HEADER TRANSFERASE 17-NOV-06 2NXJ TITLE T.THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN SPACE TITLE 2 GROUP P 21 21 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: L11 MTASE; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 GENE: PRMA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 STAR (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30B KEYWDS S-ADENOSYL-L-METHIONINE DEPENDENT METHYLTRANSFERASE, POSTRANSLATIONAL KEYWDS 2 MODIFICATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.DEMIRCI,S.T.GREGORY,A.E.DAHLBERG,G.JOGL REVDAT 5 30-AUG-23 2NXJ 1 REMARK REVDAT 4 13-JUL-11 2NXJ 1 VERSN REVDAT 3 24-FEB-09 2NXJ 1 VERSN REVDAT 2 06-FEB-07 2NXJ 1 JRNL REVDAT 1 26-DEC-06 2NXJ 0 JRNL AUTH H.DEMIRCI,S.T.GREGORY,A.E.DAHLBERG,G.JOGL JRNL TITL RECOGNITION OF RIBOSOMAL PROTEIN L11 BY THE PROTEIN JRNL TITL 2 TRIMETHYLTRANSFERASE PRMA. JRNL REF EMBO J. V. 26 567 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17215866 JRNL DOI 10.1038/SJ.EMBOJ.7601508 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 27095 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1446 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1742 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3799 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 290 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.55000 REMARK 3 B22 (A**2) : -2.10000 REMARK 3 B33 (A**2) : -2.45000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.303 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.221 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.687 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3906 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5326 ; 1.731 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 485 ; 7.031 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;33.778 ;22.470 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 595 ;20.344 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.212 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 572 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3030 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1685 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2500 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 220 ; 0.199 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 59 ; 0.217 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.237 ; 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): 2488 ; 0.836 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3869 ; 1.450 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1645 ; 1.963 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1457 ; 3.121 ; 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 : 4 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 1 A 54 REMARK 3 ORIGIN FOR THE GROUP (A): 61.1513 51.7736 -3.7215 REMARK 3 T TENSOR REMARK 3 T11: -0.2744 T22: -0.0867 REMARK 3 T33: 0.2306 T12: 0.0964 REMARK 3 T13: -0.1336 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 12.4127 L22: 6.5462 REMARK 3 L33: 4.8178 L12: -2.2253 REMARK 3 L13: -3.3472 L23: -0.7613 REMARK 3 S TENSOR REMARK 3 S11: 0.0625 S12: 1.0386 S13: 0.7573 REMARK 3 S21: -0.3805 S22: -0.1749 S23: 0.7936 REMARK 3 S31: -0.4303 S32: -0.2941 S33: 0.1124 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 57 A 254 REMARK 3 ORIGIN FOR THE GROUP (A): 28.4984 22.8683 0.1830 REMARK 3 T TENSOR REMARK 3 T11: 0.0031 T22: -0.0631 REMARK 3 T33: -0.0563 T12: 0.0274 REMARK 3 T13: -0.0050 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.2746 L22: 1.8804 REMARK 3 L33: 1.4503 L12: -0.4535 REMARK 3 L13: -0.0839 L23: -0.0520 REMARK 3 S TENSOR REMARK 3 S11: -0.0416 S12: 0.0170 S13: 0.0486 REMARK 3 S21: 0.0592 S22: 0.0418 S23: 0.0323 REMARK 3 S31: 0.1441 S32: 0.1002 S33: -0.0002 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 : B 1 B 54 REMARK 3 ORIGIN FOR THE GROUP (A): 62.9832 36.6744 5.1931 REMARK 3 T TENSOR REMARK 3 T11: -0.4202 T22: -0.2185 REMARK 3 T33: 0.7686 T12: 0.1017 REMARK 3 T13: 0.1699 T23: 0.0839 REMARK 3 L TENSOR REMARK 3 L11: 12.0676 L22: 6.6901 REMARK 3 L33: 5.1158 L12: 1.6746 REMARK 3 L13: 0.8577 L23: -2.1298 REMARK 3 S TENSOR REMARK 3 S11: -0.5562 S12: -0.8405 S13: -2.1263 REMARK 3 S21: 0.1313 S22: 0.4110 S23: 1.1780 REMARK 3 S31: 0.0458 S32: -0.1346 S33: 0.1452 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 : B 62 B 254 REMARK 3 ORIGIN FOR THE GROUP (A): 25.6591 59.8326 -1.4553 REMARK 3 T TENSOR REMARK 3 T11: 0.0449 T22: -0.0781 REMARK 3 T33: -0.0815 T12: -0.0469 REMARK 3 T13: 0.0483 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.6719 L22: 2.9804 REMARK 3 L33: 2.1814 L12: 0.5887 REMARK 3 L13: -0.6631 L23: -1.4415 REMARK 3 S TENSOR REMARK 3 S11: 0.1406 S12: 0.0124 S13: 0.0818 REMARK 3 S21: 0.2132 S22: 0.0497 S23: 0.2486 REMARK 3 S31: -0.2605 S32: 0.1223 S33: -0.1903 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 2NXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28554 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: COMO, PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1NXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULFATE, 85 MM HEPES REMARK 280 -NA, PH 7.5, 1.7% W/V PEG400, 15% V/V GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 62.09750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 76.81100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 62.09750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 76.81100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 GLY A 55 REMARK 465 ASP A 56 REMARK 465 MET A 97 REMARK 465 ALA A 98 REMARK 465 PHE A 99 REMARK 465 GLY A 100 REMARK 465 THR A 101 REMARK 465 GLY B 55 REMARK 465 ASP B 56 REMARK 465 GLU B 57 REMARK 465 MET B 97 REMARK 465 ALA B 98 REMARK 465 PHE B 99 REMARK 465 GLY B 100 REMARK 465 THR B 101 REMARK 465 GLY B 102 REMARK 465 HIS B 103 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 311 O HOH A 376 1.92 REMARK 500 NE2 HIS A 117 OE2 GLU A 240 2.11 REMARK 500 NH1 ARG A 164 O MET B 153 2.14 REMARK 500 O HOH B 281 O HOH B 365 2.16 REMARK 500 O HOH B 312 O HOH B 317 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 310 O HOH A 404 1556 2.15 REMARK 500 O HOH A 341 O HOH A 406 4555 2.18 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 226 CA - CB - CG ANGL. DEV. = 15.9 DEGREES REMARK 500 GLY B 86 N - CA - C ANGL. DEV. = 15.9 DEGREES REMARK 500 LEU B 220 CA - CB - CG ANGL. DEV. = 14.7 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 ARG A 31 72.89 -100.30 REMARK 500 GLU A 32 87.78 44.80 REMARK 500 PRO A 46 34.87 -95.89 REMARK 500 GLU A 48 71.94 58.96 REMARK 500 LEU A 60 -77.78 -105.26 REMARK 500 GLU A 61 37.36 -74.60 REMARK 500 PRO A 95 23.16 -72.74 REMARK 500 SER A 175 -154.19 -100.27 REMARK 500 PRO A 181 -15.45 -49.18 REMARK 500 LEU A 192 -118.60 -123.29 REMARK 500 PRO B 46 36.91 -88.18 REMARK 500 GLU B 48 34.55 101.95 REMARK 500 ARG B 164 -9.26 -59.09 REMARK 500 SER B 175 -163.36 -113.01 REMARK 500 LEU B 192 -117.83 -121.59 REMARK 500 LEU B 239 -51.91 -132.66 REMARK 500 GLU B 246 39.05 -91.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP B 84 GLU B 85 -134.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UFK RELATED DB: PDB REMARK 900 T. THERMOPHILUS PRMA AT 1.9A RESOLUTION REMARK 900 RELATED ID: 1NXC RELATED DB: PDB REMARK 900 T. THERMOPHILUS PRMA AT 1.59A RESOLUTION REMARK 900 RELATED ID: 2NXE RELATED DB: PDB REMARK 900 T. THERMOPHILUS PRMA IN COMPLEX WITH S-ADENOSYL-L-METHIONINE REMARK 900 RELATED ID: 2NXN RELATED DB: PDB DBREF 2NXJ A 1 254 UNP Q84BQ9 PRMA_THET8 1 254 DBREF 2NXJ B 1 254 UNP Q84BQ9 PRMA_THET8 1 254 SEQRES 1 A 254 MET TRP VAL TYR ARG LEU LYS GLY THR LEU GLU ALA LEU SEQRES 2 A 254 ASP PRO ILE LEU PRO GLY LEU PHE ASP GLY GLY ALA ARG SEQRES 3 A 254 GLY LEU TRP GLU ARG GLU GLY GLU VAL TRP ALA PHE PHE SEQRES 4 A 254 PRO ALA PRO VAL ASP LEU PRO TYR GLU GLY VAL TRP GLU SEQRES 5 A 254 GLU VAL GLY ASP GLU ASP TRP LEU GLU ALA TRP ARG ARG SEQRES 6 A 254 ASP LEU LYS PRO ALA LEU ALA PRO PRO PHE VAL VAL LEU SEQRES 7 A 254 ALA PRO TRP HIS THR TRP GLU GLY ALA GLU ILE PRO LEU SEQRES 8 A 254 VAL ILE GLU PRO GLY MET ALA PHE GLY THR GLY HIS HIS SEQRES 9 A 254 GLU THR THR ARG LEU ALA LEU LYS ALA LEU ALA ARG HIS SEQRES 10 A 254 LEU ARG PRO GLY ASP LYS VAL LEU ASP LEU GLY THR GLY SEQRES 11 A 254 SER GLY VAL LEU ALA ILE ALA ALA GLU LYS LEU GLY GLY SEQRES 12 A 254 LYS ALA LEU GLY VAL ASP ILE ASP PRO MET VAL LEU PRO SEQRES 13 A 254 GLN ALA GLU ALA ASN ALA LYS ARG ASN GLY VAL ARG PRO SEQRES 14 A 254 ARG PHE LEU GLU GLY SER LEU GLU ALA ALA LEU PRO PHE SEQRES 15 A 254 GLY PRO PHE ASP LEU LEU VAL ALA ASN LEU TYR ALA GLU SEQRES 16 A 254 LEU HIS ALA ALA LEU ALA PRO ARG TYR ARG GLU ALA LEU SEQRES 17 A 254 VAL PRO GLY GLY ARG ALA LEU LEU THR GLY ILE LEU LYS SEQRES 18 A 254 ASP ARG ALA PRO LEU VAL ARG GLU ALA MET ALA GLY ALA SEQRES 19 A 254 GLY PHE ARG PRO LEU GLU GLU ALA ALA GLU GLY GLU TRP SEQRES 20 A 254 VAL LEU LEU ALA TYR GLY ARG SEQRES 1 B 254 MET TRP VAL TYR ARG LEU LYS GLY THR LEU GLU ALA LEU SEQRES 2 B 254 ASP PRO ILE LEU PRO GLY LEU PHE ASP GLY GLY ALA ARG SEQRES 3 B 254 GLY LEU TRP GLU ARG GLU GLY GLU VAL TRP ALA PHE PHE SEQRES 4 B 254 PRO ALA PRO VAL ASP LEU PRO TYR GLU GLY VAL TRP GLU SEQRES 5 B 254 GLU VAL GLY ASP GLU ASP TRP LEU GLU ALA TRP ARG ARG SEQRES 6 B 254 ASP LEU LYS PRO ALA LEU ALA PRO PRO PHE VAL VAL LEU SEQRES 7 B 254 ALA PRO TRP HIS THR TRP GLU GLY ALA GLU ILE PRO LEU SEQRES 8 B 254 VAL ILE GLU PRO GLY MET ALA PHE GLY THR GLY HIS HIS SEQRES 9 B 254 GLU THR THR ARG LEU ALA LEU LYS ALA LEU ALA ARG HIS SEQRES 10 B 254 LEU ARG PRO GLY ASP LYS VAL LEU ASP LEU GLY THR GLY SEQRES 11 B 254 SER GLY VAL LEU ALA ILE ALA ALA GLU LYS LEU GLY GLY SEQRES 12 B 254 LYS ALA LEU GLY VAL ASP ILE ASP PRO MET VAL LEU PRO SEQRES 13 B 254 GLN ALA GLU ALA ASN ALA LYS ARG ASN GLY VAL ARG PRO SEQRES 14 B 254 ARG PHE LEU GLU GLY SER LEU GLU ALA ALA LEU PRO PHE SEQRES 15 B 254 GLY PRO PHE ASP LEU LEU VAL ALA ASN LEU TYR ALA GLU SEQRES 16 B 254 LEU HIS ALA ALA LEU ALA PRO ARG TYR ARG GLU ALA LEU SEQRES 17 B 254 VAL PRO GLY GLY ARG ALA LEU LEU THR GLY ILE LEU LYS SEQRES 18 B 254 ASP ARG ALA PRO LEU VAL ARG GLU ALA MET ALA GLY ALA SEQRES 19 B 254 GLY PHE ARG PRO LEU GLU GLU ALA ALA GLU GLY GLU TRP SEQRES 20 B 254 VAL LEU LEU ALA TYR GLY ARG FORMUL 3 HOH *290(H2 O) HELIX 1 1 THR A 9 ASP A 14 1 6 HELIX 2 2 ILE A 16 GLY A 24 1 9 HELIX 3 3 TRP A 63 LEU A 67 5 5 HELIX 4 4 HIS A 104 LEU A 118 1 15 HELIX 5 5 GLY A 132 LEU A 141 1 10 HELIX 6 6 VAL A 154 ARG A 164 1 11 HELIX 7 7 SER A 175 LEU A 180 1 6 HELIX 8 8 PRO A 181 GLY A 183 5 3 HELIX 9 9 TYR A 193 ALA A 207 1 15 HELIX 10 10 ARG A 223 ALA A 234 1 12 HELIX 11 11 THR B 9 ASP B 14 1 6 HELIX 12 12 ILE B 16 GLY B 24 1 9 HELIX 13 13 LEU B 60 LEU B 67 1 8 HELIX 14 14 HIS B 104 LEU B 118 1 15 HELIX 15 15 GLY B 132 LEU B 141 1 10 HELIX 16 16 VAL B 154 ASN B 165 1 12 HELIX 17 17 SER B 175 LEU B 180 1 6 HELIX 18 18 PRO B 181 GLY B 183 5 3 HELIX 19 19 TYR B 193 ALA B 207 1 15 HELIX 20 20 LEU B 220 ASP B 222 5 3 HELIX 21 21 ARG B 223 ALA B 234 1 12 SHEET 1 A 8 VAL A 50 GLU A 53 0 SHEET 2 A 8 TRP A 2 LYS A 7 -1 N VAL A 3 O GLU A 52 SHEET 3 A 8 GLU A 34 PHE A 39 -1 O ALA A 37 N TYR A 4 SHEET 4 A 8 GLY A 27 GLU A 30 -1 N GLY A 27 O PHE A 38 SHEET 5 A 8 GLY B 27 GLU B 30 -1 O LEU B 28 N LEU A 28 SHEET 6 A 8 GLU B 34 PHE B 38 -1 O PHE B 38 N GLY B 27 SHEET 7 A 8 TRP B 2 LYS B 7 -1 N TYR B 4 O ALA B 37 SHEET 8 A 8 VAL B 50 GLU B 53 -1 O GLU B 52 N VAL B 3 SHEET 1 B 3 ALA A 70 ALA A 72 0 SHEET 2 B 3 PHE A 75 LEU A 78 -1 O PHE A 75 N ALA A 72 SHEET 3 B 3 ILE A 89 VAL A 92 1 O LEU A 91 N LEU A 78 SHEET 1 C 7 ARG A 170 GLU A 173 0 SHEET 2 C 7 LYS A 144 ASP A 149 1 N GLY A 147 O ARG A 170 SHEET 3 C 7 LYS A 123 LEU A 127 1 N VAL A 124 O LEU A 146 SHEET 4 C 7 PHE A 185 ASN A 191 1 O VAL A 189 N LEU A 125 SHEET 5 C 7 LEU A 208 LEU A 220 1 O LEU A 215 N LEU A 188 SHEET 6 C 7 TRP A 247 GLY A 253 -1 O LEU A 250 N LEU A 216 SHEET 7 C 7 ARG A 237 GLU A 244 -1 N LEU A 239 O ALA A 251 SHEET 1 D 3 ALA B 70 ALA B 72 0 SHEET 2 D 3 PHE B 75 LEU B 78 -1 O PHE B 75 N ALA B 72 SHEET 3 D 3 ILE B 89 VAL B 92 1 O LEU B 91 N LEU B 78 SHEET 1 E 7 ARG B 170 GLU B 173 0 SHEET 2 E 7 LYS B 144 ASP B 149 1 N GLY B 147 O ARG B 170 SHEET 3 E 7 LYS B 123 LEU B 127 1 N VAL B 124 O LEU B 146 SHEET 4 E 7 PHE B 185 ASN B 191 1 O VAL B 189 N LEU B 125 SHEET 5 E 7 LEU B 208 ILE B 219 1 O LEU B 215 N LEU B 188 SHEET 6 E 7 TRP B 247 GLY B 253 -1 O VAL B 248 N ILE B 219 SHEET 7 E 7 ARG B 237 GLU B 244 -1 N ARG B 237 O GLY B 253 CISPEP 1 PRO A 73 PRO A 74 0 12.80 CISPEP 2 GLY A 183 PRO A 184 0 -0.98 CISPEP 3 PRO B 73 PRO B 74 0 6.66 CISPEP 4 GLY B 183 PRO B 184 0 1.90 CRYST1 124.195 153.622 33.255 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 0.008052 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006509 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030071 0.00000