HEADER LIGASE/RNA 20-JUL-06 2DU4 TITLE CRYSTAL STRUCTURE OF ARCHAEOGLOBUS FULGIDUS O-PHOSPHOSERYL-TRNA TITLE 2 SYNTHETASE COMPLEXED WITH TRNACYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: O-PHOSPHOSERYL-TRNA SYNTHETASE; COMPND 7 CHAIN: A, B; COMPND 8 EC: 6.1.1.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 5 ORGANISM_TAXID: 2234; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS ALPHA4 TETRAMER, LIGASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.FUKUNAGA REVDAT 5 25-OCT-23 2DU4 1 REMARK REVDAT 4 09-JUN-09 2DU4 1 REVDAT REVDAT 3 24-FEB-09 2DU4 1 VERSN REVDAT 2 06-JAN-09 2DU4 1 JRNL REVDAT 1 13-MAR-07 2DU4 0 JRNL AUTH R.FUKUNAGA,S.YOKOYAMA JRNL TITL STRUCTURAL INSIGHTS INTO THE FIRST STEP OF RNA-DEPENDENT JRNL TITL 2 CYSTEINE BIOSYNTHESIS IN ARCHAEA. JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 272 2007 JRNL REFN ISSN 1545-9993 JRNL PMID 17351629 JRNL DOI 10.1038/NSMB1219 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2997395.230 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 47199 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 SET) : 0.207 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2362 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7345 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 368 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7540 REMARK 3 NUCLEIC ACID ATOMS : 1520 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 98.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.76000 REMARK 3 B22 (A**2) : -6.76000 REMARK 3 B33 (A**2) : 13.51000 REMARK 3 B12 (A**2) : 21.67000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.46 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.58 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.330 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 8.790 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 11.520; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 12.140; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 14.230; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 51.49 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 5 : SEP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : DNA-RNA_REP.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000025845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47199 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 98.6 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) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 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: CNS REMARK 200 STARTING MODEL: 2DU3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 6000, 1.2M NACL, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 50.51067 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 101.02133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 101.02133 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.51067 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER OF O-PHOSPHOSERYL- REMARK 300 TRNA SYNTHETASE WITH TWO BOUND TRNACYS MOLECULES GENERATED FROM THE REMARK 300 DIMER O-PHOSPHOSERYL-TRNA SYNTHETASE WITH ONE BOUND TRNACYS REMARK 300 MOLECULE IN THE ASYMMETRIC UNIT BY THE OPERATIONS: Y, X, -Z 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 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 PRO A 103 REMARK 465 ASN A 104 REMARK 465 VAL A 105 REMARK 465 GLY A 106 REMARK 465 ILE A 107 REMARK 465 SER A 108 REMARK 465 ALA A 109 REMARK 465 GLU A 110 REMARK 465 LYS A 111 REMARK 465 ILE A 112 REMARK 465 ARG A 113 REMARK 465 GLN A 114 REMARK 465 ILE A 115 REMARK 465 GLU A 116 REMARK 465 ALA A 117 REMARK 465 ILE A 118 REMARK 465 THR A 119 REMARK 465 LYS A 120 REMARK 465 ARG A 121 REMARK 465 GLU A 122 REMARK 465 VAL A 123 REMARK 465 ASP A 124 REMARK 465 SER A 125 REMARK 465 LYS A 126 REMARK 465 PRO A 127 REMARK 465 LEU A 128 REMARK 465 GLN A 129 REMARK 465 GLU A 130 REMARK 465 ILE A 131 REMARK 465 PHE A 132 REMARK 465 HIS A 133 REMARK 465 ARG A 134 REMARK 465 TYR A 135 REMARK 465 LYS A 136 REMARK 465 LYS A 137 REMARK 465 GLY A 138 REMARK 465 GLU A 139 REMARK 465 ILE A 140 REMARK 465 ASP A 141 REMARK 465 GLY A 142 REMARK 465 ASP A 143 REMARK 465 ASP A 144 REMARK 465 LEU A 145 REMARK 465 SER A 146 REMARK 465 TYR A 147 REMARK 465 LEU A 148 REMARK 465 ILE A 149 REMARK 465 ALA A 150 REMARK 465 GLU A 151 REMARK 465 VAL A 152 REMARK 465 LEU A 153 REMARK 465 ASP A 154 REMARK 465 VAL A 155 REMARK 465 ASP A 156 REMARK 465 ASP A 157 REMARK 465 ILE A 158 REMARK 465 THR A 159 REMARK 465 ALA A 160 REMARK 465 VAL A 161 REMARK 465 LYS A 162 REMARK 465 ILE A 163 REMARK 465 LEU A 164 REMARK 465 ASP A 165 REMARK 465 GLU A 166 REMARK 465 VAL A 167 REMARK 465 PHE A 168 REMARK 465 PRO A 169 REMARK 465 GLU A 170 REMARK 465 VAL B 105 REMARK 465 GLY B 106 REMARK 465 ILE B 107 REMARK 465 SER B 108 REMARK 465 ALA B 109 REMARK 465 GLU B 110 REMARK 465 LYS B 111 REMARK 465 ILE B 112 REMARK 465 ARG B 113 REMARK 465 GLN B 114 REMARK 465 ILE B 115 REMARK 465 GLU B 116 REMARK 465 ALA B 117 REMARK 465 ILE B 118 REMARK 465 THR B 119 REMARK 465 LYS B 120 REMARK 465 ARG B 121 REMARK 465 GLU B 122 REMARK 465 VAL B 123 REMARK 465 ASP B 124 REMARK 465 SER B 125 REMARK 465 LYS B 126 REMARK 465 PRO B 127 REMARK 465 LEU B 128 REMARK 465 GLN B 129 REMARK 465 GLU B 130 REMARK 465 ILE B 131 REMARK 465 PHE B 132 REMARK 465 HIS B 133 REMARK 465 ARG B 134 REMARK 465 TYR B 135 REMARK 465 LYS B 136 REMARK 465 LYS B 137 REMARK 465 GLY B 138 REMARK 465 GLU B 139 REMARK 465 ILE B 140 REMARK 465 ASP B 141 REMARK 465 GLY B 142 REMARK 465 ASP B 143 REMARK 465 ASP B 144 REMARK 465 LEU B 145 REMARK 465 SER B 146 REMARK 465 TYR B 147 REMARK 465 LEU B 148 REMARK 465 ILE B 149 REMARK 465 ALA B 150 REMARK 465 GLU B 151 REMARK 465 VAL B 152 REMARK 465 LEU B 153 REMARK 465 ASP B 154 REMARK 465 VAL B 155 REMARK 465 ASP B 156 REMARK 465 ASP B 157 REMARK 465 ILE B 158 REMARK 465 THR B 159 REMARK 465 ALA B 160 REMARK 465 VAL B 161 REMARK 465 LYS B 162 REMARK 465 ILE B 163 REMARK 465 LEU B 164 REMARK 465 ASP B 165 REMARK 465 GLU B 166 REMARK 465 VAL B 167 REMARK 465 PHE B 168 REMARK 465 PRO B 169 REMARK 465 GLU B 170 REMARK 465 PHE B 171 REMARK 465 LYS B 172 REMARK 465 GLU B 173 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 SER B 185 OH TYR B 229 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 G C 901 P G C 901 OP3 -0.083 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 320 C - N - CA ANGL. DEV. = 9.4 DEGREES REMARK 500 LEU B 56 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 LEU B 326 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 PRO B 459 C - N - CA ANGL. DEV. = 10.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 32 -38.25 -37.63 REMARK 500 ASP A 76 -2.68 -56.66 REMARK 500 LYS A 172 -11.99 -49.35 REMARK 500 GLU A 173 -70.86 -66.87 REMARK 500 LEU A 174 147.15 -3.89 REMARK 500 SER A 178 167.75 -45.12 REMARK 500 ARG A 184 128.69 -31.90 REMARK 500 ARG A 216 109.32 -169.14 REMARK 500 ARG A 225 147.65 168.77 REMARK 500 LEU A 253 -61.47 -90.80 REMARK 500 ARG A 270 76.90 34.43 REMARK 500 ASP A 277 5.45 82.62 REMARK 500 GLN A 279 95.18 -65.18 REMARK 500 LYS A 288 -34.75 -37.45 REMARK 500 SER A 293 2.88 -55.47 REMARK 500 TYR A 296 42.33 -75.10 REMARK 500 GLU A 316 -10.33 -45.27 REMARK 500 HIS A 352 31.00 -99.65 REMARK 500 GLU A 354 56.81 -90.42 REMARK 500 LYS A 390 -70.39 -60.09 REMARK 500 GLU A 394 109.17 -59.35 REMARK 500 SER A 399 142.50 -175.18 REMARK 500 ARG A 410 147.06 -173.40 REMARK 500 ASN A 422 42.65 74.86 REMARK 500 THR A 423 -157.55 -166.76 REMARK 500 PRO A 428 23.67 -78.41 REMARK 500 ALA A 429 -0.07 -143.35 REMARK 500 LYS A 446 80.49 -65.00 REMARK 500 LYS A 448 8.72 -68.72 REMARK 500 ALA A 480 15.39 -58.93 REMARK 500 GLU A 483 -20.12 58.29 REMARK 500 GLN A 484 157.76 -30.13 REMARK 500 ARG A 492 -107.23 -96.59 REMARK 500 PHE A 526 75.04 29.51 REMARK 500 LEU B 11 -5.05 -47.77 REMARK 500 LYS B 14 -83.08 -82.87 REMARK 500 PHE B 16 -72.83 -58.15 REMARK 500 GLU B 17 -41.10 -26.82 REMARK 500 PRO B 103 105.00 -41.43 REMARK 500 GLN B 219 -62.59 72.79 REMARK 500 LYS B 269 1.17 -63.19 REMARK 500 ARG B 270 65.58 13.62 REMARK 500 ASP B 277 6.32 80.87 REMARK 500 THR B 294 -167.90 -118.98 REMARK 500 ILE B 380 -71.69 -79.20 REMARK 500 GLU B 386 -78.90 -64.53 REMARK 500 GLU B 394 153.49 -45.47 REMARK 500 GLU B 420 173.47 -38.73 REMARK 500 ASN B 422 -37.10 78.93 REMARK 500 THR B 423 -154.68 -66.05 REMARK 500 REMARK 500 THIS ENTRY HAS 61 RAMACHANDRAN OUTLIERS. 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 G C 956 0.05 SIDE CHAIN REMARK 500 TYR A 338 0.06 SIDE CHAIN REMARK 500 TYR B 274 0.06 SIDE CHAIN REMARK 500 TYR B 338 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DU3 RELATED DB: PDB REMARK 900 RELATED ID: 2DU5 RELATED DB: PDB REMARK 900 RELATED ID: 2DU6 RELATED DB: PDB REMARK 900 RELATED ID: 2DU7 RELATED DB: PDB DBREF 2DU4 A 1 534 UNP O30126 O30126_ARCFU 1 534 DBREF 2DU4 B 1 534 UNP O30126 O30126_ARCFU 1 534 DBREF 2DU4 C 901 971 PDB 2DU4 2DU4 901 971 SEQRES 1 C 71 G C C A G G G U G G C A G SEQRES 2 C 71 A G G G G C U U U G C G G SEQRES 3 C 71 C G G A C U G C A G A U C SEQRES 4 C 71 C G C U U U A C C C C G G SEQRES 5 C 71 U U C G A A U C C G G G C SEQRES 6 C 71 C C U G G C SEQRES 1 A 534 MET LYS PHE ASP PRO GLN LYS TYR ARG GLU LEU ALA GLU SEQRES 2 A 534 LYS ASP PHE GLU ALA ALA TRP LYS ALA GLY LYS GLU ILE SEQRES 3 A 534 LEU ALA GLU ARG SER PRO ASN GLU LEU TYR PRO ARG VAL SEQRES 4 A 534 GLY PHE SER PHE GLY LYS GLU HIS PRO LEU PHE ALA THR SEQRES 5 A 534 ILE GLN ARG LEU ARG GLU ALA TYR LEU SER ILE GLY PHE SEQRES 6 A 534 SER GLU VAL VAL ASN PRO LEU ILE VAL GLU ASP VAL HIS SEQRES 7 A 534 VAL LYS LYS GLN PHE GLY ARG GLU ALA LEU ALA VAL LEU SEQRES 8 A 534 ASP ARG CYS PHE TYR LEU ALA THR LEU PRO LYS PRO ASN SEQRES 9 A 534 VAL GLY ILE SER ALA GLU LYS ILE ARG GLN ILE GLU ALA SEQRES 10 A 534 ILE THR LYS ARG GLU VAL ASP SER LYS PRO LEU GLN GLU SEQRES 11 A 534 ILE PHE HIS ARG TYR LYS LYS GLY GLU ILE ASP GLY ASP SEQRES 12 A 534 ASP LEU SER TYR LEU ILE ALA GLU VAL LEU ASP VAL ASP SEQRES 13 A 534 ASP ILE THR ALA VAL LYS ILE LEU ASP GLU VAL PHE PRO SEQRES 14 A 534 GLU PHE LYS GLU LEU LYS PRO ILE SER SER THR LEU THR SEQRES 15 A 534 LEU ARG SER HIS MET THR THR GLY TRP PHE ILE THR LEU SEQRES 16 A 534 SER HIS ILE ALA ASP LYS LEU PRO LEU PRO ILE LYS LEU SEQRES 17 A 534 PHE SER ILE ASP ARG CYS PHE ARG ARG GLU GLN GLY GLU SEQRES 18 A 534 ASP ALA THR ARG LEU TYR THR TYR PHE SER ALA SER CYS SEQRES 19 A 534 VAL LEU VAL ASP GLU GLU LEU SER VAL ASP ASP GLY LYS SEQRES 20 A 534 ALA VAL ALA GLU ALA LEU LEU ARG GLN PHE GLY PHE GLU SEQRES 21 A 534 ASN PHE ARG PHE ARG LYS ASP GLU LYS ARG SER LYS TYR SEQRES 22 A 534 TYR ILE PRO ASP THR GLN THR GLU VAL PHE ALA PHE HIS SEQRES 23 A 534 PRO LYS LEU VAL GLY SER SER THR LYS TYR SER ASP GLY SEQRES 24 A 534 TRP ILE GLU ILE ALA THR PHE GLY ILE TYR SER PRO THR SEQRES 25 A 534 ALA LEU ALA GLU TYR ASP ILE PRO TYR PRO VAL MET ASN SEQRES 26 A 534 LEU GLY LEU GLY VAL GLU ARG LEU ALA MET ILE LEU TYR SEQRES 27 A 534 GLY TYR ASP ASP VAL ARG LYS MET VAL TYR PRO GLN ILE SEQRES 28 A 534 HIS GLY GLU ILE LYS LEU SER ASP LEU ASP ILE ALA ARG SEQRES 29 A 534 GLU ILE LYS VAL LYS GLU VAL PRO GLN THR ALA VAL GLY SEQRES 30 A 534 LEU LYS ILE ALA GLN SER ILE VAL GLU THR ALA GLU LYS SEQRES 31 A 534 HIS ALA SER GLU PRO SER PRO CYS SER PHE LEU ALA PHE SEQRES 32 A 534 GLU GLY GLU MET MET GLY ARG ASN VAL ARG VAL TYR VAL SEQRES 33 A 534 VAL GLU GLU GLU GLU ASN THR LYS LEU CYS GLY PRO ALA SEQRES 34 A 534 TYR ALA ASN GLU VAL VAL VAL TYR LYS GLY ASP ILE TYR SEQRES 35 A 534 GLY ILE PRO LYS THR LYS LYS TRP ARG SER PHE PHE GLU SEQRES 36 A 534 GLU GLY VAL PRO THR GLY ILE ARG TYR ILE ASP GLY PHE SEQRES 37 A 534 ALA TYR TYR ALA ALA ARG LYS VAL GLU GLU ALA ALA MET SEQRES 38 A 534 ARG GLU GLN GLU GLU VAL LYS VAL LYS ALA ARG ILE VAL SEQRES 39 A 534 GLU ASN LEU SER ASP ILE ASN LEU TYR ILE HIS GLU ASN SEQRES 40 A 534 VAL ARG ARG TYR ILE LEU TRP LYS LYS GLY LYS ILE ASP SEQRES 41 A 534 VAL ARG GLY PRO LEU PHE VAL THR VAL LYS ALA GLU ILE SEQRES 42 A 534 GLU SEQRES 1 B 534 MET LYS PHE ASP PRO GLN LYS TYR ARG GLU LEU ALA GLU SEQRES 2 B 534 LYS ASP PHE GLU ALA ALA TRP LYS ALA GLY LYS GLU ILE SEQRES 3 B 534 LEU ALA GLU ARG SER PRO ASN GLU LEU TYR PRO ARG VAL SEQRES 4 B 534 GLY PHE SER PHE GLY LYS GLU HIS PRO LEU PHE ALA THR SEQRES 5 B 534 ILE GLN ARG LEU ARG GLU ALA TYR LEU SER ILE GLY PHE SEQRES 6 B 534 SER GLU VAL VAL ASN PRO LEU ILE VAL GLU ASP VAL HIS SEQRES 7 B 534 VAL LYS LYS GLN PHE GLY ARG GLU ALA LEU ALA VAL LEU SEQRES 8 B 534 ASP ARG CYS PHE TYR LEU ALA THR LEU PRO LYS PRO ASN SEQRES 9 B 534 VAL GLY ILE SER ALA GLU LYS ILE ARG GLN ILE GLU ALA SEQRES 10 B 534 ILE THR LYS ARG GLU VAL ASP SER LYS PRO LEU GLN GLU SEQRES 11 B 534 ILE PHE HIS ARG TYR LYS LYS GLY GLU ILE ASP GLY ASP SEQRES 12 B 534 ASP LEU SER TYR LEU ILE ALA GLU VAL LEU ASP VAL ASP SEQRES 13 B 534 ASP ILE THR ALA VAL LYS ILE LEU ASP GLU VAL PHE PRO SEQRES 14 B 534 GLU PHE LYS GLU LEU LYS PRO ILE SER SER THR LEU THR SEQRES 15 B 534 LEU ARG SER HIS MET THR THR GLY TRP PHE ILE THR LEU SEQRES 16 B 534 SER HIS ILE ALA ASP LYS LEU PRO LEU PRO ILE LYS LEU SEQRES 17 B 534 PHE SER ILE ASP ARG CYS PHE ARG ARG GLU GLN GLY GLU SEQRES 18 B 534 ASP ALA THR ARG LEU TYR THR TYR PHE SER ALA SER CYS SEQRES 19 B 534 VAL LEU VAL ASP GLU GLU LEU SER VAL ASP ASP GLY LYS SEQRES 20 B 534 ALA VAL ALA GLU ALA LEU LEU ARG GLN PHE GLY PHE GLU SEQRES 21 B 534 ASN PHE ARG PHE ARG LYS ASP GLU LYS ARG SER LYS TYR SEQRES 22 B 534 TYR ILE PRO ASP THR GLN THR GLU VAL PHE ALA PHE HIS SEQRES 23 B 534 PRO LYS LEU VAL GLY SER SER THR LYS TYR SER ASP GLY SEQRES 24 B 534 TRP ILE GLU ILE ALA THR PHE GLY ILE TYR SER PRO THR SEQRES 25 B 534 ALA LEU ALA GLU TYR ASP ILE PRO TYR PRO VAL MET ASN SEQRES 26 B 534 LEU GLY LEU GLY VAL GLU ARG LEU ALA MET ILE LEU TYR SEQRES 27 B 534 GLY TYR ASP ASP VAL ARG LYS MET VAL TYR PRO GLN ILE SEQRES 28 B 534 HIS GLY GLU ILE LYS LEU SER ASP LEU ASP ILE ALA ARG SEQRES 29 B 534 GLU ILE LYS VAL LYS GLU VAL PRO GLN THR ALA VAL GLY SEQRES 30 B 534 LEU LYS ILE ALA GLN SER ILE VAL GLU THR ALA GLU LYS SEQRES 31 B 534 HIS ALA SER GLU PRO SER PRO CYS SER PHE LEU ALA PHE SEQRES 32 B 534 GLU GLY GLU MET MET GLY ARG ASN VAL ARG VAL TYR VAL SEQRES 33 B 534 VAL GLU GLU GLU GLU ASN THR LYS LEU CYS GLY PRO ALA SEQRES 34 B 534 TYR ALA ASN GLU VAL VAL VAL TYR LYS GLY ASP ILE TYR SEQRES 35 B 534 GLY ILE PRO LYS THR LYS LYS TRP ARG SER PHE PHE GLU SEQRES 36 B 534 GLU GLY VAL PRO THR GLY ILE ARG TYR ILE ASP GLY PHE SEQRES 37 B 534 ALA TYR TYR ALA ALA ARG LYS VAL GLU GLU ALA ALA MET SEQRES 38 B 534 ARG GLU GLN GLU GLU VAL LYS VAL LYS ALA ARG ILE VAL SEQRES 39 B 534 GLU ASN LEU SER ASP ILE ASN LEU TYR ILE HIS GLU ASN SEQRES 40 B 534 VAL ARG ARG TYR ILE LEU TRP LYS LYS GLY LYS ILE ASP SEQRES 41 B 534 VAL ARG GLY PRO LEU PHE VAL THR VAL LYS ALA GLU ILE SEQRES 42 B 534 GLU FORMUL 4 HOH *57(H2 O) HELIX 1 1 ASP A 4 GLU A 13 1 10 HELIX 2 2 ASP A 15 GLY A 23 1 9 HELIX 3 3 LYS A 24 LEU A 27 5 4 HELIX 4 4 SER A 31 LEU A 35 5 5 HELIX 5 5 HIS A 47 ILE A 63 1 17 HELIX 6 6 ASP A 76 GLY A 84 1 9 HELIX 7 7 GLU A 86 LEU A 91 1 6 HELIX 8 8 HIS A 186 HIS A 197 1 12 HELIX 9 9 VAL A 243 ARG A 255 1 13 HELIX 10 10 PRO A 287 VAL A 290 5 4 HELIX 11 11 LYS A 295 ASP A 298 5 4 HELIX 12 12 SER A 310 GLU A 316 1 7 HELIX 13 13 VAL A 330 TYR A 338 1 9 HELIX 14 14 ASP A 342 TYR A 348 1 7 HELIX 15 15 SER A 358 GLU A 365 1 8 HELIX 16 16 THR A 374 HIS A 391 1 18 HELIX 17 17 TRP A 450 GLY A 457 1 8 HELIX 18 18 TYR A 464 ALA A 480 1 17 HELIX 19 19 ASN A 496 ILE A 500 5 5 HELIX 20 20 HIS A 505 LYS A 515 1 11 HELIX 21 21 ASP B 4 LYS B 14 1 11 HELIX 22 22 ASP B 15 GLY B 23 1 9 HELIX 23 23 LYS B 24 LEU B 27 5 4 HELIX 24 24 SER B 31 LEU B 35 5 5 HELIX 25 25 HIS B 47 SER B 62 1 16 HELIX 26 26 ASP B 76 GLY B 84 1 9 HELIX 27 27 GLU B 86 LEU B 91 1 6 HELIX 28 28 ASP B 92 CYS B 94 5 3 HELIX 29 29 MET B 187 SER B 196 1 10 HELIX 30 30 SER B 242 GLN B 256 1 15 HELIX 31 31 SER B 310 GLU B 316 1 7 HELIX 32 32 VAL B 330 GLY B 339 1 10 HELIX 33 33 ASP B 342 TYR B 348 1 7 HELIX 34 34 SER B 358 GLU B 365 1 8 HELIX 35 35 THR B 374 HIS B 391 1 18 HELIX 36 36 THR B 447 LYS B 449 5 3 HELIX 37 37 TRP B 450 GLY B 457 1 8 HELIX 38 38 TYR B 464 ARG B 482 1 19 HELIX 39 39 LEU B 497 ILE B 500 5 4 HELIX 40 40 HIS B 505 LYS B 515 1 11 SHEET 1 A 7 SER A 66 GLU A 67 0 SHEET 2 A 7 ILE A 206 PHE A 215 1 O PHE A 209 N SER A 66 SHEET 3 A 7 THR A 228 VAL A 237 -1 O SER A 233 N SER A 210 SHEET 4 A 7 VAL A 323 GLY A 329 -1 O MET A 324 N LEU A 236 SHEET 5 A 7 TRP A 300 ILE A 308 -1 N GLY A 307 O ASN A 325 SHEET 6 A 7 THR A 280 PHE A 285 -1 N VAL A 282 O ALA A 304 SHEET 7 A 7 ASN A 261 LYS A 266 -1 N ARG A 265 O GLU A 281 SHEET 1 B 2 ILE A 73 GLU A 75 0 SHEET 2 B 2 LEU A 181 LEU A 183 -1 O THR A 182 N VAL A 74 SHEET 1 C 4 TYR A 96 ALA A 98 0 SHEET 2 C 4 PHE B 95 THR B 99 -1 O ALA B 98 N TYR A 96 SHEET 3 C 4 ILE B 177 LEU B 183 -1 O ILE B 177 N THR B 99 SHEET 4 C 4 ILE B 73 GLU B 75 -1 N VAL B 74 O THR B 182 SHEET 1 D 2 ILE A 366 VAL A 368 0 SHEET 2 D 2 LEU A 502 ILE A 504 -1 O TYR A 503 N LYS A 367 SHEET 1 E 4 CYS A 398 GLU A 406 0 SHEET 2 E 4 ASN A 411 GLU A 418 -1 O VAL A 414 N PHE A 403 SHEET 3 E 4 GLY A 523 ILE A 533 -1 O LYS A 530 N TYR A 415 SHEET 4 E 4 GLU A 486 VAL A 494 -1 N VAL A 494 O GLY A 523 SHEET 1 F 4 VAL A 458 ARG A 463 0 SHEET 2 F 4 GLU A 433 TYR A 437 -1 N VAL A 434 O ILE A 462 SHEET 3 F 4 ASP A 440 ILE A 444 -1 O ILE A 444 N GLU A 433 SHEET 4 F 4 ILE A 519 ASP A 520 1 O ASP A 520 N GLY A 443 SHEET 1 G 7 SER B 66 GLU B 67 0 SHEET 2 G 7 ILE B 206 PHE B 215 1 O LYS B 207 N SER B 66 SHEET 3 G 7 THR B 228 VAL B 237 -1 O TYR B 229 N CYS B 214 SHEET 4 G 7 VAL B 323 GLY B 329 -1 O LEU B 326 N CYS B 234 SHEET 5 G 7 ASP B 298 ILE B 308 -1 N GLY B 307 O ASN B 325 SHEET 6 G 7 THR B 280 VAL B 290 -1 N HIS B 286 O GLY B 299 SHEET 7 G 7 ASN B 261 LYS B 266 -1 N ARG B 265 O GLU B 281 SHEET 1 H 2 LYS B 367 VAL B 368 0 SHEET 2 H 2 LEU B 502 TYR B 503 -1 O TYR B 503 N LYS B 367 SHEET 1 I 4 CYS B 398 MET B 407 0 SHEET 2 I 4 ARG B 410 GLU B 418 -1 O VAL B 414 N ALA B 402 SHEET 3 I 4 THR B 528 ILE B 533 -1 O LYS B 530 N TYR B 415 SHEET 4 I 4 GLU B 486 VAL B 489 -1 N VAL B 489 O VAL B 529 SHEET 1 J 4 VAL B 458 ARG B 463 0 SHEET 2 J 4 GLU B 433 TYR B 437 -1 N VAL B 436 O VAL B 458 SHEET 3 J 4 ASP B 440 ILE B 444 -1 O TYR B 442 N VAL B 435 SHEET 4 J 4 ILE B 519 ASP B 520 1 O ASP B 520 N ILE B 441 SHEET 1 K 2 ILE B 493 VAL B 494 0 SHEET 2 K 2 GLY B 523 PRO B 524 -1 O GLY B 523 N VAL B 494 CISPEP 1 TYR A 36 PRO A 37 0 0.20 CISPEP 2 LEU A 204 PRO A 205 0 0.31 CISPEP 3 SER A 396 PRO A 397 0 -0.21 CISPEP 4 TYR B 36 PRO B 37 0 0.60 CISPEP 5 LEU B 204 PRO B 205 0 -0.69 CISPEP 6 SER B 396 PRO B 397 0 -0.03 CRYST1 148.433 148.433 151.532 90.00 90.00 120.00 P 31 2 1 12 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 0.006737 0.003890 0.000000 0.00000 SCALE2 0.000000 0.007779 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006599 0.00000