HEADER TRANSFERASE 11-FEB-04 1UWV TITLE CRYSTAL STRUCTURE OF RUMA, THE IRON-SULFUR CLUSTER CONTAINING E. COLI TITLE 2 23S RIBOSOMAL RNA 5-METHYLURIDINE METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 23S RRNA(M-5-U1939)-METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: IRON-SULFUR CLUSTER LINKED BY CYS81, CYS87, CYS90, AND COMPND 8 CYS162 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS METHYLTRANSFERASE, RNA MODIFICATION, IRON-SULFUR CLUSTER, KEYWDS 2 TRANSFERASE, RNA PROCESSING EXPDTA X-RAY DIFFRACTION AUTHOR T.T.LEE,S.AGARWALLA,R.M.STROUD REVDAT 3 23-OCT-24 1UWV 1 LINK REVDAT 2 24-FEB-09 1UWV 1 VERSN REVDAT 1 18-MAR-04 1UWV 0 JRNL AUTH T.T.LEE,S.AGARWALLA,R.M.STROUD JRNL TITL CRYSTAL STRUCTURE OF RUMA, AN IRON-SULFUR CLUSTER CONTAINING JRNL TITL 2 E. COLI RIBOSOMAL RNA 5-METHYLURIDINE METHYLTRANSFERASE. JRNL REF STRUCTURE V. 12 397 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15016356 JRNL DOI 10.1016/J.STR.2004.02.009 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.AGARWALLA,J.T.KEALEY,D.V.SANTI,R.M.STROUD REMARK 1 TITL CHARACTERIZATION OF THE 23 S RIBOSOMAL RNA M5U1939 REMARK 1 TITL 2 METHYLTRANSFERASE FROM ESCHERICHIA COLI REMARK 1 REF J.BIOL.CHEM. V. 277 8835 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 11779873 REMARK 1 DOI 10.1074/JBC.M111825200 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 27660 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1477 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1941 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3239 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.09000 REMARK 3 B22 (A**2) : -1.60000 REMARK 3 B33 (A**2) : 0.69000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.51000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.386 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3324 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3060 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4501 ; 1.673 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7111 ; 0.892 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 416 ; 6.389 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 506 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3683 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 645 ; 0.010 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 600 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3512 ; 0.247 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2065 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 105 ; 0.194 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.047 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 13 ; 0.267 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 60 ; 0.306 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.188 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2079 ; 0.938 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3345 ; 1.737 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1245 ; 3.506 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1144 ; 5.155 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 15 A 74 REMARK 3 ORIGIN FOR THE GROUP (A): 14.4318 -19.0110 19.9989 REMARK 3 T TENSOR REMARK 3 T11: 0.3937 T22: 0.3429 REMARK 3 T33: 0.2480 T12: 0.2112 REMARK 3 T13: -0.0344 T23: -0.1020 REMARK 3 L TENSOR REMARK 3 L11: 7.9295 L22: 29.8213 REMARK 3 L33: 3.7214 L12: 11.9100 REMARK 3 L13: 3.4672 L23: 3.6168 REMARK 3 S TENSOR REMARK 3 S11: -0.2419 S12: -0.8722 S13: 0.5785 REMARK 3 S21: 0.7810 S22: -0.4339 S23: 1.5672 REMARK 3 S31: 0.0492 S32: -0.6251 S33: 0.6758 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 75 A 93 REMARK 3 RESIDUE RANGE : F 1 F 1 REMARK 3 ORIGIN FOR THE GROUP (A): 15.9695 -1.3185 18.9468 REMARK 3 T TENSOR REMARK 3 T11: 0.2929 T22: 0.1347 REMARK 3 T33: 0.0838 T12: 0.1614 REMARK 3 T13: -0.1260 T23: -0.0326 REMARK 3 L TENSOR REMARK 3 L11: 5.9474 L22: 6.9646 REMARK 3 L33: 6.6067 L12: -5.4412 REMARK 3 L13: 0.3539 L23: 0.8802 REMARK 3 S TENSOR REMARK 3 S11: -0.2087 S12: -0.2485 S13: -0.1499 REMARK 3 S21: 0.9539 S22: 0.5126 S23: -0.3870 REMARK 3 S31: 0.1916 S32: 0.0379 S33: -0.3039 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 125 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 2.2777 15.7773 9.9425 REMARK 3 T TENSOR REMARK 3 T11: 0.1346 T22: 0.1653 REMARK 3 T33: 0.1460 T12: 0.0117 REMARK 3 T13: -0.0055 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 2.7327 L22: 2.1236 REMARK 3 L33: 0.7425 L12: -0.8533 REMARK 3 L13: -0.8632 L23: 0.4899 REMARK 3 S TENSOR REMARK 3 S11: -0.0384 S12: -0.0131 S13: 0.1375 REMARK 3 S21: 0.1261 S22: 0.2045 S23: 0.2334 REMARK 3 S31: 0.0935 S32: -0.1446 S33: -0.1660 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 94 A 124 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1141 -8.0020 3.5975 REMARK 3 T TENSOR REMARK 3 T11: 0.0878 T22: 0.1444 REMARK 3 T33: 0.1974 T12: 0.0641 REMARK 3 T13: -0.0747 T23: -0.0504 REMARK 3 L TENSOR REMARK 3 L11: 2.1226 L22: 5.2214 REMARK 3 L33: 5.5346 L12: -3.0503 REMARK 3 L13: -1.8875 L23: 1.6269 REMARK 3 S TENSOR REMARK 3 S11: -0.1256 S12: -0.0609 S13: -0.0611 REMARK 3 S21: 0.0961 S22: 0.1666 S23: -0.5257 REMARK 3 S31: 0.5168 S32: 0.2097 S33: -0.0409 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 263 A 431 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3597 0.3561 -14.5499 REMARK 3 T TENSOR REMARK 3 T11: 0.0567 T22: 0.2172 REMARK 3 T33: 0.1500 T12: -0.0323 REMARK 3 T13: 0.0230 T23: -0.0309 REMARK 3 L TENSOR REMARK 3 L11: 0.7662 L22: 4.4576 REMARK 3 L33: 2.5756 L12: -0.9717 REMARK 3 L13: 0.1948 L23: -1.3403 REMARK 3 S TENSOR REMARK 3 S11: -0.1071 S12: 0.0516 S13: -0.1198 REMARK 3 S21: -0.0835 S22: 0.1621 S23: 0.2451 REMARK 3 S31: 0.0591 S32: -0.2324 S33: -0.0550 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. B-FACTORS ARE RESIDUAL B-FACTORS, (WHICH DO NOT REMARK 3 INCLUDE THE CONTRIBUTION FROM THE TLS PARAMETERS). USE TLSANL REMARK 3 (DISTRIBUTED WITH CCP4) TO OBTAIN THE FULL B-FACTOR. REMARK 4 REMARK 4 1UWV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1290012783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786,0.9788 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD QUANTUM-4 2X2 ARRAY REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29176 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.89600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS, CCP4, SHARP ARP/WARP, QUANTA REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 50 MM REMARK 280 TRIS-CL (PH 9-9.5), 10 MM NICL2, 12.5% GLYCEROL, AND 20% REMARK 280 POLYETHYLENE GLYCOL 2000 MONOMETHYL ETHER, PH 9.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 49.72400 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 CATALYZES THE FORMATION OF 5-METHYL-URIDINE AT POSITION REMARK 400 1939 (M-5-U1939) IN 23S RRNA. REMARK 400 BELONGS TO THE RNA M5U METHYLTRANSFERASE FAMILY. RUMA 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 PHE A 4 REMARK 465 TYR A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 LYS A 8 REMARK 465 ARG A 9 REMARK 465 ARG A 10 REMARK 465 THR A 11 REMARK 465 THR A 12 REMARK 465 THR A 13 REMARK 465 ARG A 14 REMARK 465 LYS A 433 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 VAL A 432 CA C O CB CG1 CG2 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 ASP A 262 O HOH A 2082 1.97 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 ASP A 122 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 262 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 358 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 431 O - C - N ANGL. DEV. = -13.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 16 118.95 57.92 REMARK 500 LYS A 59 -83.99 -45.27 REMARK 500 GLN A 92 30.11 -142.38 REMARK 500 ASP A 122 -147.89 -143.34 REMARK 500 CYS A 162 84.19 -156.78 REMARK 500 ASP A 262 152.47 -44.95 REMARK 500 ARG A 431 -82.92 -68.97 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 SF4 A1432 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 81 SG REMARK 620 2 SF4 A1432 S1 111.7 REMARK 620 3 SF4 A1432 S2 122.4 106.5 REMARK 620 4 SF4 A1432 S3 104.1 107.4 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1432 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 87 SG REMARK 620 2 SF4 A1432 S2 112.6 REMARK 620 3 SF4 A1432 S3 116.7 104.5 REMARK 620 4 SF4 A1432 S4 114.9 104.1 102.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1432 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 SF4 A1432 S1 115.5 REMARK 620 3 SF4 A1432 S2 112.9 103.9 REMARK 620 4 SF4 A1432 S4 118.1 101.8 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1433 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 114 NE2 REMARK 620 2 HOH A2116 O 89.3 REMARK 620 3 HOH A2117 O 100.3 89.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1432 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 162 SG REMARK 620 2 SF4 A1432 S1 106.5 REMARK 620 3 SF4 A1432 S3 115.8 109.6 REMARK 620 4 SF4 A1432 S4 118.2 102.9 102.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1434 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 191 NE2 REMARK 620 2 GLU A 193 OE1 100.5 REMARK 620 N 1 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1436 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A1432 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A1434 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1435 DBREF 1UWV A 1 433 UNP P55135 RUMA_ECOLI 1 433 SEQRES 1 A 433 MSE ALA GLN PHE TYR SER ALA LYS ARG ARG THR THR THR SEQRES 2 A 433 ARG GLN ILE ILE THR VAL SER VAL ASN ASP LEU ASP SER SEQRES 3 A 433 PHE GLY GLN GLY VAL ALA ARG HIS ASN GLY LYS THR LEU SEQRES 4 A 433 PHE ILE PRO GLY LEU LEU PRO GLN GLU ASN ALA GLU VAL SEQRES 5 A 433 THR VAL THR GLU ASP LYS LYS GLN TYR ALA ARG ALA LYS SEQRES 6 A 433 VAL VAL ARG ARG LEU SER ASP SER PRO GLU ARG GLU THR SEQRES 7 A 433 PRO ARG CYS PRO HIS PHE GLY VAL CYS GLY GLY CYS GLN SEQRES 8 A 433 GLN GLN HIS ALA SER VAL ASP LEU GLN GLN ARG SER LYS SEQRES 9 A 433 SER ALA ALA LEU ALA ARG LEU MSE LYS HIS ASP VAL SER SEQRES 10 A 433 GLU VAL ILE ALA ASP VAL PRO TRP GLY TYR ARG ARG ARG SEQRES 11 A 433 ALA ARG LEU SER LEU ASN TYR LEU PRO LYS THR GLN GLN SEQRES 12 A 433 LEU GLN MSE GLY PHE ARG LYS ALA GLY SER SER ASP ILE SEQRES 13 A 433 VAL ASP VAL LYS GLN CYS PRO ILE LEU ALA PRO GLN LEU SEQRES 14 A 433 GLU ALA LEU LEU PRO LYS VAL ARG ALA CYS LEU GLY SER SEQRES 15 A 433 LEU GLN ALA MSE ARG HIS LEU GLY HIS VAL GLU LEU VAL SEQRES 16 A 433 GLN ALA THR SER GLY THR LEU MSE ILE LEU ARG HIS THR SEQRES 17 A 433 ALA PRO LEU SER SER ALA ASP ARG GLU LYS LEU GLU ARG SEQRES 18 A 433 PHE SER HIS SER GLU GLY LEU ASP LEU TYR LEU ALA PRO SEQRES 19 A 433 ASP SER GLU ILE LEU GLU THR VAL SER GLY GLU MSE PRO SEQRES 20 A 433 TRP TYR ASP SER ASN GLY LEU ARG LEU THR PHE SER PRO SEQRES 21 A 433 ARG ASP PHE ILE GLN VAL ASN ALA GLY VAL ASN GLN LYS SEQRES 22 A 433 MSE VAL ALA ARG ALA LEU GLU TRP LEU ASP VAL GLN PRO SEQRES 23 A 433 GLU ASP ARG VAL LEU ASP LEU PHE CYS GLY MSE GLY ASN SEQRES 24 A 433 PHE THR LEU PRO LEU ALA THR GLN ALA ALA SER VAL VAL SEQRES 25 A 433 GLY VAL GLU GLY VAL PRO ALA LEU VAL GLU LYS GLY GLN SEQRES 26 A 433 GLN ASN ALA ARG LEU ASN GLY LEU GLN ASN VAL THR PHE SEQRES 27 A 433 TYR HIS GLU ASN LEU GLU GLU ASP VAL THR LYS GLN PRO SEQRES 28 A 433 TRP ALA LYS ASN GLY PHE ASP LYS VAL LEU LEU ASP PRO SEQRES 29 A 433 ALA ARG ALA GLY ALA ALA GLY VAL MSE GLN GLN ILE ILE SEQRES 30 A 433 LYS LEU GLU PRO ILE ARG ILE VAL TYR VAL SER CYS ASN SEQRES 31 A 433 PRO ALA THR LEU ALA ARG ASP SER GLU ALA LEU LEU LYS SEQRES 32 A 433 ALA GLY TYR THR ILE ALA ARG LEU ALA MSE LEU ASP MSE SEQRES 33 A 433 PHE PRO HIS THR GLY HIS LEU GLU SER MSE VAL LEU PHE SEQRES 34 A 433 SER ARG VAL LYS MODRES 1UWV MSE A 112 MET SELENOMETHIONINE MODRES 1UWV MSE A 146 MET SELENOMETHIONINE MODRES 1UWV MSE A 186 MET SELENOMETHIONINE MODRES 1UWV MSE A 203 MET SELENOMETHIONINE MODRES 1UWV MSE A 246 MET SELENOMETHIONINE MODRES 1UWV MSE A 274 MET SELENOMETHIONINE MODRES 1UWV MSE A 297 MET SELENOMETHIONINE MODRES 1UWV MSE A 373 MET SELENOMETHIONINE MODRES 1UWV MSE A 413 MET SELENOMETHIONINE MODRES 1UWV MSE A 416 MET SELENOMETHIONINE MODRES 1UWV MSE A 426 MET SELENOMETHIONINE HET MSE A 112 8 HET MSE A 146 8 HET MSE A 186 8 HET MSE A 203 8 HET MSE A 246 8 HET MSE A 274 8 HET MSE A 297 8 HET MSE A 373 8 HET MSE A 413 8 HET MSE A 416 8 HET MSE A 426 8 HET SF4 A1432 8 HET NI A1433 1 HET NI A1434 1 HET PO4 A1435 5 HET CL A1436 1 HETNAM MSE SELENOMETHIONINE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM NI NICKEL (II) ION HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 2 SF4 FE4 S4 FORMUL 3 NI 2(NI 2+) FORMUL 5 PO4 O4 P 3- FORMUL 6 CL CL 1- FORMUL 7 HOH *123(H2 O) HELIX 1 1 SER A 96 LYS A 113 1 18 HELIX 2 2 ALA A 166 GLY A 181 1 16 HELIX 3 3 SER A 182 ARG A 187 5 6 HELIX 4 4 SER A 212 GLY A 227 1 16 HELIX 5 5 ASN A 267 ASP A 283 1 17 HELIX 6 6 PHE A 300 THR A 306 1 7 HELIX 7 7 VAL A 317 ASN A 331 1 15 HELIX 8 8 GLN A 350 LYS A 354 5 5 HELIX 9 9 ALA A 369 GLU A 380 1 12 HELIX 10 10 ASN A 390 ALA A 404 1 15 SHEET 1 AA 7 ILE A 17 LEU A 24 0 SHEET 2 AA 7 ASN A 49 ASP A 57 -1 O ALA A 50 N VAL A 19 SHEET 3 AA 7 TYR A 61 ARG A 69 -1 O ARG A 63 N GLU A 56 SHEET 4 AA 7 LYS A 37 PRO A 42 1 O THR A 38 N ALA A 62 SHEET 5 AA 7 GLN A 29 HIS A 34 -1 O GLY A 30 N ILE A 41 SHEET 6 AA 7 ILE A 17 LEU A 24 -1 O SER A 20 N ARG A 33 SHEET 7 AA 7 ILE A 17 LEU A 24 0 SHEET 1 AB 8 GLU A 118 ILE A 120 0 SHEET 2 AB 8 THR A 407 LEU A 414 1 O MSE A 413 N ILE A 120 SHEET 3 AB 8 GLU A 424 SER A 430 -1 O GLU A 424 N LEU A 414 SHEET 4 AB 8 ARG A 383 SER A 388 -1 O ILE A 384 N PHE A 429 SHEET 5 AB 8 LYS A 359 LEU A 362 1 O VAL A 360 N VAL A 385 SHEET 6 AB 8 ARG A 289 LEU A 293 1 O LEU A 291 N LEU A 361 SHEET 7 AB 8 SER A 310 GLU A 315 1 O SER A 310 N VAL A 290 SHEET 8 AB 8 VAL A 336 HIS A 340 1 O THR A 337 N GLY A 313 SHEET 1 AC 7 ILE A 156 ASP A 158 0 SHEET 2 AC 7 GLN A 143 ARG A 149 -1 O PHE A 148 N VAL A 157 SHEET 3 AC 7 ARG A 130 LEU A 138 -1 O SER A 134 N GLY A 147 SHEET 4 AC 7 LEU A 189 ALA A 197 -1 O GLY A 190 N LEU A 135 SHEET 5 AC 7 GLY A 200 HIS A 207 -1 O GLY A 200 N ALA A 197 SHEET 6 AC 7 ASP A 229 ALA A 233 1 O ASP A 229 N MSE A 203 SHEET 7 AC 7 GLU A 240 SER A 243 -1 O GLU A 240 N LEU A 232 SHEET 1 AD 2 TRP A 248 SER A 251 0 SHEET 2 AD 2 LEU A 254 THR A 257 -1 O LEU A 254 N SER A 251 LINK C LEU A 111 N MSE A 112 1555 1555 1.33 LINK C MSE A 112 N LYS A 113 1555 1555 1.33 LINK C GLN A 145 N MSE A 146 1555 1555 1.31 LINK C MSE A 146 N GLY A 147 1555 1555 1.33 LINK C ALA A 185 N MSE A 186 1555 1555 1.32 LINK C MSE A 186 N ARG A 187 1555 1555 1.33 LINK C LEU A 202 N MSE A 203 1555 1555 1.32 LINK C MSE A 203 N ILE A 204 1555 1555 1.33 LINK C GLU A 245 N MSE A 246 1555 1555 1.32 LINK C MSE A 246 N PRO A 247 1555 1555 1.33 LINK C LYS A 273 N MSE A 274 1555 1555 1.35 LINK C MSE A 274 N VAL A 275 1555 1555 1.33 LINK C GLY A 296 N MSE A 297 1555 1555 1.34 LINK C MSE A 297 N GLY A 298 1555 1555 1.33 LINK C VAL A 372 N MSE A 373 1555 1555 1.35 LINK C MSE A 373 N GLN A 374 1555 1555 1.33 LINK C ALA A 412 N MSE A 413 1555 1555 1.32 LINK C MSE A 413 N LEU A 414 1555 1555 1.32 LINK C ASP A 415 N MSE A 416 1555 1555 1.31 LINK C MSE A 416 N PHE A 417 1555 1555 1.31 LINK C SER A 425 N MSE A 426 1555 1555 1.32 LINK C MSE A 426 N VAL A 427 1555 1555 1.32 LINK SG CYS A 81 FE4 SF4 A1432 1555 1555 2.33 LINK SG CYS A 87 FE1 SF4 A1432 1555 1555 2.31 LINK SG CYS A 90 FE3 SF4 A1432 1555 1555 2.26 LINK NE2 HIS A 114 NI NI A1433 1555 1555 2.07 LINK SG CYS A 162 FE2 SF4 A1432 1555 1555 2.31 LINK NE2 HIS A 191 NI NI A1434 1555 1555 2.13 LINK OE1 GLU A 193 NI NI A1434 1555 1555 2.01 LINK NI NI A1433 O HOH A2116 1555 1555 1.85 LINK NI NI A1433 O HOH A2117 1555 1555 2.02 SITE 1 AC1 1 NI A1434 SITE 1 AC2 8 CYS A 81 CYS A 87 CYS A 90 GLN A 93 SITE 2 AC2 8 GLN A 161 CYS A 162 PRO A 163 ILE A 164 SITE 1 AC3 5 HIS A 114 ILE A 408 HOH A2050 HOH A2116 SITE 2 AC3 5 HOH A2117 SITE 1 AC4 4 ARG A 132 HIS A 191 GLU A 193 CL A1436 SITE 1 AC5 5 ARG A 132 HIS A 191 ARG A 206 SER A 236 SITE 2 AC5 5 LYS A 273 CRYST1 35.938 99.448 58.519 90.00 100.57 90.00 P 1 21 1 2 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 0.027826 0.000000 0.005192 0.00000 SCALE2 0.000000 0.010056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017383 0.00000