HEADER HYDROLASE 25-MAY-09 3HKM TITLE CRYSTAL STRUCTURE OF RICE(ORYZA SATIVA) RRP46 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OS03G0854200 PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: RRP46, CDNA CLONE:J023009H04, FULL INSERT SEQUENCE, 3' COMPND 5 EXORIBONUCLEASE FAMILY, DOMAIN 1 CONTAINING PROTEIN, EXPRESSED, COMPND 6 PUTATIVE EXOSOME COMPONENT; COMPND 7 EC: 3.1.13.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA JAPONICA GROUP; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 STRAIN: JAPONICA GROUP; SOURCE 6 GENE: PUTATIVE EXONUCLEASE RRP46; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(RIPL); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS RNASE PH DOMAIN, PHOSPHORYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.-C.YANG,Y.-T.WANG,Y.-Y.HSIAO,L.G.DOUDEVA,H.S.YUAN REVDAT 3 01-NOV-23 3HKM 1 SEQADV REVDAT 2 08-DEC-10 3HKM 1 JRNL REVDAT 1 26-JAN-10 3HKM 0 JRNL AUTH C.-C.YANG,Y.-T.WANG,Y.-Y.HSIAO,L.G.DOUDEVA,P.-H.KUO, JRNL AUTH 2 S.Y.CHOW,H.S.YUAN JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF CRN-5 AND JRNL TITL 2 RRP46: AN EXOSOME COMPONENT PARTICIPATING IN APOPTOTIC DNA JRNL TITL 3 DEGRADATION JRNL REF RNA V. 16 1748 2010 JRNL REFN ISSN 1355-8382 JRNL PMID 20660080 JRNL DOI 10.1261/RNA.2180810 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 54782 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2776 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 26.8096 - 5.3729 0.98 2621 137 0.1644 0.2125 REMARK 3 2 5.3729 - 4.2702 0.98 2643 144 0.1261 0.2292 REMARK 3 3 4.2702 - 3.7320 0.98 2641 125 0.1227 0.2063 REMARK 3 4 3.7320 - 3.3915 0.98 2623 131 0.1379 0.1898 REMARK 3 5 3.3915 - 3.1489 0.98 2654 138 0.1491 0.2032 REMARK 3 6 3.1489 - 2.9634 0.98 2666 138 0.1729 0.2314 REMARK 3 7 2.9634 - 2.8152 0.98 2612 148 0.1822 0.2408 REMARK 3 8 2.8152 - 2.6928 0.98 2634 140 0.1852 0.2090 REMARK 3 9 2.6928 - 2.5892 0.98 2605 137 0.1893 0.3166 REMARK 3 10 2.5892 - 2.4999 0.98 2627 142 0.1955 0.2466 REMARK 3 11 2.4999 - 2.4218 0.98 2605 142 0.1938 0.2665 REMARK 3 12 2.4218 - 2.3526 0.98 2659 143 0.2035 0.2526 REMARK 3 13 2.3526 - 2.2907 0.98 2589 140 0.2024 0.2979 REMARK 3 14 2.2907 - 2.2349 0.98 2593 135 0.2067 0.2436 REMARK 3 15 2.2349 - 2.1841 0.98 2646 138 0.2069 0.2428 REMARK 3 16 2.1841 - 2.1376 0.98 2520 132 0.2085 0.2310 REMARK 3 17 2.1376 - 2.0949 0.98 2562 146 0.2119 0.2690 REMARK 3 18 2.0949 - 2.0554 0.98 2590 139 0.2253 0.2588 REMARK 3 19 2.0554 - 2.0187 0.98 2525 132 0.2349 0.3320 REMARK 3 20 2.0187 - 1.9845 0.98 2413 127 0.2301 0.2765 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 : 0.35 REMARK 3 B_SOL : 51.86 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14800 REMARK 3 B22 (A**2) : 0.14800 REMARK 3 B33 (A**2) : -0.29700 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 TWINNING INFORMATION. REMARK 3 FRACTION: 0.5010 REMARK 3 OPERATOR: H,-H-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 4763 REMARK 3 ANGLE : 1.090 6443 REMARK 3 CHIRALITY : 0.072 752 REMARK 3 PLANARITY : 0.006 831 REMARK 3 DIHEDRAL : 18.415 1763 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3HKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053249. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 CHNNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55506 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.340 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 21.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 REMARK 200 R SYM FOR SHELL (I) : 0.35400 REMARK 200 FOR SHELL : 3.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2NN6 CHAIN D REMARK 200 REMARK 200 REMARK: THE ORIGINAL DATA WAS SCALED TO 2.0 ANGSTROM BY HKL2000. REMARK 200 THEN REFINEMENT WAS PERFORMED WITH ALL SCALED DATA AUTOMATICALLY REMARK 200 BY PHENIX.REFINE. THE HIGHEST RESOLUTION OF 1.98A WAS MADE BY REMARK 200 PHENIX.REFINE. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM MALONATE, 20% PEG 3350, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.23400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.46800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: DIMER DISSOCIATED INTO MONOMERS IN REMARK 350 THE REMARK 300 CRYSTALLIZATION CONDITION 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 2 REMARK 465 GLU A 3 REMARK 465 SER A 4 REMARK 465 SER A 174 REMARK 465 ARG A 175 REMARK 465 LYS A 176 REMARK 465 SER A 177 REMARK 465 ALA A 178 REMARK 465 SER A 179 REMARK 465 SER A 180 REMARK 465 LYS A 181 REMARK 465 GLU A 182 REMARK 465 PRO A 183 REMARK 465 ASN A 184 REMARK 465 GLN A 185 REMARK 465 LYS A 186 REMARK 465 GLU A 187 REMARK 465 GLU A 188 REMARK 465 ASP A 189 REMARK 465 SER A 190 REMARK 465 GLU A 191 REMARK 465 ARG A 192 REMARK 465 GLY A 193 REMARK 465 LYS A 232 REMARK 465 GLN A 233 REMARK 465 ALA A 234 REMARK 465 PRO A 235 REMARK 465 GLY A 236 REMARK 465 ASP A 237 REMARK 465 VAL A 238 REMARK 465 LEU A 239 REMARK 465 GLU A 240 REMARK 465 HIS A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 SER B 4 REMARK 465 SER B 177 REMARK 465 ALA B 178 REMARK 465 SER B 179 REMARK 465 SER B 180 REMARK 465 LYS B 181 REMARK 465 GLU B 182 REMARK 465 PRO B 183 REMARK 465 ASN B 184 REMARK 465 GLN B 185 REMARK 465 LYS B 186 REMARK 465 GLU B 187 REMARK 465 GLU B 188 REMARK 465 ASP B 189 REMARK 465 SER B 190 REMARK 465 GLU B 191 REMARK 465 GLN B 233 REMARK 465 ALA B 234 REMARK 465 PRO B 235 REMARK 465 GLY B 236 REMARK 465 ASP B 237 REMARK 465 VAL B 238 REMARK 465 LEU B 239 REMARK 465 GLU B 240 REMARK 465 HIS B 241 REMARK 465 HIS B 242 REMARK 465 HIS B 243 REMARK 465 HIS B 244 REMARK 465 HIS B 245 REMARK 465 HIS B 246 REMARK 465 MET C 1 REMARK 465 GLU C 2 REMARK 465 GLU C 3 REMARK 465 SER C 4 REMARK 465 ASP C 25 REMARK 465 LYS C 53 REMARK 465 GLY C 54 REMARK 465 GLU C 55 REMARK 465 ASN C 56 REMARK 465 PRO C 57 REMARK 465 GLU C 58 REMARK 465 LEU C 146 REMARK 465 GLU C 147 REMARK 465 ASP C 148 REMARK 465 GLY C 149 REMARK 465 GLU C 150 REMARK 465 ASN C 173 REMARK 465 SER C 174 REMARK 465 ARG C 175 REMARK 465 LYS C 176 REMARK 465 SER C 177 REMARK 465 ALA C 178 REMARK 465 SER C 179 REMARK 465 SER C 180 REMARK 465 LYS C 181 REMARK 465 GLU C 182 REMARK 465 PRO C 183 REMARK 465 ASN C 184 REMARK 465 GLN C 185 REMARK 465 LYS C 186 REMARK 465 GLU C 187 REMARK 465 GLU C 188 REMARK 465 ASP C 189 REMARK 465 SER C 190 REMARK 465 GLU C 191 REMARK 465 ARG C 192 REMARK 465 GLY C 193 REMARK 465 VAL C 202 REMARK 465 ALA C 234 REMARK 465 PRO C 235 REMARK 465 GLY C 236 REMARK 465 ASP C 237 REMARK 465 VAL C 238 REMARK 465 LEU C 239 REMARK 465 GLU C 240 REMARK 465 HIS C 241 REMARK 465 HIS C 242 REMARK 465 HIS C 243 REMARK 465 HIS C 244 REMARK 465 HIS C 245 REMARK 465 HIS C 246 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 362 O HOH A 366 3554 2.05 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 PRO A 57 C - N - CD ANGL. DEV. = -15.8 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 ASN A 22 80.56 19.09 REMARK 500 TYR A 45 62.59 -113.20 REMARK 500 ARG A 52 140.31 -31.37 REMARK 500 PRO A 57 -5.05 18.83 REMARK 500 GLU A 147 -58.66 -27.73 REMARK 500 ILE A 195 -83.00 -84.91 REMARK 500 THR A 228 -80.82 -114.91 REMARK 500 ALA B 6 -7.19 -59.02 REMARK 500 PRO B 47 92.78 -64.67 REMARK 500 LYS B 53 108.94 -58.38 REMARK 500 ASP B 154 75.42 48.78 REMARK 500 THR B 228 -83.06 -129.98 REMARK 500 GLN B 231 6.53 -67.40 REMARK 500 ALA C 31 116.64 -162.04 REMARK 500 PRO C 47 93.99 -63.75 REMARK 500 ILE C 73 107.67 -41.44 REMARK 500 THR C 228 -77.55 -106.06 REMARK 500 LYS C 232 -177.60 -63.48 REMARK 500 REMARK 500 REMARK: NULL DBREF 3HKM A 1 238 UNP Q84T68 Q84T68_ORYSJ 1 238 DBREF 3HKM B 1 238 UNP Q84T68 Q84T68_ORYSJ 1 238 DBREF 3HKM C 1 238 UNP Q84T68 Q84T68_ORYSJ 1 238 SEQADV 3HKM LEU A 239 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM GLU A 240 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS A 241 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS A 242 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS A 243 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS A 244 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS A 245 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS A 246 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM LEU B 239 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM GLU B 240 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS B 241 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS B 242 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS B 243 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS B 244 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS B 245 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS B 246 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM LEU C 239 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM GLU C 240 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS C 241 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS C 242 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS C 243 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS C 244 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS C 245 UNP Q84T68 EXPRESSION TAG SEQADV 3HKM HIS C 246 UNP Q84T68 EXPRESSION TAG SEQRES 1 A 246 MET GLU GLU SER ARG ALA ASP GLY ARG ASN PRO ASN GLN SEQRES 2 A 246 LEU ARG PRO PHE SER CYS THR ARG ASN PRO LEU ASP ARG SEQRES 3 A 246 ALA HIS GLY SER ALA ARG TRP ALA GLN GLY ASP THR ILE SEQRES 4 A 246 VAL LEU ALA ALA VAL TYR GLY PRO LYS PRO GLY THR ARG SEQRES 5 A 246 LYS GLY GLU ASN PRO GLU LYS ALA SER ILE GLU VAL VAL SEQRES 6 A 246 TRP LYS PRO MET THR GLY GLN ILE GLY LYS GLN GLU LYS SEQRES 7 A 246 GLU TYR GLU MET THR LEU LYS ARG THR LEU GLN SER ILE SEQRES 8 A 246 CYS LEU LEU THR VAL HIS PRO ASN THR THR THR SER VAL SEQRES 9 A 246 ILE LEU GLN VAL VAL GLY ASN ASP GLY SER LEU LEU PRO SEQRES 10 A 246 CYS ALA ILE ASN ALA CYS CYS ALA ALA LEU VAL PHE ALA SEQRES 11 A 246 GLY ILE PRO LEU LYS HIS LEU ALA VAL ALA ILE GLY CYS SEQRES 12 A 246 GLY VAL LEU GLU ASP GLY GLU VAL ILE LEU ASP THR ASN SEQRES 13 A 246 LYS ALA GLU GLU GLN GLN LEU LYS SER PHE ALA HIS LEU SEQRES 14 A 246 VAL PHE PRO ASN SER ARG LYS SER ALA SER SER LYS GLU SEQRES 15 A 246 PRO ASN GLN LYS GLU GLU ASP SER GLU ARG GLY LEU ILE SEQRES 16 A 246 THR SER ILE THR HIS GLY VAL MET SER GLU GLU ASP TYR SEQRES 17 A 246 PHE SER CYS ILE GLU ARG GLY LEU ALA ALA SER SER ARG SEQRES 18 A 246 ILE SER ASP PHE MET ARG THR THR LEU GLN LYS GLN ALA SEQRES 19 A 246 PRO GLY ASP VAL LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 246 MET GLU GLU SER ARG ALA ASP GLY ARG ASN PRO ASN GLN SEQRES 2 B 246 LEU ARG PRO PHE SER CYS THR ARG ASN PRO LEU ASP ARG SEQRES 3 B 246 ALA HIS GLY SER ALA ARG TRP ALA GLN GLY ASP THR ILE SEQRES 4 B 246 VAL LEU ALA ALA VAL TYR GLY PRO LYS PRO GLY THR ARG SEQRES 5 B 246 LYS GLY GLU ASN PRO GLU LYS ALA SER ILE GLU VAL VAL SEQRES 6 B 246 TRP LYS PRO MET THR GLY GLN ILE GLY LYS GLN GLU LYS SEQRES 7 B 246 GLU TYR GLU MET THR LEU LYS ARG THR LEU GLN SER ILE SEQRES 8 B 246 CYS LEU LEU THR VAL HIS PRO ASN THR THR THR SER VAL SEQRES 9 B 246 ILE LEU GLN VAL VAL GLY ASN ASP GLY SER LEU LEU PRO SEQRES 10 B 246 CYS ALA ILE ASN ALA CYS CYS ALA ALA LEU VAL PHE ALA SEQRES 11 B 246 GLY ILE PRO LEU LYS HIS LEU ALA VAL ALA ILE GLY CYS SEQRES 12 B 246 GLY VAL LEU GLU ASP GLY GLU VAL ILE LEU ASP THR ASN SEQRES 13 B 246 LYS ALA GLU GLU GLN GLN LEU LYS SER PHE ALA HIS LEU SEQRES 14 B 246 VAL PHE PRO ASN SER ARG LYS SER ALA SER SER LYS GLU SEQRES 15 B 246 PRO ASN GLN LYS GLU GLU ASP SER GLU ARG GLY LEU ILE SEQRES 16 B 246 THR SER ILE THR HIS GLY VAL MET SER GLU GLU ASP TYR SEQRES 17 B 246 PHE SER CYS ILE GLU ARG GLY LEU ALA ALA SER SER ARG SEQRES 18 B 246 ILE SER ASP PHE MET ARG THR THR LEU GLN LYS GLN ALA SEQRES 19 B 246 PRO GLY ASP VAL LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 246 MET GLU GLU SER ARG ALA ASP GLY ARG ASN PRO ASN GLN SEQRES 2 C 246 LEU ARG PRO PHE SER CYS THR ARG ASN PRO LEU ASP ARG SEQRES 3 C 246 ALA HIS GLY SER ALA ARG TRP ALA GLN GLY ASP THR ILE SEQRES 4 C 246 VAL LEU ALA ALA VAL TYR GLY PRO LYS PRO GLY THR ARG SEQRES 5 C 246 LYS GLY GLU ASN PRO GLU LYS ALA SER ILE GLU VAL VAL SEQRES 6 C 246 TRP LYS PRO MET THR GLY GLN ILE GLY LYS GLN GLU LYS SEQRES 7 C 246 GLU TYR GLU MET THR LEU LYS ARG THR LEU GLN SER ILE SEQRES 8 C 246 CYS LEU LEU THR VAL HIS PRO ASN THR THR THR SER VAL SEQRES 9 C 246 ILE LEU GLN VAL VAL GLY ASN ASP GLY SER LEU LEU PRO SEQRES 10 C 246 CYS ALA ILE ASN ALA CYS CYS ALA ALA LEU VAL PHE ALA SEQRES 11 C 246 GLY ILE PRO LEU LYS HIS LEU ALA VAL ALA ILE GLY CYS SEQRES 12 C 246 GLY VAL LEU GLU ASP GLY GLU VAL ILE LEU ASP THR ASN SEQRES 13 C 246 LYS ALA GLU GLU GLN GLN LEU LYS SER PHE ALA HIS LEU SEQRES 14 C 246 VAL PHE PRO ASN SER ARG LYS SER ALA SER SER LYS GLU SEQRES 15 C 246 PRO ASN GLN LYS GLU GLU ASP SER GLU ARG GLY LEU ILE SEQRES 16 C 246 THR SER ILE THR HIS GLY VAL MET SER GLU GLU ASP TYR SEQRES 17 C 246 PHE SER CYS ILE GLU ARG GLY LEU ALA ALA SER SER ARG SEQRES 18 C 246 ILE SER ASP PHE MET ARG THR THR LEU GLN LYS GLN ALA SEQRES 19 C 246 PRO GLY ASP VAL LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 4 HOH *416(H2 O) HELIX 1 1 GLN A 76 CYS A 92 1 17 HELIX 2 2 SER A 114 GLY A 131 1 18 HELIX 3 3 ASN A 156 GLN A 161 1 6 HELIX 4 4 GLU A 205 THR A 228 1 24 HELIX 5 5 GLN B 76 CYS B 92 1 17 HELIX 6 6 SER B 114 GLY B 131 1 18 HELIX 7 7 ASN B 156 LEU B 163 1 8 HELIX 8 8 GLU B 205 THR B 228 1 24 HELIX 9 9 LYS C 75 CYS C 92 1 18 HELIX 10 10 SER C 114 GLY C 131 1 18 HELIX 11 11 ASN C 156 GLN C 162 1 7 HELIX 12 12 SER C 204 SER C 219 1 16 HELIX 13 13 SER C 219 THR C 228 1 10 SHEET 1 A 5 PHE A 17 ARG A 21 0 SHEET 2 A 5 GLY A 29 GLN A 35 -1 O ALA A 34 N SER A 18 SHEET 3 A 5 THR A 38 VAL A 44 -1 O VAL A 44 N GLY A 29 SHEET 4 A 5 THR A 100 GLY A 110 -1 O GLN A 107 N LEU A 41 SHEET 5 A 5 LYS A 48 PRO A 49 -1 N LYS A 48 O THR A 101 SHEET 1 B 5 PHE A 17 ARG A 21 0 SHEET 2 B 5 GLY A 29 GLN A 35 -1 O ALA A 34 N SER A 18 SHEET 3 B 5 THR A 38 VAL A 44 -1 O VAL A 44 N GLY A 29 SHEET 4 B 5 THR A 100 GLY A 110 -1 O GLN A 107 N LEU A 41 SHEET 5 B 5 SER A 61 LYS A 67 1 N GLU A 63 O VAL A 104 SHEET 1 C 6 VAL A 151 LEU A 153 0 SHEET 2 C 6 LEU A 137 VAL A 145 -1 N GLY A 144 O ILE A 152 SHEET 3 C 6 SER A 165 ASN A 173 -1 O ALA A 167 N CYS A 143 SHEET 4 C 6 SER A 197 GLY A 201 -1 O ILE A 198 N HIS A 168 SHEET 5 C 6 THR B 196 SER B 204 -1 O MET B 203 N THR A 199 SHEET 6 C 6 MET A 203 SER A 204 -1 N MET A 203 O THR B 199 SHEET 1 D 8 VAL A 151 LEU A 153 0 SHEET 2 D 8 LEU A 137 VAL A 145 -1 N GLY A 144 O ILE A 152 SHEET 3 D 8 SER A 165 ASN A 173 -1 O ALA A 167 N CYS A 143 SHEET 4 D 8 SER A 197 GLY A 201 -1 O ILE A 198 N HIS A 168 SHEET 5 D 8 THR B 196 SER B 204 -1 O MET B 203 N THR A 199 SHEET 6 D 8 SER B 165 ASN B 173 -1 N PHE B 166 O HIS B 200 SHEET 7 D 8 LEU B 137 VAL B 145 -1 N VAL B 139 O PHE B 171 SHEET 8 D 8 VAL B 151 LEU B 153 -1 O ILE B 152 N GLY B 144 SHEET 1 E 5 PHE B 17 ARG B 21 0 SHEET 2 E 5 GLY B 29 GLN B 35 -1 O ALA B 34 N SER B 18 SHEET 3 E 5 THR B 38 PRO B 49 -1 O VAL B 44 N GLY B 29 SHEET 4 E 5 THR B 100 GLY B 110 -1 O GLN B 107 N LEU B 41 SHEET 5 E 5 ALA B 60 LYS B 67 1 N SER B 61 O THR B 100 SHEET 1 F 5 PHE C 17 ARG C 21 0 SHEET 2 F 5 GLY C 29 GLN C 35 -1 O ALA C 34 N SER C 18 SHEET 3 F 5 THR C 38 PRO C 49 -1 O THR C 38 N GLN C 35 SHEET 4 F 5 THR C 100 GLY C 110 -1 O GLN C 107 N LEU C 41 SHEET 5 F 5 ALA C 60 LYS C 67 1 N SER C 61 O THR C 100 SHEET 1 G 3 VAL C 139 GLY C 144 0 SHEET 2 G 3 PHE C 166 PHE C 171 -1 O PHE C 171 N VAL C 139 SHEET 3 G 3 THR C 196 HIS C 200 -1 O ILE C 198 N HIS C 168 CRYST1 111.607 111.607 57.702 90.00 90.00 120.00 P 31 9 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 0.008960 0.005173 0.000000 0.00000 SCALE2 0.000000 0.010346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017330 0.00000