HEADER TRANSFERASE 02-OCT-02 1MXI TITLE STRUCTURE OF YIBK FROM HAEMOPHILUS INFLUENZAE (HI0766): A TITLE 2 METHYLTRANSFERASE WITH A COFACTOR BOUND AT A SITE FORMED BY A KNOT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE HI0766; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: YIBK; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 GENE: HI0766; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS METHYLTRANSFERASE, S-ADENOSYLHOMOCYSTEINE, SPOU FAMILY, STRUCTURE 2 KEYWDS 2 FUNCTION PROJECT, S2F, STRUCTURAL GENOMICS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.LIM,H.ZHANG,A.TEMPCZYK,N.BONANDER,J.TOEDT,A.HOWARD,E.EISENSTEIN, AUTHOR 2 O.HERZBERG,STRUCTURE 2 FUNCTION PROJECT (S2F) REVDAT 3 14-FEB-24 1MXI 1 REMARK REVDAT 2 24-FEB-09 1MXI 1 VERSN REVDAT 1 25-FEB-03 1MXI 0 JRNL AUTH K.LIM,H.ZHANG,A.TEMPCZYK,W.KRAJEWSKI,N.BONANDER,J.TOEDT, JRNL AUTH 2 A.HOWARD,E.EISENSTEIN,O.HERZBERG JRNL TITL STRUCTURE OF THE YIBK METHYLTRANSFERASE FROM HAEMOPHILUS JRNL TITL 2 INFLUENZAE (HI0766): A COFACTOR BOUND AT A SITE FORMED BY A JRNL TITL 3 KNOT JRNL REF PROTEINS V. 51 56 2003 JRNL REFN ISSN 0887-3585 JRNL PMID 12596263 JRNL DOI 10.1002/PROT.10323 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14742 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 SET) : 0.196 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1593 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MXI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15394 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22300 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: CNS REMARK 200 STARTING MODEL: PDB 1J85 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PMME 2000, 0.1 M SODIUM ACETATE, REMARK 280 0.2 M AMMONIUM ACETATE, 3 % ETHYLENE GLYCOL, PH 4.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, SOAKING OF CRYSTAL WITH COFACTOR SAH, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 82.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.40000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.45000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.40000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.40000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 124.35000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.40000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.40000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.45000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.40000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.40000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 124.35000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 82.90000 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 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 PRO A 157 REMARK 465 GLU A 158 REMARK 465 VAL A 159 REMARK 465 LYS A 160 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 43 12.82 -59.09 REMARK 500 PHE A 54 -162.81 -104.51 REMARK 500 ALA A 55 -16.30 63.34 REMARK 500 ARG A 104 -12.25 -152.98 REMARK 500 SER A 130 173.08 176.58 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 IOD A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J85 RELATED DB: PDB REMARK 900 1J85 IS YIBK METHYLTRANSFERASE FROM HAEMOPHILIUS INFLUENZAE (HI0766) REMARK 900 , APO-METHYLTRANSFERASE WITH A KNOT-CONTAINING FOLD REMARK 900 RELATED ID: HI0766 RELATED DB: TARGETDB DBREF 1MXI A 1 160 UNP P44868 Y766_HAEIN 1 160 SEQRES 1 A 160 MET LEU ASP ILE VAL LEU TYR GLU PRO GLU ILE PRO GLN SEQRES 2 A 160 ASN THR GLY ASN ILE ILE ARG LEU CYS ALA ASN THR GLY SEQRES 3 A 160 PHE ARG LEU HIS LEU ILE GLU PRO LEU GLY PHE THR TRP SEQRES 4 A 160 ASP ASP LYS ARG LEU ARG ARG SER GLY LEU ASP TYR HIS SEQRES 5 A 160 GLU PHE ALA GLU ILE LYS ARG HIS LYS THR PHE GLU ALA SEQRES 6 A 160 PHE LEU GLU SER GLU LYS PRO LYS ARG LEU PHE ALA LEU SEQRES 7 A 160 THR THR LYS GLY CYS PRO ALA HIS SER GLN VAL LYS PHE SEQRES 8 A 160 LYS LEU GLY ASP TYR LEU MET PHE GLY PRO GLU THR ARG SEQRES 9 A 160 GLY ILE PRO MET SER ILE LEU ASN GLU MET PRO MET GLU SEQRES 10 A 160 GLN LYS ILE ARG ILE PRO MET THR ALA ASN SER ARG SER SEQRES 11 A 160 MET ASN LEU SER ASN SER VAL ALA VAL THR VAL TYR GLU SEQRES 12 A 160 ALA TRP ARG GLN LEU GLY TYR LYS GLY ALA VAL ASN LEU SEQRES 13 A 160 PRO GLU VAL LYS HET IOD A2001 1 HET SAH A 302 26 HETNAM IOD IODIDE ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 IOD I 1- FORMUL 3 SAH C14 H20 N6 O5 S FORMUL 4 HOH *153(H2 O) HELIX 1 1 ILE A 11 GLY A 26 1 16 HELIX 2 2 ASP A 41 ARG A 46 1 6 HELIX 3 3 ASP A 50 PHE A 54 5 5 HELIX 4 4 THR A 62 LYS A 71 1 10 HELIX 5 5 ALA A 85 VAL A 89 5 5 HELIX 6 6 PRO A 107 ASN A 112 1 6 HELIX 7 7 GLU A 113 MET A 114 5 2 HELIX 8 8 PRO A 115 GLU A 117 5 3 HELIX 9 9 ASN A 132 LEU A 148 1 17 SHEET 1 A 6 LYS A 58 HIS A 60 0 SHEET 2 A 6 ARG A 28 ILE A 32 1 N LEU A 31 O HIS A 60 SHEET 3 A 6 ASP A 3 TYR A 7 1 N ILE A 4 O ARG A 28 SHEET 4 A 6 ASP A 95 PHE A 99 1 O LEU A 97 N VAL A 5 SHEET 5 A 6 ARG A 74 LEU A 78 1 N PHE A 76 O TYR A 96 SHEET 6 A 6 LYS A 119 ILE A 120 1 O ILE A 120 N ALA A 77 CISPEP 1 GLU A 33 PRO A 34 0 0.35 SITE 1 AC1 1 MET A 131 SITE 1 AC2 16 LEU A 78 THR A 79 THR A 80 PHE A 99 SITE 2 AC2 16 GLY A 100 PRO A 101 GLU A 102 ARG A 104 SITE 3 AC2 16 GLY A 105 ARG A 121 ILE A 122 MET A 124 SITE 4 AC2 16 SER A 130 MET A 131 SER A 136 HOH A1002 CRYST1 40.800 40.800 165.800 90.00 90.00 90.00 P 41 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 0.024510 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024510 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006031 0.00000