PDB Short entry for 1QMH HEADER LIGASE 28-SEP-99 1QMH TITLE CRYSTAL STRUCTURE OF RNA 3'-TERMINAL PHOSPHATE CYCLASE, AN TITLE 2 UBIQUITOUS ENZYME WITH UNUSUAL TOPOLOGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA 3'-TERMINAL PHOSPHATE CYCLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNA CYCLASE, RNA-3'-PHOSPHATE CYCLASE; COMPND 5 EC: 6.5.1.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: RTCA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_VECTOR: PET-11D; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET-11D_ECOLI CYCLASE; SOURCE 14 EXPRESSION_SYSTEM_GENE: RTCA KEYWDS 2'3'CYCLIC PHOSPHATE RNA, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR G.J.PALM,E.BILLY,W.FILIPOWICZ,A.WLODAWER REVDAT 3 17-APR-13 1QMH 1 HEADER COMPND SOURCE KEYWDS REVDAT 3 2 REMARK VERSN DBREF SEQADV REVDAT 3 3 FORMUL REVDAT 2 24-FEB-09 1QMH 1 VERSN REVDAT 1 11-JAN-00 1QMH 0 JRNL AUTH G.J.PALM,E.BILLY,W.FILIPOWICZ,A.WLODAWER JRNL TITL CRYSTAL STRUCTURE OF RNA 3'-TERMINAL PHOSPHATE JRNL TITL 2 CYCLASE, A UBIQUITOUS ENZYME WITH UNUSUAL TOPOLOGY JRNL REF STRUCTURE V. 8 13 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10673421 JRNL DOI 10.1016/S0969-2126(00)00076-9 REMARK 2 REMARK 2 RESOLUTION. 2.1 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.1 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.0 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 48203 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 2286 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4973 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 424 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.1 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.228 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.47 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.022 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.046 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.056 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.029 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.185 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.196 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.261 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.171 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.3 ; 7.0 REMARK 3 STAGGERED (DEGREES) : 17.5 ; 15.0 REMARK 3 TRANSVERSE (DEGREES) : 21.1 ; 20.0 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.6 ; 2.0 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.8 ; 3.0 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.0 ; 2.0 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.6 ; 3.0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT WAS STARTED WITH XPLOR REMARK 3 3.1, THE HIS TAG OF CHAINS A AND B WERE NOT VISIBLE IN THE REMARK 3 ELECTRON DENSITY. THE ELECTRON DENSITY AROUND RESIDUES 94 TO REMARK 3 97 COULD NOT BE MODELLED WITH STANDARD BACKBONE GEOMETRY. REMARK 4 REMARK 4 1QMH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-SEP-99. REMARK 100 THE PDBE ID CODE IS EBI-2830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-98 REMARK 200 TEMPERATURE (KELVIN) : 105.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96456 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50057 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 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 1QMI, CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN WAS CRYSTALLIZED REMARK 280 FROM 13-15% MPEG 2000, 200 MM NA-CITRATE PH 4.0, 200 MM REMARK 280 TRIS/HCL PH 8.0, 2 MM DTT. PROTEIN CONCENTRATION WAS REMARK 280 CA. 15 MG/ML. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 62.90000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 62.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 VAL A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 GLU A 339 REMARK 465 GLY A 340 REMARK 465 SER A 341 REMARK 465 HIS A 342 REMARK 465 HIS A 343 REMARK 465 HIS A 344 REMARK 465 HIS A 345 REMARK 465 HIS A 346 REMARK 465 HIS A 347 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 LYS B 3 REMARK 465 ARG B 4 REMARK 465 GLY B 340 REMARK 465 SER B 341 REMARK 465 HIS B 342 REMARK 465 HIS B 343 REMARK 465 HIS B 344 REMARK 465 HIS B 345 REMARK 465 HIS B 346 REMARK 465 HIS B 347 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 ARG A 203 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 185 CG CD OE1 OE2 REMARK 470 ARG B 257 CG CD NE CZ NH1 NH2 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 ALA B 7 NH2 ARG B 319 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 ARG A 193 CD ARG A 193 NE -0.124 REMARK 500 SER B 25 CA SER B 25 CB 0.098 REMARK 500 ASP B 230 CA ASP B 230 CB 0.161 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 LEU A 24 CB - CG - CD2 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 SER A 95 N - CA - CB ANGL. DEV. = -10.0 DEGREES REMARK 500 ALA A 96 N - CA - CB ANGL. DEV. = 8.5 DEGREES REMARK 500 ASP A 114 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 118 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 GLU A 120 OE1 - CD - OE2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 137 CD - NE - CZ ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG A 137 CG - CD - NE ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG A 137 NE - CZ - NH1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 137 NH1 - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 138 CD - NE - CZ ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 GLU A 141 OE1 - CD - OE2 ANGL. DEV. = -15.4 DEGREES REMARK 500 GLY A 148 O - C - N ANGL. DEV. = -9.6 DEGREES REMARK 500 LEU A 155 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG A 157 CA - CB - CG ANGL. DEV. = 19.0 DEGREES REMARK 500 ARG A 157 CG - CD - NE ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG A 157 NE - CZ - NH1 ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG A 157 NH1 - CZ - NH2 ANGL. DEV. = 9.7 DEGREES REMARK 500 GLY A 164 N - CA - C ANGL. DEV. = -15.8 DEGREES REMARK 500 VAL A 172 CA - CB - CG2 ANGL. DEV. = 12.5 DEGREES REMARK 500 ARG A 193 CD - NE - CZ ANGL. DEV. = 39.1 DEGREES REMARK 500 ARG A 193 CG - CD - NE ANGL. DEV. = 16.5 DEGREES REMARK 500 ARG A 193 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 229 CD - NE - CZ ANGL. DEV. = 33.0 DEGREES REMARK 500 ARG A 229 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 229 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 LEU A 239 CA - CB - CG ANGL. DEV. = -14.8 DEGREES REMARK 500 ARG A 257 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 257 NE - CZ - NH2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG A 273 CD - NE - CZ ANGL. DEV. = 36.1 DEGREES REMARK 500 ARG A 273 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 GLU A 283 OE1 - CD - OE2 ANGL. DEV. = -8.5 DEGREES REMARK 500 LEU A 291 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 CYS A 308 CA - CB - SG ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 324 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 331 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP B 9 CB - CG - OD2 ANGL. DEV. = 13.2 DEGREES REMARK 500 ASP B 9 OD1 - CG - OD2 ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 PHE B 34 CB - CG - CD2 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 40 CD - NE - CZ ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG B 43 CD - NE - CZ ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG B 43 NE - CZ - NH1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 50 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 96 ANGLE DEVIATIONS. 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 SER A 95 -137.32 15.12 REMARK 500 SER B 95 -137.64 21.29 REMARK 500 GLN B 222 58.08 -141.71 REMARK 500 LYS B 256 -77.64 -33.19 REMARK 500 ARG B 257 73.28 -105.80 REMARK 500 THR B 330 -61.71 -127.84 REMARK 500 ASP B 331 55.46 -110.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE B 29 12.02 REMARK 500 LEU B 198 -10.99 REMARK 500 ALA B 211 -10.87 REMARK 500 GLU B 244 10.99 REMARK 500 ASP B 287 -11.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL A 106 24.9 L L OUTSIDE RANGE REMARK 500 GLU A 141 21.0 L L OUTSIDE RANGE REMARK 500 THR B 330 24.2 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTO B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QMI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RNA 3'-TERMINAL PHOSPHATE CYCLASE, AN REMARK 900 UBIQUITOUS ENZYME WITH UNUSUAL TOPOLOGY REMARK 999 REMARK 999 SEQUENCE REMARK 999 C-TERMINAL HIS TAG ADDED DBREF 1QMH A 3 339 UNP P46849 RTCA_ECOLI 2 338 DBREF 1QMH B 3 339 UNP P46849 RTCA_ECOLI 2 338 SEQADV 1QMH MET A 1 UNP P46849 EXPRESSION TAG SEQADV 1QMH VAL A 2 UNP P46849 EXPRESSION TAG SEQADV 1QMH GLY A 340 UNP P46849 EXPRESSION TAG SEQADV 1QMH SER A 341 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS A 342 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS A 343 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS A 344 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS A 345 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS A 346 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS A 347 UNP P46849 EXPRESSION TAG SEQADV 1QMH MET B 1 UNP P46849 EXPRESSION TAG SEQADV 1QMH VAL B 2 UNP P46849 EXPRESSION TAG SEQADV 1QMH GLY B 340 UNP P46849 EXPRESSION TAG SEQADV 1QMH SER B 341 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS B 342 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS B 343 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS B 344 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS B 345 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS B 346 UNP P46849 EXPRESSION TAG SEQADV 1QMH HIS B 347 UNP P46849 EXPRESSION TAG SEQRES 1 A 347 MET VAL LYS ARG MET ILE ALA LEU ASP GLY ALA GLN GLY SEQRES 2 A 347 GLU GLY GLY GLY GLN ILE LEU ARG SER ALA LEU SER LEU SEQRES 3 A 347 SER MET ILE THR GLY GLN PRO PHE THR ILE THR SER ILE SEQRES 4 A 347 ARG ALA GLY ARG ALA LYS PRO GLY LEU LEU ARG GLN HIS SEQRES 5 A 347 LEU THR ALA VAL LYS ALA ALA THR GLU ILE CYS GLY ALA SEQRES 6 A 347 THR VAL GLU GLY ALA GLU LEU GLY SER GLN ARG LEU LEU SEQRES 7 A 347 PHE ARG PRO GLY THR VAL ARG GLY GLY ASP TYR ARG PHE SEQRES 8 A 347 ALA ILE GLY SER ALA GLY SER CYS THR LEU VAL LEU GLN SEQRES 9 A 347 THR VAL LEU PRO ALA LEU TRP PHE ALA ASP GLY PRO SER SEQRES 10 A 347 ARG VAL GLU VAL SER GLY GLY THR ASP ASN PRO SER ALA SEQRES 11 A 347 PRO PRO ALA ASP PHE ILE ARG ARG VAL LEU GLU PRO LEU SEQRES 12 A 347 LEU ALA LYS ILE GLY ILE HIS GLN GLN THR THR LEU LEU SEQRES 13 A 347 ARG HIS GLY PHE TYR PRO ALA GLY GLY GLY VAL VAL ALA SEQRES 14 A 347 THR GLU VAL SER PRO VAL ALA SER PHE ASN THR LEU GLN SEQRES 15 A 347 LEU GLY GLU ARG GLY ASN ILE VAL GLN MET ARG GLY GLU SEQRES 16 A 347 VAL LEU LEU ALA GLY VAL PRO ARG HIS VAL ALA GLU ARG SEQRES 17 A 347 GLU ILE ALA THR LEU ALA GLY SER PHE SER LEU HIS GLU SEQRES 18 A 347 GLN ASN ILE HIS ASN LEU PRO ARG ASP GLN GLY PRO GLY SEQRES 19 A 347 ASN THR VAL SER LEU GLU VAL GLU SER GLU ASN ILE THR SEQRES 20 A 347 GLU ARG PHE PHE VAL VAL GLY GLU LYS ARG VAL SER ALA SEQRES 21 A 347 GLU VAL VAL ALA ALA GLN LEU VAL LYS GLU VAL LYS ARG SEQRES 22 A 347 TYR LEU ALA SER THR ALA ALA VAL GLY GLU TYR LEU ALA SEQRES 23 A 347 ASP GLN LEU VAL LEU PRO MET ALA LEU ALA GLY ALA GLY SEQRES 24 A 347 GLU PHE THR VAL ALA HIS PRO SER CYS HIS LEU LEU THR SEQRES 25 A 347 ASN ILE ALA VAL VAL GLU ARG PHE LEU PRO VAL ARG PHE SEQRES 26 A 347 SER LEU ILE GLU THR ASP GLY VAL THR ARG VAL SER ILE SEQRES 27 A 347 GLU GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 347 MET VAL LYS ARG MET ILE ALA LEU ASP GLY ALA GLN GLY SEQRES 2 B 347 GLU GLY GLY GLY GLN ILE LEU ARG SER ALA LEU SER LEU SEQRES 3 B 347 SER MET ILE THR GLY GLN PRO PHE THR ILE THR SER ILE SEQRES 4 B 347 ARG ALA GLY ARG ALA LYS PRO GLY LEU LEU ARG GLN HIS SEQRES 5 B 347 LEU THR ALA VAL LYS ALA ALA THR GLU ILE CYS GLY ALA SEQRES 6 B 347 THR VAL GLU GLY ALA GLU LEU GLY SER GLN ARG LEU LEU SEQRES 7 B 347 PHE ARG PRO GLY THR VAL ARG GLY GLY ASP TYR ARG PHE SEQRES 8 B 347 ALA ILE GLY SER ALA GLY SER CYS THR LEU VAL LEU GLN SEQRES 9 B 347 THR VAL LEU PRO ALA LEU TRP PHE ALA ASP GLY PRO SER SEQRES 10 B 347 ARG VAL GLU VAL SER GLY GLY THR ASP ASN PRO SER ALA SEQRES 11 B 347 PRO PRO ALA ASP PHE ILE ARG ARG VAL LEU GLU PRO LEU SEQRES 12 B 347 LEU ALA LYS ILE GLY ILE HIS GLN GLN THR THR LEU LEU SEQRES 13 B 347 ARG HIS GLY PHE TYR PRO ALA GLY GLY GLY VAL VAL ALA SEQRES 14 B 347 THR GLU VAL SER PRO VAL ALA SER PHE ASN THR LEU GLN SEQRES 15 B 347 LEU GLY GLU ARG GLY ASN ILE VAL GLN MET ARG GLY GLU SEQRES 16 B 347 VAL LEU LEU ALA GLY VAL PRO ARG HIS VAL ALA GLU ARG SEQRES 17 B 347 GLU ILE ALA THR LEU ALA GLY SER PHE SER LEU HIS GLU SEQRES 18 B 347 GLN ASN ILE HIS ASN LEU PRO ARG ASP GLN GLY PRO GLY SEQRES 19 B 347 ASN THR VAL SER LEU GLU VAL GLU SER GLU ASN ILE THR SEQRES 20 B 347 GLU ARG PHE PHE VAL VAL GLY GLU LYS ARG VAL SER ALA SEQRES 21 B 347 GLU VAL VAL ALA ALA GLN LEU VAL LYS GLU VAL LYS ARG SEQRES 22 B 347 TYR LEU ALA SER THR ALA ALA VAL GLY GLU TYR LEU ALA SEQRES 23 B 347 ASP GLN LEU VAL LEU PRO MET ALA LEU ALA GLY ALA GLY SEQRES 24 B 347 GLU PHE THR VAL ALA HIS PRO SER CYS HIS LEU LEU THR SEQRES 25 B 347 ASN ILE ALA VAL VAL GLU ARG PHE LEU PRO VAL ARG PHE SEQRES 26 B 347 SER LEU ILE GLU THR ASP GLY VAL THR ARG VAL SER ILE SEQRES 27 B 347 GLU GLY SER HIS HIS HIS HIS HIS HIS HET CIT A 401 13 HET CIT B 401 13 HET DTO B 402 9 HETNAM CIT CITRIC ACID HETNAM DTO 1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL FORMUL 3 CIT 2(C6 H8 O7) FORMUL 5 DTO C4 H10 O3 S2 FORMUL 6 HOH *424(H2 O) HELIX 1 1 GLY A 16 GLY A 31 1 16 HELIX 2 2 LEU A 49 CYS A 63 1 15 HELIX 3 3 CYS A 99 TRP A 111 1 13 HELIX 4 4 ALA A 133 VAL A 139 1 7 HELIX 5 5 VAL A 139 ILE A 147 1 9 HELIX 6 6 PRO A 202 PHE A 217 1 16 HELIX 7 7 PRO A 228 GLY A 232 5 5 HELIX 8 8 SER A 259 SER A 277 1 19 HELIX 9 9 GLY A 282 GLY A 297 1 16 HELIX 10 10 SER A 307 LEU A 321 1 15 HELIX 11 11 GLY B 16 GLY B 31 1 16 HELIX 12 12 LEU B 49 GLY B 64 1 16 HELIX 13 13 CYS B 99 TRP B 111 1 13 HELIX 14 14 ASP B 134 VAL B 139 1 6 HELIX 15 15 VAL B 139 GLY B 148 1 10 HELIX 16 16 PRO B 202 PHE B 217 1 16 HELIX 17 17 PRO B 228 GLY B 232 5 5 HELIX 18 18 SER B 259 LEU B 275 1 17 HELIX 19 19 GLY B 282 GLY B 297 1 16 HELIX 20 20 SER B 307 LEU B 321 1 15 SHEET 1 A 4 ILE A 6 ASP A 9 0 SHEET 2 A 4 PHE A 34 THR A 37 1 N THR A 35 O ILE A 6 SHEET 3 A 4 LEU A 77 ARG A 80 -1 N PHE A 79 O PHE A 34 SHEET 4 A 4 THR A 66 GLU A 68 -1 N GLU A 68 O LEU A 78 SHEET 1 B 4 GLY A 87 GLY A 94 0 SHEET 2 B 4 SER A 117 GLY A 123 1 N ARG A 118 O GLY A 87 SHEET 3 B 4 GLY A 166 SER A 173 -1 N VAL A 172 O SER A 117 SHEET 4 B 4 HIS A 150 ARG A 157 -1 N ARG A 157 O VAL A 167 SHEET 1 C 4 GLU A 221 LEU A 227 0 SHEET 2 C 4 ILE A 189 ALA A 199 1 N GLY A 194 O GLU A 221 SHEET 3 C 4 GLY A 234 SER A 243 -1 N GLU A 242 O VAL A 190 SHEET 4 C 4 THR A 247 VAL A 253 -1 N VAL A 252 O VAL A 237 SHEET 1 D 3 GLU A 300 VAL A 303 0 SHEET 2 D 3 THR A 334 SER A 337 -1 N VAL A 336 O PHE A 301 SHEET 3 D 3 SER A 326 GLU A 329 -1 N ILE A 328 O ARG A 335 SHEET 1 E 4 ILE B 6 ASP B 9 0 SHEET 2 E 4 PHE B 34 THR B 37 1 N THR B 35 O ILE B 6 SHEET 3 E 4 LEU B 77 ARG B 80 -1 N PHE B 79 O PHE B 34 SHEET 4 E 4 THR B 66 GLU B 68 -1 N GLU B 68 O LEU B 78 SHEET 1 F 4 ASP B 88 GLY B 94 0 SHEET 2 F 4 SER B 117 GLY B 123 1 N ARG B 118 O TYR B 89 SHEET 3 F 4 GLY B 166 VAL B 172 -1 N VAL B 172 O SER B 117 SHEET 4 F 4 GLN B 151 ARG B 157 -1 N ARG B 157 O VAL B 167 SHEET 1 G 4 GLU B 221 LEU B 227 0 SHEET 2 G 4 ILE B 189 ALA B 199 1 N GLY B 194 O GLU B 221 SHEET 3 G 4 GLY B 234 SER B 243 -1 N GLU B 242 O VAL B 190 SHEET 4 G 4 THR B 247 VAL B 253 -1 N VAL B 252 O VAL B 237 SHEET 1 H 3 GLY B 299 VAL B 303 0 SHEET 2 H 3 THR B 334 GLU B 339 -1 N ILE B 338 O GLY B 299 SHEET 3 H 3 ARG B 324 GLU B 329 -1 N ILE B 328 O ARG B 335 SSBOND 1 CYS A 308 CYS B 308 1555 1555 2.15 CISPEP 1 TYR A 161 PRO A 162 0 2.10 CISPEP 2 GLY A 232 PRO A 233 0 2.90 CISPEP 3 TYR B 161 PRO B 162 0 3.93 CISPEP 4 GLY B 232 PRO B 233 0 2.13 SITE 1 AC1 8 GLU A 14 GLY A 16 GLY A 17 ARG A 21 SITE 2 AC1 8 ARG A 40 ARG A 43 GLN A 51 HIS A 52 SITE 1 AC2 8 GLY B 16 GLY B 17 ARG B 21 ARG B 40 SITE 2 AC2 8 ARG B 43 HIS B 52 HOH B2215 HOH B2216 SITE 1 AC3 8 GLY B 234 ASN B 235 GLY B 254 GLU B 255 SITE 2 AC3 8 LYS B 256 VAL B 258 VAL B 263 HOH B2176 CRYST1 125.800 133.500 51.000 90.00 90.00 90.00 P 21 21 2 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 0.007949 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019608 0.00000 MTRIX1 1 -0.515842 -0.671843 -0.531539 148.35341 1 MTRIX2 1 -0.689428 -0.042742 0.723092 113.33745 1 MTRIX3 1 -0.508523 0.739459 -0.441140 -10.30362 1