HEADER TRANSFERASE 17-APR-08 2VS1 TITLE THE CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI TRNA (URACIL-54, C5)- TITLE 2 METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED RNA METHYLTRANSFERASE PYRAB10780; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRNA M5U54-METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 3 ORGANISM_TAXID: 29292; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METAL-BINDING, METHYLTRANSFERASE, TRNA METHYLTRANSFERASE, S-ADENOSYL- KEYWDS 2 L-METHIONINE, IRON, TRANSFERASE, IRON-SULFUR EXPDTA X-RAY DIFFRACTION AUTHOR H.WALBOTT,N.LEULLIOT,H.GROSJEAN,B.GOLINELLI-PIMPANEAU REVDAT 4 12-JUL-17 2VS1 1 REVDAT 3 24-FEB-09 2VS1 1 VERSN REVDAT 2 09-SEP-08 2VS1 1 JRNL REVDAT 1 05-AUG-08 2VS1 0 JRNL AUTH H.WALBOTT,N.LEULLIOT,H.GROSJEAN,B.GOLINELLI-PIMPANEAU JRNL TITL THE CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI TRNA (URACIL-54, JRNL TITL 2 C5)-METHYLTRANSFERASE PROVIDES INSIGHTS INTO ITS TRNA JRNL TITL 3 SPECIFICITY. JRNL REF NUCLEIC ACIDS RES. V. 36 4929 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18653523 JRNL DOI 10.1093/NAR/GKN437 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 27517 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1473 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2014 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 99 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.35000 REMARK 3 B22 (A**2) : 1.07000 REMARK 3 B33 (A**2) : -0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.93000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.201 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.192 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.970 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3358 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4526 ; 2.342 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 7.586 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;33.152 ;23.174 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 609 ;17.413 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;20.824 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 486 ; 0.157 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2536 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1982 ; 1.433 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3219 ; 2.489 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1376 ; 3.873 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1307 ; 5.990 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2VS1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-APR-08. REMARK 100 THE DEPOSITION ID IS D_1290035966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28215 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28990 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 68.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 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) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 8000, 0.05 M AMMONIUM SULFATE, REMARK 280 0.1 M SODIUM CITRATE PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 49.76450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.20750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.76450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.20750 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 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 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A 58 REMARK 465 PRO A 59 REMARK 465 ARG A 60 REMARK 465 CYS A 61 REMARK 465 LYS A 62 REMARK 465 ALA A 63 REMARK 465 PHE A 64 REMARK 465 GLY A 65 REMARK 465 ARG A 125 REMARK 465 GLY A 126 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 710 O HOH A 788 1.89 REMARK 500 CB VAL A 4 O HOH A 738 2.03 REMARK 500 O PRO A 359 OH TYR A 381 2.10 REMARK 500 OD2 ASP A 224 O HOH A 601 2.11 REMARK 500 O LEU A 244 O HOH A 602 2.14 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 745 O HOH A 758 2656 2.11 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 GLU A 95 CG GLU A 95 CD 0.106 REMARK 500 GLU A 149 CG GLU A 149 CD 0.093 REMARK 500 TYR A 243 CE1 TYR A 243 CZ 0.085 REMARK 500 CYS A 367 CB CYS A 367 SG -0.110 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 28 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 51 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 56 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 240 CB - CG - OD1 ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 263 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 309 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 PRO A 341 C - N - CA ANGL. DEV. = 9.4 DEGREES REMARK 500 ASP A 375 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 90 -73.94 -64.82 REMARK 500 SER A 221 35.88 -98.26 REMARK 500 ASP A 239 -113.21 60.21 REMARK 500 GLN A 252 124.00 -36.59 REMARK 500 PRO A 342 -178.15 -64.98 REMARK 500 LYS A 358 77.80 24.81 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 SAH A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JJQ RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI TRNA (URACIL-54, C5)- REMARK 900 METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE DBREF 2VS1 A -19 0 PDB 2VS1 2VS1 -19 0 DBREF 2VS1 A 1 405 UNP Q9UZR7 Y1078_PYRAB 1 405 SEQRES 1 A 425 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 425 LEU VAL PRO ARG GLY SER HIS MET ARG GLY VAL ILE ARG SEQRES 3 A 425 LYS LEU ASN ASP ASP GLY PHE GLY VAL LEU LYS GLY ILE SEQRES 4 A 425 LEU VAL PRO PHE SER ALA PRO GLY ASP GLU ILE ILE VAL SEQRES 5 A 425 GLU ARG VAL GLU ARG VAL LYS LYS ARG ARG VAL ALA SER SEQRES 6 A 425 GLN TRP LYS LEU VAL ARG SER SER PRO LEU ARG VAL GLY SEQRES 7 A 425 PRO ARG CYS LYS ALA PHE GLY LYS CYS GLY GLY CYS THR SEQRES 8 A 425 LEU GLN HIS LEU ASN TYR ASP TYR GLN LEU GLU PHE LYS SEQRES 9 A 425 ARG LYS LYS LEU LYS ARG ILE LEU GLY PHE GLU VAL GLU SEQRES 10 A 425 VAL VAL PRO SER PRO LYS ILE PHE GLY HIS ARG ASN ARG SEQRES 11 A 425 ILE ASP LEU ALA ILE THR LYS ASP GLY ILE GLY PHE ARG SEQRES 12 A 425 GLU ARG GLY LYS TRP TRP LYS ILE VAL ASP ILE ASP GLU SEQRES 13 A 425 CSS PRO VAL PHE GLY LYS THR SER ARG GLU ALA ILE GLU SEQRES 14 A 425 ARG LEU LYS GLU PHE ILE GLU GLU GLU LYS ILE SER VAL SEQRES 15 A 425 TRP ASN ILE LYS LYS ASP GLU GLY PHE LEU ARG TYR MET SEQRES 16 A 425 VAL LEU ARG GLU GLY LYS PHE THR GLU GLU VAL MET VAL SEQRES 17 A 425 ASN PHE VAL THR LYS GLU GLY ASN LEU PRO ASP PRO THR SEQRES 18 A 425 ASN TYR PHE ASP PHE ASP SER ILE TYR TRP SER VAL ASN SEQRES 19 A 425 ARG SER LYS SER ASP VAL SER TYR GLY ASP ILE GLU ARG SEQRES 20 A 425 PHE TRP GLY LYS GLU PHE ILE ARG GLU ARG LEU ASP ASP SEQRES 21 A 425 VAL ASP TYR LEU ILE HIS PRO ASN SER PHE PHE GLN THR SEQRES 22 A 425 ASN SER TYR GLN ALA VAL ASN LEU VAL ARG LYS VAL SER SEQRES 23 A 425 GLU LEU VAL GLU GLY GLU LYS ILE LEU ASP MET TYR SER SEQRES 24 A 425 GLY VAL GLY THR PHE GLY ILE TYR LEU ALA LYS ARG GLY SEQRES 25 A 425 PHE ASN VAL LYS GLY PHE ASP SER ASN GLU PHE ALA ILE SEQRES 26 A 425 GLU MET ALA ARG ARG ASN VAL GLU ILE ASN ASN VAL ASP SEQRES 27 A 425 ALA GLU PHE GLU VAL ALA SER ASP ARG GLU VAL SER VAL SEQRES 28 A 425 LYS GLY PHE ASP THR VAL ILE VAL ASP PRO PRO ARG ALA SEQRES 29 A 425 GLY LEU HIS PRO ARG LEU VAL LYS ARG LEU ASN ARG GLU SEQRES 30 A 425 LYS PRO GLY VAL ILE VAL TYR VAL SER CYS ASN PRO GLU SEQRES 31 A 425 THR PHE ALA ARG ASP VAL LYS MET LEU ASP TYR ARG ILE SEQRES 32 A 425 ASP GLU ILE VAL ALA LEU ASP MET PHE PRO HIS THR PRO SEQRES 33 A 425 HIS VAL GLU LEU VAL ALA LYS LEU VAL MODRES 2VS1 CSS A 137 CYS S-MERCAPTOCYSTEINE HET CSS A 137 7 HET SAH A 501 26 HET PO4 A 502 5 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM PO4 PHOSPHATE ION FORMUL 1 CSS C3 H7 N O2 S2 FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *188(H2 O) HELIX 1 1 GLY A -2 HIS A 0 5 3 HELIX 2 2 ASN A 76 GLY A 93 1 18 HELIX 3 3 LYS A 142 LYS A 159 1 18 HELIX 4 4 PRO A 200 PHE A 204 5 5 HELIX 5 5 ASN A 254 VAL A 269 1 16 HELIX 6 6 GLY A 282 LYS A 290 1 9 HELIX 7 7 ASN A 301 ASN A 315 1 15 HELIX 8 8 HIS A 347 LYS A 358 1 12 HELIX 9 9 ASN A 368 LEU A 379 1 12 SHEET 1 AA 3 ARG A 2 VAL A 4 0 SHEET 2 AA 3 GLU A 29 VAL A 38 -1 O ILE A 30 N GLY A 3 SHEET 3 AA 3 ARG A 41 ARG A 51 -1 O ARG A 41 N VAL A 38 SHEET 1 AB 2 GLY A 14 LEU A 16 0 SHEET 2 AB 2 ILE A 19 VAL A 21 -1 O ILE A 19 N LEU A 16 SHEET 1 AC 8 VAL A 98 VAL A 99 0 SHEET 2 AC 8 ARG A 382 LEU A 389 1 O ALA A 388 N VAL A 99 SHEET 3 AC 8 GLU A 399 VAL A 405 -1 O GLU A 399 N LEU A 389 SHEET 4 AC 8 VAL A 361 SER A 366 -1 O ILE A 362 N LEU A 404 SHEET 5 AC 8 THR A 336 VAL A 339 1 O VAL A 337 N VAL A 363 SHEET 6 AC 8 LYS A 273 MET A 277 1 O LYS A 273 N THR A 336 SHEET 7 AC 8 ASN A 294 ASP A 299 1 O ASN A 294 N ILE A 274 SHEET 8 AC 8 GLU A 320 VAL A 323 1 O GLU A 320 N GLY A 297 SHEET 1 AD 7 ILE A 131 ASP A 133 0 SHEET 2 AD 7 GLY A 119 ARG A 123 -1 O PHE A 122 N VAL A 132 SHEET 3 AD 7 ARG A 110 THR A 116 -1 O ALA A 114 N GLY A 121 SHEET 4 AD 7 LEU A 172 GLU A 179 -1 O ARG A 173 N ILE A 115 SHEET 5 AD 7 VAL A 186 THR A 192 -1 O MET A 187 N ARG A 178 SHEET 6 AD 7 SER A 208 VAL A 213 1 O SER A 208 N VAL A 188 SHEET 7 AD 7 ASP A 224 GLY A 230 -1 O ASP A 224 N VAL A 213 SHEET 1 AE 2 ILE A 234 LEU A 238 0 SHEET 2 AE 2 VAL A 241 ILE A 245 -1 O VAL A 241 N LEU A 238 SSBOND 1 CYS A 67 CYS A 70 1555 1555 2.01 LINK C GLU A 136 N CSS A 137 1555 1555 1.32 LINK C CSS A 137 N PRO A 138 1555 1555 1.36 SITE 1 AC1 16 PHE A 250 GLN A 252 TYR A 278 SER A 279 SITE 2 AC1 16 GLY A 280 THR A 283 ASP A 299 SER A 300 SITE 3 AC1 16 ASN A 301 ALA A 324 ASP A 326 ASP A 340 SITE 4 AC1 16 HOH A 664 HOH A 627 HOH A 628 HOH A 629 SITE 1 AC2 5 ARG A 6 ARG A 51 ARG A 85 LYS A 86 SITE 2 AC2 5 HOH A 635 CRYST1 99.529 100.415 55.737 90.00 111.61 90.00 C 1 2 1 4 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 0.010047 0.000000 0.003980 0.00000 SCALE2 0.000000 0.009959 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019298 0.00000