HEADER TRANSFERASE/RNA 17-APR-18 5ZQ1 TITLE CRYSTAL STRUCTURE OF SPRLMCD WITH U1939LOOP RNA AT 3.10 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED RNA METHYLTRANSFERASE SP_1029; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE SEROTYPE 4 (STRAIN SOURCE 3 ATCC BAA-334 / TIGR4); SOURCE 4 ORGANISM_TAXID: 170187; SOURCE 5 STRAIN: ATCC BAA-334 / TIGR4; SOURCE 6 GENE: SP_1029; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE TIGR4; SOURCE 12 ORGANISM_TAXID: 170187 KEYWDS METHYLTRANSFERASE, RIBOSOME, 23S RNA, STREPTOCOCCUS PNEUMONIAE, KEYWDS 2 TRANSFERASE, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.L.YU,Y.Y.JIANG REVDAT 3 22-NOV-23 5ZQ1 1 REMARK REVDAT 2 14-NOV-18 5ZQ1 1 TITLE JRNL REVDAT 1 24-OCT-18 5ZQ1 0 JRNL AUTH Y.JIANG,H.YU,F.LI,L.CHENG,L.ZHU,Y.SHI,Q.GONG JRNL TITL UNVEILING THE STRUCTURAL FEATURES THAT DETERMINE THE DUAL JRNL TITL 2 METHYLTRANSFERASE ACTIVITIES OF STREPTOCOCCUS PNEUMONIAE JRNL TITL 3 RLMCD JRNL REF PLOS PATHOG. V. 14 07379 2018 JRNL REFN ESSN 1553-7374 JRNL PMID 30388185 JRNL DOI 10.1371/JOURNAL.PPAT.1007379 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9422 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 511 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 677 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3600 REMARK 3 NUCLEIC ACID ATOMS : 163 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.08000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.475 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.320 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.692 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3874 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3621 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5267 ; 1.256 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8417 ; 0.909 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 451 ; 6.198 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;36.778 ;25.059 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 680 ;15.141 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;15.447 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 606 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4128 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 732 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5ZQ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-APR-18. REMARK 100 THE DEPOSITION ID IS D_1300007470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-DEC-17 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10101 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.16300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : 0.84400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5XJ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 5.5, 0.15 M AMMONIUM REMARK 280 SULFATE, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.69300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.08100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.04850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.08100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.69300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.04850 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: 2200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 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 A B1936 O5' 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 O2' A B 1937 O5' A B 1938 1.43 REMARK 500 O ARG A 147 OG SER A 150 2.15 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 A B1938 O3' MUM B1939 P -0.120 REMARK 500 MUM B1939 O3' U B1940 P -0.100 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 ARG A 77 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 MUM B1939 O3' - P - O5' ANGL. DEV. = 16.6 DEGREES REMARK 500 MUM B1939 C3' - O3' - P ANGL. DEV. = 18.8 DEGREES REMARK 500 U B1940 O3' - P - OP2 ANGL. DEV. = 16.0 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 ASP A 26 55.58 24.51 REMARK 500 SER A 38 -2.87 75.34 REMARK 500 ASP A 70 112.06 -39.03 REMARK 500 SER A 78 49.43 -74.23 REMARK 500 PHE A 160 -55.06 71.41 REMARK 500 LEU A 270 -131.04 53.82 REMARK 500 GLN A 374 76.14 -114.92 REMARK 500 PRO A 383 -174.29 -67.45 REMARK 500 LYS A 428 -67.69 -94.51 REMARK 500 PHE A 436 71.36 -118.98 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 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XJ1 RELATED DB: PDB DBREF 5ZQ1 A 1 452 UNP Q97R12 Y1029_STRPN 1 452 DBREF 5ZQ1 B 1936 1943 PDB 5ZQ1 5ZQ1 1936 1943 SEQADV 5ZQ1 GLN A 443 UNP Q97R12 GLU 443 ENGINEERED MUTATION SEQRES 1 A 452 MET LEU LYS LYS ASN ASP ILE VAL GLU VAL GLU ILE VAL SEQRES 2 A 452 ASP LEU THR HIS GLU GLY ALA GLY VAL ALA LYS VAL ASP SEQRES 3 A 452 GLY LEU VAL PHE PHE VAL GLU ASN ALA LEU PRO SER GLU SEQRES 4 A 452 LYS ILE LEU MET ARG VAL LEU LYS VAL ASN LYS LYS ILE SEQRES 5 A 452 GLY PHE GLY LYS VAL GLU LYS TYR LEU VAL GLN SER PRO SEQRES 6 A 452 HIS ARG ASN GLN ASP LEU ASP LEU ALA TYR LEU ARG SER SEQRES 7 A 452 GLY ILE ALA ASP LEU GLY HIS LEU SER TYR PRO GLU GLN SEQRES 8 A 452 LEU LYS PHE LYS THR LYS GLN VAL LYS ASP SER LEU TYR SEQRES 9 A 452 LYS ILE ALA GLY ILE ALA ASP VAL GLU VAL ALA GLU THR SEQRES 10 A 452 LEU GLY MET GLU HIS PRO VAL LYS TYR ARG ASN LYS ALA SEQRES 11 A 452 GLN VAL PRO VAL ARG ARG VAL ASN GLY VAL LEU GLU THR SEQRES 12 A 452 GLY PHE PHE ARG LYS ASN SER HIS ASN LEU MET PRO LEU SEQRES 13 A 452 GLU ASP PHE PHE ILE GLN ASP PRO VAL ILE ASP GLN VAL SEQRES 14 A 452 VAL VAL ALA LEU ARG ASP LEU LEU ARG ARG PHE ASP LEU SEQRES 15 A 452 LYS PRO TYR ASP GLU LYS GLU GLN SER GLY LEU ILE ARG SEQRES 16 A 452 ASN LEU VAL VAL ARG ARG GLY HIS TYR SER GLY GLN ILE SEQRES 17 A 452 MET VAL VAL LEU VAL THR THR ARG PRO LYS VAL PHE ARG SEQRES 18 A 452 VAL ASP GLN LEU ILE GLU GLN VAL ILE LYS GLN PHE PRO SEQRES 19 A 452 GLU ILE VAL SER VAL MET GLN ASN ILE ASN ASP GLN ASN SEQRES 20 A 452 THR ASN ALA ILE PHE GLY LYS GLU TRP ARG THR LEU TYR SEQRES 21 A 452 GLY GLN ASP TYR ILE THR ASP GLN MET LEU GLY ASN ASP SEQRES 22 A 452 PHE GLN ILE ALA GLY PRO ALA PHE TYR GLN VAL ASN THR SEQRES 23 A 452 GLU MET ALA GLU LYS LEU TYR GLN THR ALA ILE ASP PHE SEQRES 24 A 452 ALA GLU LEU LYS LYS ASP ASP VAL ILE ILE ASP ALA TYR SEQRES 25 A 452 SER GLY ILE GLY THR ILE GLY LEU SER VAL ALA LYS HIS SEQRES 26 A 452 VAL LYS GLU VAL TYR GLY VAL GLU LEU ILE PRO GLU ALA SEQRES 27 A 452 VAL GLU ASN SER GLN LYS ASN ALA SER LEU ASN LYS ILE SEQRES 28 A 452 THR ASN ALA HIS TYR VAL CYS ASP THR ALA GLU ASN ALA SEQRES 29 A 452 MET LYS LYS TRP LEU LYS GLU GLY ILE GLN PRO THR VAL SEQRES 30 A 452 ILE LEU VAL ASP PRO PRO ARG LYS GLY LEU THR GLU SER SEQRES 31 A 452 PHE ILE LYS ALA SER ALA GLN THR GLY ALA ASP ARG ILE SEQRES 32 A 452 ALA TYR ILE SER CYS ASN VAL ALA THR MET ALA ARG ASP SEQRES 33 A 452 ILE LYS LEU TYR GLN GLU LEU GLY TYR GLU LEU LYS LYS SEQRES 34 A 452 VAL GLN PRO VAL ASP LEU PHE PRO GLN THR HIS HIS VAL SEQRES 35 A 452 GLN THR VAL ALA LEU LEU SER LYS LEU ASP SEQRES 1 B 8 A A A MUM U C C U HET MUM B1939 21 HET SAH A 501 26 HETNAM MUM 5'-O-(DIHYDROXYPHOSPHANYL)-5-METHYL-5,6-DIHYDROURIDINE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 MUM C10 H17 N2 O8 P FORMUL 3 SAH C14 H20 N6 O5 S HELIX 1 AA1 ASP A 70 SER A 78 1 9 HELIX 2 AA2 SER A 87 ILE A 106 1 20 HELIX 3 AA3 ASP A 163 PHE A 180 1 18 HELIX 4 AA4 ARG A 221 PHE A 233 1 13 HELIX 5 AA5 ASN A 285 GLU A 301 1 17 HELIX 6 AA6 GLY A 316 ALA A 323 1 8 HELIX 7 AA7 LYS A 324 VAL A 326 5 3 HELIX 8 AA8 ILE A 335 ASN A 349 1 15 HELIX 9 AA9 THR A 360 GLY A 372 1 13 HELIX 10 AB1 THR A 388 THR A 398 1 11 HELIX 11 AB2 ASN A 409 GLU A 422 1 14 SHEET 1 AA1 6 ILE A 7 GLU A 11 0 SHEET 2 AA1 6 LYS A 40 VAL A 48 -1 O MET A 43 N VAL A 8 SHEET 3 AA1 6 ILE A 52 VAL A 62 -1 O GLU A 58 N LEU A 42 SHEET 4 AA1 6 LEU A 28 VAL A 32 1 N VAL A 29 O GLY A 53 SHEET 5 AA1 6 GLY A 21 VAL A 25 -1 N ALA A 23 O PHE A 30 SHEET 6 AA1 6 ASP A 14 LEU A 15 -1 N ASP A 14 O VAL A 22 SHEET 1 AA2 8 GLU A 113 VAL A 114 0 SHEET 2 AA2 8 TYR A 425 VAL A 433 1 O LYS A 428 N GLU A 113 SHEET 3 AA2 8 GLN A 443 LYS A 450 -1 O SER A 449 N GLU A 426 SHEET 4 AA2 8 ARG A 402 SER A 407 -1 N ILE A 403 O LEU A 448 SHEET 5 AA2 8 VAL A 377 VAL A 380 1 N VAL A 380 O ILE A 406 SHEET 6 AA2 8 VAL A 307 ALA A 311 1 N ILE A 309 O LEU A 379 SHEET 7 AA2 8 GLU A 328 GLU A 333 1 O TYR A 330 N ASP A 310 SHEET 8 AA2 8 ALA A 354 CYS A 358 1 O HIS A 355 N VAL A 329 SHEET 1 AA3 7 LEU A 153 PRO A 155 0 SHEET 2 AA3 7 LEU A 141 PHE A 146 -1 N PHE A 145 O MET A 154 SHEET 3 AA3 7 LYS A 129 ARG A 136 -1 N ARG A 135 O GLU A 142 SHEET 4 AA3 7 ILE A 194 ARG A 201 -1 O LEU A 197 N VAL A 132 SHEET 5 AA3 7 ILE A 208 THR A 214 -1 O VAL A 211 N VAL A 198 SHEET 6 AA3 7 ILE A 236 ILE A 243 1 O ASN A 242 N THR A 214 SHEET 7 AA3 7 TRP A 256 GLY A 261 -1 O ARG A 257 N GLN A 241 SHEET 1 AA4 2 ILE A 265 MET A 269 0 SHEET 2 AA4 2 ASN A 272 ILE A 276 -1 O ILE A 276 N ILE A 265 LINK SG CYS A 408 C6 MUM B1939 1555 1555 1.64 LINK O3' A B1938 P MUM B1939 1555 1555 1.49 LINK O3' MUM B1939 P U B1940 1555 1555 1.51 SITE 1 AC1 18 PHE A 281 GLN A 283 TYR A 293 TYR A 312 SITE 2 AC1 18 SER A 313 GLY A 314 THR A 317 ILE A 318 SITE 3 AC1 18 GLU A 333 LEU A 334 ILE A 335 THR A 360 SITE 4 AC1 18 ALA A 361 GLU A 362 ASP A 381 PRO A 383 SITE 5 AC1 18 LYS A 385 MUM B1939 CRYST1 47.386 96.097 114.162 90.00 90.00 90.00 P 21 21 21 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 0.021103 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008759 0.00000