ILE GLN ILE ASP PHE MET LYS SEQRES 58 A 1101 ASP PHE GLU ALA ILE ALA ASP ASP GLU THR SER LEU TYR SEQRES 59 A 1101 TYR PHE ASN MET LYS TYR CYS LYS LEU LEU GLN SER SER SEQRES 60 A 1101 ILE ARG ASN HIS SER SER GLN ALA LYS GLU TYR ARG GLU SEQRES 61 A 1101 GLU ILE PHE GLU LEU LEU ARG ASP GLY LYS LEU SER VAL SEQRES 62 A 1101 LEU LYS LEU SER SER LEU SER ASN LEU SER PHE VAL MET SEQRES 63 A 1101 PHE LYS VAL ALA LYS SER LEU ILE GLY THR TYR PHE GLY SEQRES 64 A 1101 HIS LEU LEU LYS LYS PRO LYS ASN SER LYS SER ASP VAL SEQRES 65 A 1101 LYS ALA PRO PRO ILE THR ASP GLU ASP LYS GLN LYS ALA SEQRES 66 A 1101 ASP PRO GLU MET PHE ALA LEU ARG LEU ALA LEU GLU GLU SEQRES 67 A 1101 LYS ARG LEU ASN LYS VAL LYS SER LYS LYS GLU VAL ILE SEQRES 68 A 1101 ALA ASN LYS ILE VAL ALA LYS ALA LEU GLU LEU ARG ASP SEQRES 69 A 1101 LYS TYR GLY PRO VAL LEU ILE LYS GLY GLU ASN ILE SER SEQRES 70 A 1101 ASP THR THR LYS LYS GLY LYS LYS SER SER THR ASN SER SEQRES 71 A 1101 PHE LEU MET ASP TRP LEU ALA ARG GLY VAL ALA ASN LYS SEQRES 72 A 1101 VAL LYS GLU MET VAL MET MET HIS GLN GLY LEU GLU PHE SEQRES 73 A 1101 VAL GLU VAL ASN PRO ASN PHE THR SER HIS GLN ASP PRO SEQRES 74 A 1101 PHE VAL HIS LYS ASN PRO GLU ASN THR PHE ARG ALA ARG SEQRES 75 A 1101 TYR SER ARG CYS THR PRO SER GLU LEU THR GLU LYS ASN SEQRES 76 A 1101 ARG LYS GLU ILE LEU SER PHE LEU SER ASP LYS PRO SER SEQRES 77 A 1101 LYS ARG PRO THR ASN ALA TYR TYR ASN GLU GLY ALA MET SEQRES 78 A 1101 ALA PHE LEU ALA THR TYR GLY LEU LYS LYS ASN ASP VAL SEQRES 79 A 1101 LEU GLY VAL SER LEU GLU LYS PHE LYS GLN ILE MET ALA SEQRES 80 A 1101 ASN ILE LEU HIS GLN ARG SER GLU ASP GLN LEU LEU PHE SEQRES 81 A 1101 PRO SER ARG GLY GLY MET PHE TYR LEU ALA THR TYR LYS SEQRES 82 A 1101 LEU ASP ALA ASP ALA THR SER VAL ASN TRP ASN GLY LYS SEQRES 83 A 1101 GLN PHE TRP VAL CYS ASN ALA ASP LEU VAL ALA ALA TYR SEQRES 84 A 1101 ASN VAL GLY LEU VAL ASP ILE GLN LYS ASP PHE LYS LYS SEQRES 85 A 1101 LYS LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 43 A U U U U U G U G C C C A SEQRES 2 B 43 U C G U U G G C A C U A U SEQRES 3 B 43 U A A G G A A U G G A A U SEQRES 4 B 43 A U A G SEQRES 1 C 40 DG DG DG DG DG DA DG DC DT DT DG DC DT SEQRES 2 C 40 DA DT DA DT DT DC DC DA DT DT DC DC DT SEQRES 3 C 40 DT DA DA DT DA DG DA DA DC DT DA DG DA SEQRES 4 C 40 DC SEQRES 1 D 40 DG DT DC DT DA DG DT DT DC DT DA DT DT SEQRES 2 D 40 DA DA DA DA DG DG DC DA DA DG DG DC DG SEQRES 3 D 40 DC DT DG DC DA DA DG DC DT DC DC DC DC SEQRES 4 D 40 DC HET CIT A1201 13 HETNAM CIT CITRIC ACID FORMUL 5 CIT C6 H8 O7 FORMUL 6 HOH *12(H2 O) HELIX 1 AA1 SER A 23 GLY A 54 1 32 HELIX 2 AA2 SER A 70 TRP A 79 1 10 HELIX 3 AA3 SER A 93 SER A 95 5 3 HELIX 4 AA4 ASN A 96 GLY A 106 1 11 HELIX 5 AA5 ASP A 110 SER A 119 1 10 HELIX 6 AA6 MET A 131 GLN A 143 1 13 HELIX 7 AA7 SER A 145 GLU A 159 1 15 HELIX 8 AA8 THR A 168 GLY A 178 1 11 HELIX 9 AA9 ASN A 184 SER A 202 1 19 HELIX 10 AB1 SER A 207 ASP A 220 1 14 HELIX 11 AB2 SER A 223 SER A 232 1 10 HELIX 12 AB3 PRO A 238 LEU A 249 1 12 HELIX 13 AB4 ASN A 258 LYS A 269 1 12 HELIX 14 AB5 LEU A 270 GLU A 274 5 5 HELIX 15 AB6 CYS A 281 GLY A 294 1 14 HELIX 16 AB7 TYR A 297 ILE A 333 1 37 HELIX 17 AB8 LYS A 334 GLU A 336 5 3 HELIX 18 AB9 ASN A 337 GLY A 346 1 10 HELIX 19 AC1 PHE A 347 SER A 350 5 4 HELIX 20 AC2 HIS A 364 ILE A 368 5 5 HELIX 21 AC3 GLY A 369 SER A 371 5 3 HELIX 22 AC4 ASN A 372 SER A 393 1 22 HELIX 23 AC5 LYS A 399 ALA A 425 1 27 HELIX 24 AC6 LEU A 429 ARG A 439 1 11 HELIX 25 AC7 ALA A 444 GLN A 464 1 21 HELIX 26 AC8 SER A 490 CYS A 501 1 12 HELIX 27 AC9 SER A 533 VAL A 540 1 8 HELIX 28 AD1 THR A 559 GLY A 563 5 5 HELIX 29 AD2 SER A 571 ALA A 581 1 11 HELIX 30 AD3 PRO A 582 GLN A 601 1 20 HELIX 31 AD4 LYS A 704 TYR A 707 5 4 HELIX 32 AD5 CYS A 708 TYR A 722 1 15 HELIX 33 AD6 PHE A 739 ALA A 747 1 9 HELIX 34 AD7 SER A 752 HIS A 771 1 20 HELIX 35 AD8 GLN A 774 ARG A 787 1 14 HELIX 36 AD9 SER A 800 LEU A 822 1 23 HELIX 37 AE1 THR A 838 ASP A 846 1 9 HELIX 38 AE2 ASP A 846 TYR A 886 1 41 HELIX 39 AE3 LYS A 905 MET A 913 1 9 HELIX 40 AE4 LEU A 916 MET A 929 1 14 HELIX 41 AE5 THR A 972 PHE A 982 1 11 HELIX 42 AE6 THR A 992 TYR A 1007 1 16 HELIX 43 AE7 LYS A 1010 LEU A 1015 1 6 HELIX 44 AE8 SER A 1018 ARG A 1033 1 16 HELIX 45 AE9 ALA A 1073 LEU A 1083 1 11 HELIX 46 AF1 ASP A 1085 PHE A 1090 1 6 SHEET 1 AA1 8 ALA A 8 THR A 16 0 SHEET 2 AA1 8 ASN A 623 LYS A 635 -1 O VAL A 632 N THR A 11 SHEET 3 AA1 8 ASN A 614 ARG A 620 -1 N CYS A 618 O GLU A 625 SHEET 4 AA1 8 PHE A 476 GLY A 479 -1 N PHE A 476 O ILE A 617 SHEET 5 AA1 8 LEU A 484 ILE A 488 1 O LEU A 484 N GLY A 479 SHEET 6 AA1 8 ILE A 510 ASN A 518 -1 O LYS A 515 N LEU A 485 SHEET 7 AA1 8 ARG A 523 SER A 532 -1 O LEU A 531 N ILE A 510 SHEET 8 AA1 8 LYS A 18 ILE A 20 -1 N ILE A 20 O ALA A 530 SHEET 1 AA2 3 PHE A 80 PRO A 84 0 SHEET 2 AA2 3 HIS A 126 ASP A 130 -1 O GLN A 127 N MET A 83 SHEET 3 AA2 3 GLY A 91 VAL A 92 -1 N VAL A 92 O TRP A 128 SHEET 1 AA3 6 ILE A 669 TYR A 671 0 SHEET 2 AA3 6 LEU A 674 PHE A 683 -1 O LEU A 674 N TYR A 671 SHEET 3 AA3 6 THR A 655 ALA A 661 -1 N GLU A 660 O LYS A 677 SHEET 4 AA3 6 VAL A 642 ALA A 647 -1 N GLY A 645 O ALA A 657 SHEET 5 AA3 6 VAL A 889 GLU A 894 1 O LYS A 892 N LEU A 644 SHEET 6 AA3 6 LEU A 934 VAL A 939 1 O GLU A 935 N ILE A 891 SHEET 1 AA4 2 GLU A 687 VAL A 690 0 SHEET 2 AA4 2 LYS A 693 ASP A 696 -1 O LYS A 693 N VAL A 690 SHEET 1 AA5 2 ASN A 724 GLY A 725 0 SHEET 2 AA5 2 ILE A 737 ASP A 738 -1 O ILE A 737 N GLY A 725 SHEET 1 AA6 2 TYR A 963 CYS A 966 0 SHEET 2 AA6 2 LEU A1038 PRO A1041 -1 O PHE A1040 N SER A 964 SHEET 1 AA7 3 PHE A1047 ALA A1050 0 SHEET 2 AA7 3 LYS A1066 ASN A1072 -1 O TRP A1069 N ALA A1050 SHEET 3 AA7 3 THR A1059 TRP A1063 -1 N TRP A1063 O LYS A1066 CISPEP 1 ASN A 954 PRO A 955 0 -21.36 CRYST1 129.192 142.644 209.517 90.00 90.00 90.00 C 2 2 21 8 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 0.007740 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007010 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004773 0.00000