HEADER HYDROLASE/RNA 10-APR-18 6D06 TITLE HUMAN ADAR2D E488Y MUTANT COMPLEXED WITH DSRNA CONTAINING AN ABASIC TITLE 2 SITE OPPOSITE THE EDITED BASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE-STRANDED RNA-SPECIFIC EDITASE 1; COMPND 3 CHAIN: A, D; COMPND 4 SYNONYM: RNA-EDITING DEAMINASE 1,RNA-EDITING ENZYME 1,DSRNA ADENOSINE COMPND 5 DEAMINASE; COMPND 6 EC: 3.5.4.37; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA (5'-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ) COMPND 11 P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: RNA (5'- COMPND 16 R(*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*NP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP* COMPND 17 C)-3'); COMPND 18 CHAIN: C; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ADARB1, ADAR2, DRADA2, RED1; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BCY123; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSC; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606 KEYWDS ADENOSINE DEAMINASE, RNA EDITING, HYDROLASE, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.M.MATTHEWS,A.J.FISHER,P.A.BEAL REVDAT 5 04-OCT-23 6D06 1 REMARK REVDAT 4 30-SEP-20 6D06 1 HETSYN LINK REVDAT 3 01-JAN-20 6D06 1 SEQRES REVDAT 2 06-MAR-19 6D06 1 JRNL REVDAT 1 20-FEB-19 6D06 0 JRNL AUTH L.R.MONTELEONE,M.M.MATTHEWS,C.M.PALUMBO,J.M.THOMAS,Y.ZHENG, JRNL AUTH 2 Y.CHIANG,A.J.FISHER,P.A.BEAL JRNL TITL A BUMP-HOLE APPROACH FOR DIRECTED RNA EDITING. JRNL REF CELL CHEM BIOL V. 26 269 2019 JRNL REFN ESSN 2451-9448 JRNL PMID 30581135 JRNL DOI 10.1016/J.CHEMBIOL.2018.10.025 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 105.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 35463 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1862 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2610 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 135 REMARK 3 BIN FREE R VALUE : 0.3860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5760 REMARK 3 NUCLEIC ACID ATOMS : 967 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.05000 REMARK 3 B22 (A**2) : -4.83000 REMARK 3 B33 (A**2) : 0.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.20000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.462 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.294 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.245 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.895 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7069 ; 0.012 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 6052 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9796 ; 1.739 ; 1.866 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14068 ; 1.101 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 738 ; 7.166 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 255 ;36.143 ;22.902 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1043 ;16.634 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;20.478 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1088 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7069 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1473 ; 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): 2955 ; 4.698 ; 6.477 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2954 ; 4.695 ; 6.475 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3689 ; 7.002 ; 9.704 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3690 ; 7.001 ; 9.706 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4113 ; 4.817 ; 6.689 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4109 ; 4.815 ; 6.687 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 6101 ; 7.055 ; 9.923 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7956 ; 9.171 ;72.561 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7957 ; 9.171 ;72.566 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 REMARK 4 REMARK 4 6D06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000231682. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37329 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 106.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.440 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.72300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.070 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1ZY7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES:NAOH PH 6.5, 14% PEG 20,000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 87.34000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.72000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 87.34000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.72000 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 LEU A 299 REMARK 465 HIS A 300 REMARK 465 LEU A 301 REMARK 465 ASP A 302 REMARK 465 GLN A 303 REMARK 465 THR A 304 REMARK 465 PRO A 305 REMARK 465 SER A 306 REMARK 465 ARG A 307 REMARK 465 GLN A 308 REMARK 465 PRO A 309 REMARK 465 ILE A 310 REMARK 465 PRO A 311 REMARK 465 SER A 312 REMARK 465 GLU A 313 REMARK 465 GLY A 314 REMARK 465 LEU A 315 REMARK 465 GLN A 316 REMARK 465 PRO A 701 REMARK 465 LEU D 299 REMARK 465 HIS D 300 REMARK 465 LEU D 301 REMARK 465 ASP D 302 REMARK 465 GLN D 303 REMARK 465 THR D 304 REMARK 465 PRO D 305 REMARK 465 SER D 306 REMARK 465 ARG D 307 REMARK 465 GLN D 308 REMARK 465 PRO D 309 REMARK 465 ILE D 310 REMARK 465 PRO D 311 REMARK 465 SER D 312 REMARK 465 GLU D 313 REMARK 465 GLY D 314 REMARK 465 LEU D 315 REMARK 465 GLN D 316 REMARK 465 LEU D 317 REMARK 465 HIS D 318 REMARK 465 LEU D 464 REMARK 465 GLU D 465 REMARK 465 GLU D 466 REMARK 465 PRO D 467 REMARK 465 ALA D 468 REMARK 465 ASP D 469 REMARK 465 ARG D 470 REMARK 465 HIS D 471 REMARK 465 PRO D 472 REMARK 465 ASN D 473 REMARK 465 ARG D 474 REMARK 465 LYS D 475 REMARK 465 ALA D 476 REMARK 465 SER D 495 REMARK 465 ASN D 496 REMARK 465 ALA D 497 REMARK 465 SER D 498 REMARK 465 ILE D 499 REMARK 465 GLN D 500 REMARK 465 THR D 501 REMARK 465 TRP D 502 REMARK 465 ASP D 503 REMARK 465 GLY D 504 REMARK 465 VAL D 505 REMARK 465 LEU D 506 REMARK 465 GLN D 507 REMARK 465 GLY D 508 REMARK 465 GLU D 509 REMARK 465 ARG D 510 REMARK 465 LEU D 511 REMARK 465 PRO D 701 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 LEU A 317 CG CD1 CD2 REMARK 470 HIS A 318 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 590 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 485 CG CD OE1 OE2 REMARK 470 ARG D 494 CG CD NE CZ NH1 NH2 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 C 13 O3' C C 14 P -0.079 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 ARG A 455 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 481 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 481 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 U B 12 O5' - P - OP2 ANGL. DEV. = -6.2 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 GLU A 430 -7.71 -57.46 REMARK 500 GLU A 438 150.94 -45.11 REMARK 500 PRO A 459 45.14 -85.58 REMARK 500 GLU A 465 -78.41 -57.94 REMARK 500 TYR A 561 -48.23 -161.85 REMARK 500 ASN A 566 0.28 -66.92 REMARK 500 LEU A 573 -24.14 73.40 REMARK 500 GLN A 696 58.46 -98.99 REMARK 500 ASP D 365 65.32 -102.32 REMARK 500 ASN D 439 -6.24 71.43 REMARK 500 ILE D 456 72.30 -106.08 REMARK 500 SER D 486 7.40 80.91 REMARK 500 PRO D 492 -171.72 -65.16 REMARK 500 VAL D 525 -58.89 -128.78 REMARK 500 TYR D 561 -45.60 -158.19 REMARK 500 ASN D 566 1.77 -59.35 REMARK 500 GLU D 568 -86.10 -117.79 REMARK 500 LEU D 573 -27.41 92.91 REMARK 500 ASN D 586 71.61 -114.68 REMARK 500 LEU D 621 32.76 -98.88 REMARK 500 ILE D 652 128.85 -176.39 REMARK 500 THR D 653 -54.40 -122.71 REMARK 500 ASN D 656 -59.88 -150.81 REMARK 500 GLN D 696 64.59 -102.24 REMARK 500 LEU D 699 -139.21 -77.55 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 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 394 ND1 REMARK 620 2 CYS A 451 SG 110.2 REMARK 620 3 CYS A 516 SG 106.1 107.5 REMARK 620 4 8AZ B 13 O6 123.6 106.9 101.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 394 ND1 REMARK 620 2 CYS D 451 SG 111.7 REMARK 620 3 CYS D 516 SG 113.4 114.1 REMARK 620 4 HOH D 901 O 121.1 96.1 99.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHP A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHP D 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 802 DBREF 6D06 A 299 701 UNP P78563 RED1_HUMAN 327 729 DBREF 6D06 B 1 23 PDB 6D06 6D06 1 23 DBREF 6D06 C 1 23 PDB 6D06 6D06 1 23 DBREF 6D06 D 299 701 UNP P78563 RED1_HUMAN 327 729 SEQADV 6D06 TYR A 488 UNP P78563 GLU 516 ENGINEERED MUTATION SEQADV 6D06 TYR D 488 UNP P78563 GLU 516 ENGINEERED MUTATION SEQRES 1 A 403 LEU HIS LEU ASP GLN THR PRO SER ARG GLN PRO ILE PRO SEQRES 2 A 403 SER GLU GLY LEU GLN LEU HIS LEU PRO GLN VAL LEU ALA SEQRES 3 A 403 ASP ALA VAL SER ARG LEU VAL LEU GLY LYS PHE GLY ASP SEQRES 4 A 403 LEU THR ASP ASN PHE SER SER PRO HIS ALA ARG ARG LYS SEQRES 5 A 403 VAL LEU ALA GLY VAL VAL MET THR THR GLY THR ASP VAL SEQRES 6 A 403 LYS ASP ALA LYS VAL ILE SER VAL SER THR GLY THR LYS SEQRES 7 A 403 CYS ILE ASN GLY GLU TYR MET SER ASP ARG GLY LEU ALA SEQRES 8 A 403 LEU ASN ASP CYS HIS ALA GLU ILE ILE SER ARG ARG SER SEQRES 9 A 403 LEU LEU ARG PHE LEU TYR THR GLN LEU GLU LEU TYR LEU SEQRES 10 A 403 ASN ASN LYS ASP ASP GLN LYS ARG SER ILE PHE GLN LYS SEQRES 11 A 403 SER GLU ARG GLY GLY PHE ARG LEU LYS GLU ASN VAL GLN SEQRES 12 A 403 PHE HIS LEU TYR ILE SER THR SER PRO CYS GLY ASP ALA SEQRES 13 A 403 ARG ILE PHE SER PRO HIS GLU PRO ILE LEU GLU GLU PRO SEQRES 14 A 403 ALA ASP ARG HIS PRO ASN ARG LYS ALA ARG GLY GLN LEU SEQRES 15 A 403 ARG THR LYS ILE GLU SER GLY TYR GLY THR ILE PRO VAL SEQRES 16 A 403 ARG SER ASN ALA SER ILE GLN THR TRP ASP GLY VAL LEU SEQRES 17 A 403 GLN GLY GLU ARG LEU LEU THR MET SER CYS SER ASP LYS SEQRES 18 A 403 ILE ALA ARG TRP ASN VAL VAL GLY ILE GLN GLY SER LEU SEQRES 19 A 403 LEU SER ILE PHE VAL GLU PRO ILE TYR PHE SER SER ILE SEQRES 20 A 403 ILE LEU GLY SER LEU TYR HIS GLY ASP HIS LEU SER ARG SEQRES 21 A 403 ALA MET TYR GLN ARG ILE SER ASN ILE GLU ASP LEU PRO SEQRES 22 A 403 PRO LEU TYR THR LEU ASN LYS PRO LEU LEU SER GLY ILE SEQRES 23 A 403 SER ASN ALA GLU ALA ARG GLN PRO GLY LYS ALA PRO ASN SEQRES 24 A 403 PHE SER VAL ASN TRP THR VAL GLY ASP SER ALA ILE GLU SEQRES 25 A 403 VAL ILE ASN ALA THR THR GLY LYS ASP GLU LEU GLY ARG SEQRES 26 A 403 ALA SER ARG LEU CYS LYS HIS ALA LEU TYR CYS ARG TRP SEQRES 27 A 403 MET ARG VAL HIS GLY LYS VAL PRO SER HIS LEU LEU ARG SEQRES 28 A 403 SER LYS ILE THR LYS PRO ASN VAL TYR HIS GLU SER LYS SEQRES 29 A 403 LEU ALA ALA LYS GLU TYR GLN ALA ALA LYS ALA ARG LEU SEQRES 30 A 403 PHE THR ALA PHE ILE LYS ALA GLY LEU GLY ALA TRP VAL SEQRES 31 A 403 GLU LYS PRO THR GLU GLN ASP GLN PHE SER LEU THR PRO SEQRES 1 B 23 G C U C G C G A U G C U 8AZ SEQRES 2 B 23 G A G G G C U C U G SEQRES 1 C 23 C A G A G C C C C C N A G SEQRES 2 C 23 C A U C G C G A G C SEQRES 1 D 403 LEU HIS LEU ASP GLN THR PRO SER ARG GLN PRO ILE PRO SEQRES 2 D 403 SER GLU GLY LEU GLN LEU HIS LEU PRO GLN VAL LEU ALA SEQRES 3 D 403 ASP ALA VAL SER ARG LEU VAL LEU GLY LYS PHE GLY ASP SEQRES 4 D 403 LEU THR ASP ASN PHE SER SER PRO HIS ALA ARG ARG LYS SEQRES 5 D 403 VAL LEU ALA GLY VAL VAL MET THR THR GLY THR ASP VAL SEQRES 6 D 403 LYS ASP ALA LYS VAL ILE SER VAL SER THR GLY THR LYS SEQRES 7 D 403 CYS ILE ASN GLY GLU TYR MET SER ASP ARG GLY LEU ALA SEQRES 8 D 403 LEU ASN ASP CYS HIS ALA GLU ILE ILE SER ARG ARG SER SEQRES 9 D 403 LEU LEU ARG PHE LEU TYR THR GLN LEU GLU LEU TYR LEU SEQRES 10 D 403 ASN ASN LYS ASP ASP GLN LYS ARG SER ILE PHE GLN LYS SEQRES 11 D 403 SER GLU ARG GLY GLY PHE ARG LEU LYS GLU ASN VAL GLN SEQRES 12 D 403 PHE HIS LEU TYR ILE SER THR SER PRO CYS GLY ASP ALA SEQRES 13 D 403 ARG ILE PHE SER PRO HIS GLU PRO ILE LEU GLU GLU PRO SEQRES 14 D 403 ALA ASP ARG HIS PRO ASN ARG LYS ALA ARG GLY GLN LEU SEQRES 15 D 403 ARG THR LYS ILE GLU SER GLY TYR GLY THR ILE PRO VAL SEQRES 16 D 403 ARG SER ASN ALA SER ILE GLN THR TRP ASP GLY VAL LEU SEQRES 17 D 403 GLN GLY GLU ARG LEU LEU THR MET SER CYS SER ASP LYS SEQRES 18 D 403 ILE ALA ARG TRP ASN VAL VAL GLY ILE GLN GLY SER LEU SEQRES 19 D 403 LEU SER ILE PHE VAL GLU PRO ILE TYR PHE SER SER ILE SEQRES 20 D 403 ILE LEU GLY SER LEU TYR HIS GLY ASP HIS LEU SER ARG SEQRES 21 D 403 ALA MET TYR GLN ARG ILE SER ASN ILE GLU ASP LEU PRO SEQRES 22 D 403 PRO LEU TYR THR LEU ASN LYS PRO LEU LEU SER GLY ILE SEQRES 23 D 403 SER ASN ALA GLU ALA ARG GLN PRO GLY LYS ALA PRO ASN SEQRES 24 D 403 PHE SER VAL ASN TRP THR VAL GLY ASP SER ALA ILE GLU SEQRES 25 D 403 VAL ILE ASN ALA THR THR GLY LYS ASP GLU LEU GLY ARG SEQRES 26 D 403 ALA SER ARG LEU CYS LYS HIS ALA LEU TYR CYS ARG TRP SEQRES 27 D 403 MET ARG VAL HIS GLY LYS VAL PRO SER HIS LEU LEU ARG SEQRES 28 D 403 SER LYS ILE THR LYS PRO ASN VAL TYR HIS GLU SER LYS SEQRES 29 D 403 LEU ALA ALA LYS GLU TYR GLN ALA ALA LYS ALA ARG LEU SEQRES 30 D 403 PHE THR ALA PHE ILE LYS ALA GLY LEU GLY ALA TRP VAL SEQRES 31 D 403 GLU LYS PRO THR GLU GLN ASP GLN PHE SER LEU THR PRO HET 8AZ B 13 22 HET IHP A 801 36 HET ZN A 802 1 HET IHP D 801 36 HET ZN D 802 1 HETNAM 8AZ 8-AZA-NEBULARINE-5'-MONOPHOSPHATE HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETNAM ZN ZINC ION HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 2 8AZ C9 H14 N5 O8 P FORMUL 5 IHP 2(C6 H18 O24 P6) FORMUL 6 ZN 2(ZN 2+) FORMUL 9 HOH *48(H2 O) HELIX 1 AA1 LEU A 319 THR A 339 1 21 HELIX 2 AA2 SER A 344 ARG A 348 5 5 HELIX 3 AA3 ASP A 362 ALA A 366 5 5 HELIX 4 AA4 ASN A 379 MET A 383 5 5 HELIX 5 AA5 HIS A 394 ASN A 417 1 24 HELIX 6 AA6 ASP A 419 ARG A 423 5 5 HELIX 7 AA7 ARG A 494 ASN A 496 5 3 HELIX 8 AA8 THR A 501 GLY A 508 1 8 HELIX 9 AA9 SER A 515 GLY A 527 1 13 HELIX 10 AB1 GLN A 529 ILE A 535 1 7 HELIX 11 AB2 HIS A 552 TYR A 561 1 10 HELIX 12 AB3 GLN A 562 SER A 565 5 4 HELIX 13 AB4 CYS A 628 LYS A 642 1 15 HELIX 14 AB5 VAL A 643 LEU A 648 5 6 HELIX 15 AB6 VAL A 657 ALA A 664 1 8 HELIX 16 AB7 ALA A 665 ALA A 682 1 18 HELIX 17 AB8 PRO A 691 GLN A 696 5 6 HELIX 18 AB9 PRO D 320 LEU D 338 1 19 HELIX 19 AC1 ASN D 379 MET D 383 5 5 HELIX 20 AC2 HIS D 394 ASN D 417 1 24 HELIX 21 AC3 LYS D 418 ARG D 423 5 6 HELIX 22 AC4 GLY D 452 ILE D 456 5 5 HELIX 23 AC5 SER D 515 ASN D 524 1 10 HELIX 24 AC6 GLN D 529 VAL D 537 1 9 HELIX 25 AC7 HIS D 552 TYR D 561 1 10 HELIX 26 AC8 GLN D 562 SER D 565 5 4 HELIX 27 AC9 CYS D 628 VAL D 643 1 16 HELIX 28 AD1 PRO D 644 LEU D 648 5 5 HELIX 29 AD2 VAL D 657 ALA D 665 1 9 HELIX 30 AD3 ALA D 665 LYS D 681 1 17 SHEET 1 AA1 7 LEU A 580 GLY A 583 0 SHEET 2 AA1 7 PHE A 542 LEU A 547 1 N SER A 543 O LEU A 580 SHEET 3 AA1 7 GLN A 441 ILE A 446 1 N LEU A 444 O ILE A 546 SHEET 4 AA1 7 LEU A 352 THR A 358 -1 N GLY A 354 O TYR A 445 SHEET 5 AA1 7 LYS A 367 THR A 373 -1 O LYS A 367 N MET A 357 SHEET 6 AA1 7 PHE A 598 THR A 603 -1 O TRP A 602 N VAL A 371 SHEET 7 AA1 7 GLU A 610 ASN A 613 -1 O ILE A 612 N SER A 599 SHEET 1 AA2 2 PHE A 426 LYS A 428 0 SHEET 2 AA2 2 PHE A 434 LEU A 436 -1 O ARG A 435 N GLN A 427 SHEET 1 AA3 3 THR A 490 PRO A 492 0 SHEET 2 AA3 3 ARG A 481 ILE A 484 -1 N THR A 482 O ILE A 491 SHEET 3 AA3 3 LEU A 512 MET A 514 -1 O THR A 513 N LYS A 483 SHEET 1 AA4 8 LEU D 580 GLY D 583 0 SHEET 2 AA4 8 PHE D 542 LEU D 547 1 N LEU D 547 O SER D 582 SHEET 3 AA4 8 GLN D 441 ILE D 446 1 N LEU D 444 O ILE D 546 SHEET 4 AA4 8 LEU D 352 THR D 358 -1 N VAL D 356 O HIS D 443 SHEET 5 AA4 8 ALA D 366 THR D 373 -1 O SER D 372 N ALA D 353 SHEET 6 AA4 8 PHE D 598 THR D 603 -1 O TRP D 602 N VAL D 371 SHEET 7 AA4 8 GLU D 610 ASN D 613 -1 O ILE D 612 N SER D 599 SHEET 8 AA4 8 LYS D 618 ASP D 619 -1 O LYS D 618 N ASN D 613 SHEET 1 AA5 2 PHE D 426 LYS D 428 0 SHEET 2 AA5 2 PHE D 434 LEU D 436 -1 O ARG D 435 N GLN D 427 SHEET 1 AA6 2 ARG D 481 LYS D 483 0 SHEET 2 AA6 2 THR D 490 PRO D 492 -1 O ILE D 491 N THR D 482 LINK O3' U B 12 P 8AZ B 13 1555 1555 1.59 LINK O3' 8AZ B 13 P G B 14 1555 1555 1.59 LINK O3' C C 10 P N C 11 1555 1555 1.59 LINK O3' N C 11 P A C 12 1555 1555 1.55 LINK ND1 HIS A 394 ZN ZN A 802 1555 1555 2.01 LINK SG CYS A 451 ZN ZN A 802 1555 1555 2.29 LINK SG CYS A 516 ZN ZN A 802 1555 1555 2.30 LINK ZN ZN A 802 O6 8AZ B 13 1555 1555 1.98 LINK ND1 HIS D 394 ZN ZN D 802 1555 1555 1.95 LINK SG CYS D 451 ZN ZN D 802 1555 1555 2.30 LINK SG CYS D 516 ZN ZN D 802 1555 1555 2.26 LINK ZN ZN D 802 O HOH D 901 1555 1555 1.98 SITE 1 AC1 21 ASN A 391 ILE A 397 ARG A 400 ARG A 401 SITE 2 AC1 21 LYS A 519 ARG A 522 GLY A 530 SER A 531 SITE 3 AC1 21 LYS A 629 TYR A 658 LYS A 662 TYR A 668 SITE 4 AC1 21 LYS A 672 TRP A 687 GLU A 689 LYS A 690 SITE 5 AC1 21 HOH A 901 HOH A 905 HOH A 906 HOH A 912 SITE 6 AC1 21 HOH A 913 SITE 1 AC2 5 HIS A 394 CYS A 451 LYS A 483 CYS A 516 SITE 2 AC2 5 8AZ B 13 SITE 1 AC3 18 ASN D 391 ILE D 397 ARG D 400 ARG D 401 SITE 2 AC3 18 THR D 513 LYS D 519 ARG D 522 GLY D 530 SITE 3 AC3 18 SER D 531 LYS D 629 TYR D 658 LYS D 662 SITE 4 AC3 18 TYR D 668 LYS D 672 TRP D 687 GLU D 689 SITE 5 AC3 18 LYS D 690 ASP D 695 SITE 1 AC4 4 HIS D 394 CYS D 451 CYS D 516 HOH D 901 CRYST1 174.680 63.440 132.060 90.00 126.64 90.00 C 1 2 1 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 0.005725 0.000000 0.004258 0.00000 SCALE2 0.000000 0.015763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009437 0.00000