HEADER HYDROLASE/RNA 06-JAN-14 4OAU TITLE COMPLETE HUMAN RNASE L IN COMPLEX WITH BIOLOGICAL ACTIVATORS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-5A-DEPENDENT RIBONUCLEASE; COMPND 3 CHAIN: C; COMPND 4 FRAGMENT: UNP RESIDUES 21-719; COMPND 5 SYNONYM: 2-5A-DEPENDENT RNASE, RIBONUCLEASE 4, RIBONUCLEASE L, RNASE COMPND 6 L; COMPND 7 EC: 3.1.26.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: RNA (5'-R(P*A*AP*A)-2'); COMPND 12 CHAIN: A; COMPND 13 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: RNASEL, RNS4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS RNASE L, RNASEL, 2-5A, 2', 5'-OLIGOADENYLATE, INTERFERON, KEN, KEYWDS 2 PSEUDOKINASE, KINASE, INFLAMMATION, IRE1, RIDD, REGULATED RNA DECAY, KEYWDS 3 SPLICING CLEAVAGE, HPC1, HEREDITARY PROSTATE CANCER 1, RNASE L KEYWDS 4 KINASE-HOMOLOGY AND KEN DOMAIN-CONTAINING, INNATE IMMUNITY, KEYWDS 5 INTERFERON RESPONSE, ANTIVIRAL RESPONSE, 2-5A (2', 5'-LINKED KEYWDS 6 OLIGOADENYLATE)AND RNA, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.HAN,J.DONOVAN,S.RATH,G.WHITNEY,A.CHITRAKAR,A.KORENNYKH REVDAT 3 28-FEB-24 4OAU 1 REMARK SEQADV LINK REVDAT 2 02-APR-14 4OAU 1 JRNL REVDAT 1 12-MAR-14 4OAU 0 JRNL AUTH Y.HAN,J.DONOVAN,S.RATH,G.WHITNEY,A.CHITRAKAR,A.KORENNYKH JRNL TITL STRUCTURE OF HUMAN RNASE L REVEALS THE BASIS FOR REGULATED JRNL TITL 2 RNA DECAY IN THE IFN RESPONSE. JRNL REF SCIENCE V. 343 1244 2014 JRNL REFN ISSN 0036-8075 JRNL PMID 24578532 JRNL DOI 10.1126/SCIENCE.1249845 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 53.4535 - 6.1107 0.99 2801 147 0.1919 0.2073 REMARK 3 2 6.1107 - 4.8513 1.00 2691 142 0.2011 0.2138 REMARK 3 3 4.8513 - 4.2383 1.00 2651 140 0.1588 0.2258 REMARK 3 4 4.2383 - 3.8509 1.00 2626 138 0.1777 0.2084 REMARK 3 5 3.8509 - 3.5750 1.00 2630 139 0.1868 0.2515 REMARK 3 6 3.5750 - 3.3642 1.00 2594 136 0.2010 0.2542 REMARK 3 7 3.3642 - 3.1958 1.00 2611 138 0.2402 0.3036 REMARK 3 8 3.1958 - 3.0567 1.00 2600 136 0.2463 0.3034 REMARK 3 9 3.0567 - 2.9390 1.00 2604 138 0.2715 0.3235 REMARK 3 10 2.9390 - 2.8376 1.00 2585 136 0.2919 0.3292 REMARK 3 11 2.8376 - 2.7489 1.00 2574 135 0.3124 0.3750 REMARK 3 12 2.7489 - 2.6703 1.00 2583 136 0.3239 0.3457 REMARK 3 13 2.6703 - 2.6000 1.00 2594 137 0.3247 0.3430 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 5747 REMARK 3 ANGLE : 0.788 7761 REMARK 3 CHIRALITY : 0.061 853 REMARK 3 PLANARITY : 0.003 990 REMARK 3 DIHEDRAL : 20.991 3594 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 1:3) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1477 -7.8617 -17.1830 REMARK 3 T TENSOR REMARK 3 T11: 0.4256 T22: 0.4407 REMARK 3 T33: 0.3948 T12: -0.0337 REMARK 3 T13: -0.0839 T23: 0.0431 REMARK 3 L TENSOR REMARK 3 L11: 1.9528 L22: 0.5120 REMARK 3 L33: 3.6844 L12: 0.0566 REMARK 3 L13: -2.2491 L23: -0.2371 REMARK 3 S TENSOR REMARK 3 S11: -0.0712 S12: 0.1831 S13: 0.0541 REMARK 3 S21: -0.0723 S22: 0.0537 S23: 0.0961 REMARK 3 S31: 0.0847 S32: -0.3113 S33: 0.0300 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN C AND RESID 331:437 REMARK 3 ORIGIN FOR THE GROUP (A): -2.0124 -32.9871 12.3325 REMARK 3 T TENSOR REMARK 3 T11: 0.7326 T22: 0.4646 REMARK 3 T33: 0.3941 T12: 0.0537 REMARK 3 T13: 0.0038 T23: -0.0331 REMARK 3 L TENSOR REMARK 3 L11: 9.0326 L22: 7.2187 REMARK 3 L33: 4.6573 L12: 0.2735 REMARK 3 L13: -0.8627 L23: 1.4975 REMARK 3 S TENSOR REMARK 3 S11: 0.0714 S12: -0.1739 S13: -0.0632 REMARK 3 S21: -0.0653 S22: -0.3649 S23: 0.1608 REMARK 3 S31: 0.4149 S32: -0.2258 S33: 0.2316 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C AND (RESID 438:584 OR RESID 801 OR RESID REMARK 3 802:803) REMARK 3 ORIGIN FOR THE GROUP (A): 12.0602 -55.0227 13.8441 REMARK 3 T TENSOR REMARK 3 T11: 1.1017 T22: 0.4811 REMARK 3 T33: 0.7815 T12: 0.1808 REMARK 3 T13: 0.0659 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 4.9714 L22: 7.7501 REMARK 3 L33: 2.3704 L12: -1.2853 REMARK 3 L13: 1.3603 L23: -0.8334 REMARK 3 S TENSOR REMARK 3 S11: 0.0100 S12: -0.2132 S13: -0.8229 REMARK 3 S21: 0.4748 S22: -0.0342 S23: -0.6503 REMARK 3 S31: 0.5047 S32: 0.3231 S33: -0.0118 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN C AND RESID 585:719 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1432 -86.2206 9.0501 REMARK 3 T TENSOR REMARK 3 T11: 1.8347 T22: 0.5853 REMARK 3 T33: 1.5589 T12: 0.1614 REMARK 3 T13: 0.2195 T23: 0.0284 REMARK 3 L TENSOR REMARK 3 L11: 3.4794 L22: 0.6338 REMARK 3 L33: 2.3859 L12: 0.7786 REMARK 3 L13: 0.0611 L23: 0.2491 REMARK 3 S TENSOR REMARK 3 S11: -0.3026 S12: -0.0162 S13: -0.4112 REMARK 3 S21: -0.1138 S22: 0.1845 S23: 0.5986 REMARK 3 S31: 0.5937 S32: -0.0360 S33: 0.2577 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4OAU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28947 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 53.442 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RNASE L (21-719) (15 MG/ML IN BUFFER REMARK 280 CONTAINING 20 MM HEPES PH 7.5, 109 MM NACL, 5 MM MGCL 2, 5 MM REMARK 280 DTT, 2.8 MM ATP OR AMP-PCP, AND 10% GLYCEROL) WAS MIXED WITH 2- REMARK 280 5A AND RNA18 AT MOLAR RATIO 1:1.5:1.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277K, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 30.06500 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.20000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.06500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 81.20000 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: 12060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 60980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ALA C 21 REMARK 465 ALA C 22 REMARK 465 VAL C 23 REMARK 465 GLU C 24 REMARK 465 GLY C 621 REMARK 465 PRO C 622 REMARK 465 SER C 623 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH C 979 O HOH C 990 1.91 REMARK 500 OD2 ASP C 541 O HOH C 961 1.96 REMARK 500 OE2 GLU C 327 O HOH C 931 2.01 REMARK 500 O HOH C 906 O HOH C 918 2.04 REMARK 500 O LYS C 496 O HOH C 1007 2.13 REMARK 500 OD1 ASN C 601 NH1 ARG C 667 2.16 REMARK 500 OE1 GLN C 473 OG SER C 578 2.17 REMARK 500 O HIS C 263 O HOH C 959 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 A A 1 O4' A A 1 C1' 0.086 REMARK 500 A A 1 N1 A A 1 C2 0.066 REMARK 500 A A 1 C2 A A 1 N3 0.134 REMARK 500 A A 1 N3 A A 1 C4 0.079 REMARK 500 A A 1 C4 A A 1 C5 0.066 REMARK 500 A A 1 C6 A A 1 N1 0.111 REMARK 500 A A 1 N7 A A 1 C8 0.196 REMARK 500 A A 1 N9 A A 1 C4 0.120 REMARK 500 A A 1 C6 A A 1 N6 0.107 REMARK 500 A A 2 O4' A A 2 C1' 0.102 REMARK 500 A A 2 N3 A A 2 C4 0.136 REMARK 500 A A 2 C6 A A 2 N1 0.136 REMARK 500 A A 2 C5 A A 2 N7 0.122 REMARK 500 A A 2 N7 A A 2 C8 0.143 REMARK 500 A A 2 N9 A A 2 C4 0.158 REMARK 500 A A 2 C6 A A 2 N6 0.100 REMARK 500 A A 3 O4' A A 3 C1' 0.082 REMARK 500 A A 3 C2 A A 3 N3 0.116 REMARK 500 A A 3 N3 A A 3 C4 0.056 REMARK 500 A A 3 C6 A A 3 N1 0.074 REMARK 500 A A 3 N7 A A 3 C8 0.102 REMARK 500 A A 3 C6 A A 3 N6 0.101 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 A A 1 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 A A 1 C5' - C4' - O4' ANGL. DEV. = 8.4 DEGREES REMARK 500 A A 1 N9 - C1' - C2' ANGL. DEV. = 34.3 DEGREES REMARK 500 A A 1 O4' - C1' - N9 ANGL. DEV. = -12.9 DEGREES REMARK 500 A A 1 N1 - C2 - N3 ANGL. DEV. = -9.4 DEGREES REMARK 500 A A 1 C2 - N3 - C4 ANGL. DEV. = 9.0 DEGREES REMARK 500 A A 1 N3 - C4 - C5 ANGL. DEV. = -6.4 DEGREES REMARK 500 A A 1 C5 - N7 - C8 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 1 N7 - C8 - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 A A 2 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES REMARK 500 A A 2 N9 - C1' - C2' ANGL. DEV. = 21.9 DEGREES REMARK 500 A A 2 O4' - C1' - N9 ANGL. DEV. = -8.1 DEGREES REMARK 500 A A 2 N1 - C2 - N3 ANGL. DEV. = -9.2 DEGREES REMARK 500 A A 2 C2 - N3 - C4 ANGL. DEV. = 8.5 DEGREES REMARK 500 A A 2 N3 - C4 - C5 ANGL. DEV. = -5.8 DEGREES REMARK 500 A A 2 C4 - C5 - N7 ANGL. DEV. = -3.1 DEGREES REMARK 500 A A 2 C5 - N7 - C8 ANGL. DEV. = 4.4 DEGREES REMARK 500 A A 2 N7 - C8 - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 A A 2 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 A A 3 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES REMARK 500 A A 3 N9 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 A A 3 O4' - C1' - N9 ANGL. DEV. = 16.5 DEGREES REMARK 500 A A 3 N1 - C2 - N3 ANGL. DEV. = -9.2 DEGREES REMARK 500 A A 3 C2 - N3 - C4 ANGL. DEV. = 9.2 DEGREES REMARK 500 A A 3 N3 - C4 - C5 ANGL. DEV. = -6.7 DEGREES REMARK 500 A A 3 C4 - C5 - C6 ANGL. DEV. = 3.1 DEGREES REMARK 500 A A 3 C4 - C5 - N7 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 3 C5 - N7 - C8 ANGL. DEV. = 4.2 DEGREES REMARK 500 A A 3 N7 - C8 - N9 ANGL. DEV. = -5.5 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 C 160 -70.95 -53.57 REMARK 500 ASP C 270 -166.79 -75.38 REMARK 500 ALA C 333 57.69 -67.90 REMARK 500 TRP C 343 -150.39 -79.00 REMARK 500 HIS C 426 -68.32 -123.34 REMARK 500 ARG C 427 39.71 -140.76 REMARK 500 ASP C 485 48.38 -153.21 REMARK 500 ASP C 494 -176.28 -65.10 REMARK 500 ASP C 503 103.61 59.98 REMARK 500 LYS C 509 -93.91 -69.67 REMARK 500 PRO C 555 -75.10 -56.52 REMARK 500 CYS C 576 37.47 -78.17 REMARK 500 LEU C 577 -31.52 -136.82 REMARK 500 THR C 607 75.94 -100.15 REMARK 500 ASN C 657 40.05 -78.96 REMARK 500 GLU C 676 58.81 -99.57 REMARK 500 LYS C 677 17.73 -153.27 REMARK 500 TYR C 712 34.93 -77.25 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 C 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN C 490 OD1 REMARK 620 2 ASP C 503 OD2 91.3 REMARK 620 3 ADP C 801 O1B 140.6 82.4 REMARK 620 4 ADP C 801 O2A 76.6 77.1 64.0 REMARK 620 5 HOH C 923 O 72.7 147.0 91.9 71.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 503 OD2 REMARK 620 2 ASP C 503 OD1 54.7 REMARK 620 3 ASP C 505 OD1 121.1 66.4 REMARK 620 4 ADP C 801 O3B 83.4 75.5 84.1 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 ADP C 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 803 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OAV RELATED DB: PDB DBREF 4OAU C 21 719 UNP Q05823 RN5A_HUMAN 21 719 DBREF 4OAU A 1 3 PDB 4OAU 4OAU 1 3 SEQADV 4OAU ASN C 672 UNP Q05823 HIS 672 ENGINEERED MUTATION SEQRES 1 C 699 ALA ALA VAL GLU ASP ASN HIS LEU LEU ILE LYS ALA VAL SEQRES 2 C 699 GLN ASN GLU ASP VAL ASP LEU VAL GLN GLN LEU LEU GLU SEQRES 3 C 699 GLY GLY ALA ASN VAL ASN PHE GLN GLU GLU GLU GLY GLY SEQRES 4 C 699 TRP THR PRO LEU HIS ASN ALA VAL GLN MET SER ARG GLU SEQRES 5 C 699 ASP ILE VAL GLU LEU LEU LEU ARG HIS GLY ALA ASP PRO SEQRES 6 C 699 VAL LEU ARG LYS LYS ASN GLY ALA THR PRO PHE ILE LEU SEQRES 7 C 699 ALA ALA ILE ALA GLY SER VAL LYS LEU LEU LYS LEU PHE SEQRES 8 C 699 LEU SER LYS GLY ALA ASP VAL ASN GLU CYS ASP PHE TYR SEQRES 9 C 699 GLY PHE THR ALA PHE MET GLU ALA ALA VAL TYR GLY LYS SEQRES 10 C 699 VAL LYS ALA LEU LYS PHE LEU TYR LYS ARG GLY ALA ASN SEQRES 11 C 699 VAL ASN LEU ARG ARG LYS THR LYS GLU ASP GLN GLU ARG SEQRES 12 C 699 LEU ARG LYS GLY GLY ALA THR ALA LEU MET ASP ALA ALA SEQRES 13 C 699 GLU LYS GLY HIS VAL GLU VAL LEU LYS ILE LEU LEU ASP SEQRES 14 C 699 GLU MET GLY ALA ASP VAL ASN ALA CYS ASP ASN MET GLY SEQRES 15 C 699 ARG ASN ALA LEU ILE HIS ALA LEU LEU SER SER ASP ASP SEQRES 16 C 699 SER ASP VAL GLU ALA ILE THR HIS LEU LEU LEU ASP HIS SEQRES 17 C 699 GLY ALA ASP VAL ASN VAL ARG GLY GLU ARG GLY LYS THR SEQRES 18 C 699 PRO LEU ILE LEU ALA VAL GLU LYS LYS HIS LEU GLY LEU SEQRES 19 C 699 VAL GLN ARG LEU LEU GLU GLN GLU HIS ILE GLU ILE ASN SEQRES 20 C 699 ASP THR ASP SER ASP GLY LYS THR ALA LEU LEU LEU ALA SEQRES 21 C 699 VAL GLU LEU LYS LEU LYS LYS ILE ALA GLU LEU LEU CYS SEQRES 22 C 699 LYS ARG GLY ALA SER THR ASP CYS GLY ASP LEU VAL MET SEQRES 23 C 699 THR ALA ARG ARG ASN TYR ASP HIS SER LEU VAL LYS VAL SEQRES 24 C 699 LEU LEU SER HIS GLY ALA LYS GLU ASP PHE HIS PRO PRO SEQRES 25 C 699 ALA GLU ASP TRP LYS PRO GLN SER SER HIS TRP GLY ALA SEQRES 26 C 699 ALA LEU LYS ASP LEU HIS ARG ILE TYR ARG PRO MET ILE SEQRES 27 C 699 GLY LYS LEU LYS PHE PHE ILE ASP GLU LYS TYR LYS ILE SEQRES 28 C 699 ALA ASP THR SER GLU GLY GLY ILE TYR LEU GLY PHE TYR SEQRES 29 C 699 GLU LYS GLN GLU VAL ALA VAL LYS THR PHE CYS GLU GLY SEQRES 30 C 699 SER PRO ARG ALA GLN ARG GLU VAL SER CYS LEU GLN SER SEQRES 31 C 699 SER ARG GLU ASN SER HIS LEU VAL THR PHE TYR GLY SER SEQRES 32 C 699 GLU SER HIS ARG GLY HIS LEU PHE VAL CYS VAL THR LEU SEQRES 33 C 699 CYS GLU GLN THR LEU GLU ALA CYS LEU ASP VAL HIS ARG SEQRES 34 C 699 GLY GLU ASP VAL GLU ASN GLU GLU ASP GLU PHE ALA ARG SEQRES 35 C 699 ASN VAL LEU SER SER ILE PHE LYS ALA VAL GLN GLU LEU SEQRES 36 C 699 HIS LEU SER CYS GLY TYR THR HIS GLN ASP LEU GLN PRO SEQRES 37 C 699 GLN ASN ILE LEU ILE ASP SER LYS LYS ALA ALA HIS LEU SEQRES 38 C 699 ALA ASP PHE ASP LYS SER ILE LYS TRP ALA GLY ASP PRO SEQRES 39 C 699 GLN GLU VAL LYS ARG ASP LEU GLU ASP LEU GLY ARG LEU SEQRES 40 C 699 VAL LEU TYR VAL VAL LYS LYS GLY SER ILE SER PHE GLU SEQRES 41 C 699 ASP LEU LYS ALA GLN SER ASN GLU GLU VAL VAL GLN LEU SEQRES 42 C 699 SER PRO ASP GLU GLU THR LYS ASP LEU ILE HIS ARG LEU SEQRES 43 C 699 PHE HIS PRO GLY GLU HIS VAL ARG ASP CYS LEU SER ASP SEQRES 44 C 699 LEU LEU GLY HIS PRO PHE PHE TRP THR TRP GLU SER ARG SEQRES 45 C 699 TYR ARG THR LEU ARG ASN VAL GLY ASN GLU SER ASP ILE SEQRES 46 C 699 LYS THR ARG LYS SER GLU SER GLU ILE LEU ARG LEU LEU SEQRES 47 C 699 GLN PRO GLY PRO SER GLU HIS SER LYS SER PHE ASP LYS SEQRES 48 C 699 TRP THR THR LYS ILE ASN GLU CYS VAL MET LYS LYS MET SEQRES 49 C 699 ASN LYS PHE TYR GLU LYS ARG GLY ASN PHE TYR GLN ASN SEQRES 50 C 699 THR VAL GLY ASP LEU LEU LYS PHE ILE ARG ASN LEU GLY SEQRES 51 C 699 GLU ASN ILE ASP GLU GLU LYS HIS LYS LYS MET LYS LEU SEQRES 52 C 699 LYS ILE GLY ASP PRO SER LEU TYR PHE GLN LYS THR PHE SEQRES 53 C 699 PRO ASP LEU VAL ILE TYR VAL TYR THR LYS LEU GLN ASN SEQRES 54 C 699 THR GLU TYR ARG LYS HIS PHE PRO GLN THR SEQRES 1 A 3 A A A HET ADP C 801 27 HET MG C 802 1 HET MG C 803 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *139(H2 O) HELIX 1 1 HIS C 27 ASN C 35 1 9 HELIX 2 2 ASP C 37 GLY C 48 1 12 HELIX 3 3 THR C 61 MET C 69 1 9 HELIX 4 4 ARG C 71 HIS C 81 1 11 HELIX 5 5 THR C 94 GLY C 103 1 10 HELIX 6 6 SER C 104 SER C 113 1 10 HELIX 7 7 THR C 127 TYR C 135 1 9 HELIX 8 8 LYS C 137 ARG C 147 1 11 HELIX 9 9 LYS C 158 LEU C 164 1 7 HELIX 10 10 THR C 170 GLY C 179 1 10 HELIX 11 11 HIS C 180 GLU C 190 1 11 HELIX 12 12 ASN C 204 SER C 212 1 9 HELIX 13 13 ASP C 217 HIS C 228 1 12 HELIX 14 14 THR C 241 LYS C 249 1 9 HELIX 15 15 HIS C 251 LEU C 259 1 9 HELIX 16 16 THR C 275 LEU C 283 1 9 HELIX 17 17 LEU C 285 ARG C 295 1 11 HELIX 18 18 ASP C 303 ASN C 311 1 9 HELIX 19 19 ASP C 313 HIS C 323 1 11 HELIX 20 20 GLY C 344 ILE C 353 1 10 HELIX 21 21 SER C 398 SER C 410 1 13 HELIX 22 22 LEU C 441 ASP C 452 1 12 HELIX 23 23 ASP C 458 SER C 478 1 21 HELIX 24 24 GLN C 487 GLN C 489 5 3 HELIX 25 25 ASP C 513 LYS C 533 1 21 HELIX 26 26 SER C 538 LYS C 543 1 6 HELIX 27 27 GLU C 548 LEU C 553 1 6 HELIX 28 28 ASP C 556 HIS C 568 1 13 HELIX 29 29 SER C 578 TRP C 587 5 10 HELIX 30 30 THR C 588 GLY C 600 1 13 HELIX 31 31 GLU C 602 THR C 607 1 6 HELIX 32 32 SER C 612 LEU C 618 1 7 HELIX 33 33 LYS C 631 ILE C 636 1 6 HELIX 34 34 GLU C 638 LYS C 646 1 9 HELIX 35 35 PHE C 647 GLU C 649 5 3 HELIX 36 36 THR C 658 ILE C 673 1 16 HELIX 37 37 LYS C 679 GLY C 686 1 8 HELIX 38 38 ASP C 687 PHE C 696 1 10 HELIX 39 39 ASP C 698 GLN C 708 1 11 SHEET 1 A 3 LYS C 362 PHE C 363 0 SHEET 2 A 3 GLY C 377 PHE C 383 -1 O PHE C 383 N LYS C 362 SHEET 3 A 3 LYS C 370 THR C 374 -1 N ALA C 372 O ILE C 379 SHEET 1 B 5 LYS C 362 PHE C 363 0 SHEET 2 B 5 GLY C 377 PHE C 383 -1 O PHE C 383 N LYS C 362 SHEET 3 B 5 GLU C 388 CYS C 395 -1 O VAL C 391 N TYR C 380 SHEET 4 B 5 HIS C 429 THR C 435 -1 O VAL C 434 N ALA C 390 SHEET 5 B 5 PHE C 420 SER C 425 -1 N GLY C 422 O CYS C 433 SHEET 1 C 3 GLN C 439 THR C 440 0 SHEET 2 C 3 ILE C 491 ILE C 493 -1 O ILE C 493 N GLN C 439 SHEET 3 C 3 ALA C 499 LEU C 501 -1 O HIS C 500 N LEU C 492 LINK O2' A A 1 P A A 2 1555 1555 1.58 LINK O2' A A 2 P A A 3 1555 1555 1.58 LINK OD1 ASN C 490 MG MG C 802 1555 1555 2.14 LINK OD2 ASP C 503 MG MG C 802 1555 1555 2.19 LINK OD2 ASP C 503 MG MG C 803 1555 1555 2.30 LINK OD1 ASP C 503 MG MG C 803 1555 1555 2.46 LINK OD1 ASP C 505 MG MG C 803 1555 1555 2.30 LINK O1B ADP C 801 MG MG C 802 1555 1555 2.08 LINK O2A ADP C 801 MG MG C 802 1555 1555 2.46 LINK O3B ADP C 801 MG MG C 803 1555 1555 2.11 LINK MG MG C 802 O HOH C 923 1555 1555 2.21 CISPEP 1 LYS C 496 LYS C 497 0 0.95 CISPEP 2 ASN C 637 GLU C 638 0 8.64 SITE 1 AC1 20 ILE C 371 ALA C 372 THR C 374 ILE C 379 SITE 2 AC1 20 ALA C 390 LYS C 392 VAL C 434 THR C 435 SITE 3 AC1 20 CYS C 437 THR C 440 GLN C 489 ASN C 490 SITE 4 AC1 20 LEU C 492 ASP C 503 ASP C 505 MG C 802 SITE 5 AC1 20 MG C 803 HOH C 923 HOH C 925 HOH C 993 SITE 1 AC2 6 GLN C 487 ASN C 490 ASP C 503 ADP C 801 SITE 2 AC2 6 MG C 803 HOH C 923 SITE 1 AC3 4 ASP C 503 ASP C 505 ADP C 801 MG C 802 CRYST1 60.130 116.600 162.400 90.00 90.00 90.00 P 21 2 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 0.016631 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008576 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006158 0.00000