HEADER TRANSFERASE 28-JUL-16 5L0Z TITLE CRYSTAL STRUCTURE OF ADOMET BOUND RRNA METHYLTRANSFERASE FROM TITLE 2 SINORHIZOBIUM MELILOTI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE RNA METHYLTRANSFERASE, TRMH FAMILY; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOBIUM MELILOTI (STRAIN 1021); SOURCE 3 ORGANISM_COMMON: ENSIFER MELILOTI; SOURCE 4 ORGANISM_TAXID: 266834; SOURCE 5 STRAIN: 1021; SOURCE 6 GENE: SMC01130; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: BC-PSGX4(BC) KEYWDS SPOUT METHYLTRANSFERASE, ADOMET BINDING, TREFOIL KNOT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.DEY,R.P.HEGDE,S.C.ALMO,S.RAMAKUMAR,U.A.RAMAGOPAL REVDAT 2 20-NOV-19 5L0Z 1 LINK REVDAT 1 02-AUG-17 5L0Z 0 JRNL AUTH D.DEY,R.P.HEGDE,S.C.ALMO,S.RAMAKUMAR,U.A.RAMAGOPAL JRNL TITL CRYSTAL STRUCTURE OF ADOMET BOUND RRNA METHYLTRANSFERASE JRNL TITL 2 FROM SINORHIZOBIUM MELILOTI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 12403 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 634 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 587 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 25 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3951 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 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) : 56.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : -0.89000 REMARK 3 B33 (A**2) : 0.34000 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): 0.451 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.343 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.924 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4091 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4044 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5566 ; 1.667 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9240 ; 1.015 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 523 ; 7.549 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;37.897 ;23.374 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 648 ;18.907 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;19.716 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 677 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4594 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 893 ; 0.002 ; 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): 2104 ; 1.957 ; 4.334 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2104 ; 1.955 ; 4.334 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2623 ; 3.404 ; 6.481 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2624 ; 3.404 ; 6.483 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1987 ; 2.086 ; 4.576 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1988 ; 2.085 ; 4.576 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2944 ; 3.491 ; 6.782 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4343 ; 5.616 ;52.265 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4344 ; 5.615 ;52.260 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 : 2 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 16 A 284 REMARK 3 ORIGIN FOR THE GROUP (A): 34.8978 44.8742 8.8879 REMARK 3 T TENSOR REMARK 3 T11: 0.0080 T22: 0.1836 REMARK 3 T33: 0.1150 T12: -0.0267 REMARK 3 T13: -0.0100 T23: 0.0249 REMARK 3 L TENSOR REMARK 3 L11: 1.0091 L22: 0.5221 REMARK 3 L33: 0.9466 L12: 0.0032 REMARK 3 L13: -0.3146 L23: -0.6376 REMARK 3 S TENSOR REMARK 3 S11: -0.0801 S12: 0.1560 S13: 0.0456 REMARK 3 S21: 0.0023 S22: 0.0320 S23: -0.0658 REMARK 3 S31: 0.0147 S32: 0.0131 S33: 0.0481 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 : B 16 B 283 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5011 39.4904 22.3585 REMARK 3 T TENSOR REMARK 3 T11: 0.0329 T22: 0.1628 REMARK 3 T33: 0.0923 T12: -0.0068 REMARK 3 T13: 0.0058 T23: 0.0212 REMARK 3 L TENSOR REMARK 3 L11: 1.3755 L22: 0.6013 REMARK 3 L33: 0.5767 L12: 0.3607 REMARK 3 L13: 0.1865 L23: 0.1089 REMARK 3 S TENSOR REMARK 3 S11: -0.1061 S12: 0.0453 S13: -0.0654 REMARK 3 S21: 0.0181 S22: 0.0868 S23: 0.0531 REMARK 3 S31: -0.0963 S32: -0.1002 S33: 0.0192 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: 1.542, HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 5L0Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13571 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 65.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5MM COBALT CHLORIDE , 5MM MAGNESIUM REMARK 280 CHLORIDE HEXAHYDRATE, 0.1M HEPES PH 7.5, 9% WT/VOL POLYETHYLENE REMARK 280 GLYCOL 3,350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 300K 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 32.42750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.40300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.44800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.40300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.42750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.44800 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: 3670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 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 ILE A 2 REMARK 465 ASN A 3 REMARK 465 ASP A 4 REMARK 465 ARG A 5 REMARK 465 SER A 6 REMARK 465 ASP A 7 REMARK 465 HIS A 8 REMARK 465 GLY A 9 REMARK 465 THR A 10 REMARK 465 GLY A 11 REMARK 465 THR A 12 REMARK 465 ALA A 13 REMARK 465 ARG A 14 REMARK 465 VAL A 15 REMARK 465 ALA A 71 REMARK 465 LYS A 72 REMARK 465 ALA A 73 REMARK 465 ALA A 74 REMARK 465 LYS A 75 REMARK 465 GLY A 76 REMARK 465 LYS A 77 REMARK 465 ASP A 285 REMARK 465 GLY A 286 REMARK 465 GLY A 287 REMARK 465 ARG A 288 REMARK 465 MSE B 1 REMARK 465 ILE B 2 REMARK 465 ASN B 3 REMARK 465 ASP B 4 REMARK 465 ARG B 5 REMARK 465 SER B 6 REMARK 465 ASP B 7 REMARK 465 HIS B 8 REMARK 465 GLY B 9 REMARK 465 THR B 10 REMARK 465 GLY B 11 REMARK 465 THR B 12 REMARK 465 ALA B 13 REMARK 465 ARG B 14 REMARK 465 VAL B 15 REMARK 465 ALA B 71 REMARK 465 LYS B 72 REMARK 465 ALA B 73 REMARK 465 ALA B 74 REMARK 465 LYS B 75 REMARK 465 GLY B 76 REMARK 465 LYS B 77 REMARK 465 LEU B 284 REMARK 465 ASP B 285 REMARK 465 GLY B 286 REMARK 465 GLY B 287 REMARK 465 ARG B 288 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 LYS A 39 CE NZ REMARK 470 ARG A 45 CD NE CZ NH1 NH2 REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 96 CG CD OE1 OE2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 ARG A 143 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 20 CG CD OE1 OE2 REMARK 470 SER B 23 OG REMARK 470 LYS B 53 CG CD CE NZ REMARK 470 GLN B 82 CD OE1 NE2 REMARK 470 LYS B 86 CE NZ REMARK 470 GLU B 99 CG CD OE1 OE2 REMARK 470 LYS B 100 CG CD CE NZ REMARK 470 ARG B 108 NE CZ NH1 NH2 REMARK 470 ARG B 260 CG CD NE CZ NH1 NH2 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 ASN A 26 84.04 -2.37 REMARK 500 PRO A 27 -43.89 -24.14 REMARK 500 ASN A 110 54.16 -140.59 REMARK 500 ARG A 247 -38.97 -38.66 REMARK 500 ALA A 258 52.17 -154.35 REMARK 500 ALA A 261 126.16 -33.88 REMARK 500 PRO B 130 102.87 -45.73 REMARK 500 GLN B 238 -61.79 -90.14 REMARK 500 VAL B 243 -38.94 -37.68 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 CO A 301 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 40 ND1 REMARK 620 2 GLU A 43 OE2 101.7 REMARK 620 3 HIS B 129 NE2 37.4 118.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 301 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 40 ND1 REMARK 620 2 HIS A 129 NE2 28.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KZK RELATED DB: PDB DBREF 5L0Z A 2 288 UNP Q92SJ4 Q92SJ4_RHIME 2 288 DBREF 5L0Z B 2 288 UNP Q92SJ4 Q92SJ4_RHIME 2 288 SEQADV 5L0Z MSE A 1 UNP Q92SJ4 INITIATING METHIONINE SEQADV 5L0Z MSE B 1 UNP Q92SJ4 INITIATING METHIONINE SEQRES 1 A 288 MSE ILE ASN ASP ARG SER ASP HIS GLY THR GLY THR ALA SEQRES 2 A 288 ARG VAL GLY GLN VAL LYS GLU VAL THR SER LEU THR ASN SEQRES 3 A 288 PRO ILE VAL LYS ASP ILE ARG ALA LEU THR GLN LYS LYS SEQRES 4 A 288 HIS ARG ASP GLU THR ARG SER PHE MSE ALA GLU GLY LEU SEQRES 5 A 288 LYS LEU VAL ILE ASP ALA LEU ASP LEU GLY TRP LYS ILE SEQRES 6 A 288 LYS THR LEU VAL TYR ALA LYS ALA ALA LYS GLY LYS PRO SEQRES 7 A 288 GLN VAL GLU GLN VAL ALA ALA LYS THR VAL ALA ARG GLY SEQRES 8 A 288 GLY LEU VAL LEU GLU VAL ASN GLU LYS VAL ILE SER THR SEQRES 9 A 288 ILE THR ARG ARG ASP ASN PRO GLN MSE VAL VAL GLY ILE SEQRES 10 A 288 PHE GLU GLN ARG TYR SER PRO LEU ARG ASP ILE HIS PRO SEQRES 11 A 288 GLN GLU GLY GLU THR TYR VAL ALA LEU ASP ARG VAL ARG SEQRES 12 A 288 ASP PRO GLY ASN LEU GLY THR ILE ILE ARG THR ALA ASP SEQRES 13 A 288 ALA ALA GLY ALA SER GLY ILE ILE LEU VAL GLY GLU THR SEQRES 14 A 288 THR ASP PRO PHE SER LEU GLU THR VAL ARG ALA THR MSE SEQRES 15 A 288 GLY SER VAL PHE ALA ILE PRO ILE ALA ARG ALA ASN THR SEQRES 16 A 288 GLU ASP PHE ILE ARG TRP GLN ARG ALA ALA GLY VAL GLN SEQRES 17 A 288 VAL VAL ALA THR HIS LEU ALA GLY SER VAL ASP TYR ARG SEQRES 18 A 288 THR ILE ASP TYR LYS SER LYS PRO VAL VAL LEU LEU MSE SEQRES 19 A 288 GLY ASN GLU GLN ALA GLY LEU PRO VAL GLU LEU ALA ARG SEQRES 20 A 288 GLU ALA GLY ALA LEU ALA ARG ILE PRO GLN ALA GLY ARG SEQRES 21 A 288 ALA ASP SER LEU ASN LEU ALA ILE ALA THR GLY ILE MSE SEQRES 22 A 288 LEU PHE GLU ALA ARG ARG HIS LEU LEU SER LEU ASP GLY SEQRES 23 A 288 GLY ARG SEQRES 1 B 288 MSE ILE ASN ASP ARG SER ASP HIS GLY THR GLY THR ALA SEQRES 2 B 288 ARG VAL GLY GLN VAL LYS GLU VAL THR SER LEU THR ASN SEQRES 3 B 288 PRO ILE VAL LYS ASP ILE ARG ALA LEU THR GLN LYS LYS SEQRES 4 B 288 HIS ARG ASP GLU THR ARG SER PHE MSE ALA GLU GLY LEU SEQRES 5 B 288 LYS LEU VAL ILE ASP ALA LEU ASP LEU GLY TRP LYS ILE SEQRES 6 B 288 LYS THR LEU VAL TYR ALA LYS ALA ALA LYS GLY LYS PRO SEQRES 7 B 288 GLN VAL GLU GLN VAL ALA ALA LYS THR VAL ALA ARG GLY SEQRES 8 B 288 GLY LEU VAL LEU GLU VAL ASN GLU LYS VAL ILE SER THR SEQRES 9 B 288 ILE THR ARG ARG ASP ASN PRO GLN MSE VAL VAL GLY ILE SEQRES 10 B 288 PHE GLU GLN ARG TYR SER PRO LEU ARG ASP ILE HIS PRO SEQRES 11 B 288 GLN GLU GLY GLU THR TYR VAL ALA LEU ASP ARG VAL ARG SEQRES 12 B 288 ASP PRO GLY ASN LEU GLY THR ILE ILE ARG THR ALA ASP SEQRES 13 B 288 ALA ALA GLY ALA SER GLY ILE ILE LEU VAL GLY GLU THR SEQRES 14 B 288 THR ASP PRO PHE SER LEU GLU THR VAL ARG ALA THR MSE SEQRES 15 B 288 GLY SER VAL PHE ALA ILE PRO ILE ALA ARG ALA ASN THR SEQRES 16 B 288 GLU ASP PHE ILE ARG TRP GLN ARG ALA ALA GLY VAL GLN SEQRES 17 B 288 VAL VAL ALA THR HIS LEU ALA GLY SER VAL ASP TYR ARG SEQRES 18 B 288 THR ILE ASP TYR LYS SER LYS PRO VAL VAL LEU LEU MSE SEQRES 19 B 288 GLY ASN GLU GLN ALA GLY LEU PRO VAL GLU LEU ALA ARG SEQRES 20 B 288 GLU ALA GLY ALA LEU ALA ARG ILE PRO GLN ALA GLY ARG SEQRES 21 B 288 ALA ASP SER LEU ASN LEU ALA ILE ALA THR GLY ILE MSE SEQRES 22 B 288 LEU PHE GLU ALA ARG ARG HIS LEU LEU SER LEU ASP GLY SEQRES 23 B 288 GLY ARG MODRES 5L0Z MSE A 48 MET MODIFIED RESIDUE MODRES 5L0Z MSE A 113 MET MODIFIED RESIDUE MODRES 5L0Z MSE A 182 MET MODIFIED RESIDUE MODRES 5L0Z MSE A 234 MET MODIFIED RESIDUE MODRES 5L0Z MSE A 273 MET MODIFIED RESIDUE MODRES 5L0Z MSE B 48 MET MODIFIED RESIDUE MODRES 5L0Z MSE B 113 MET MODIFIED RESIDUE MODRES 5L0Z MSE B 182 MET MODIFIED RESIDUE MODRES 5L0Z MSE B 234 MET MODIFIED RESIDUE MODRES 5L0Z MSE B 273 MET MODIFIED RESIDUE HET MSE A 48 16 HET MSE A 113 8 HET MSE A 182 8 HET MSE A 234 8 HET MSE A 273 8 HET MSE B 48 8 HET MSE B 113 8 HET MSE B 182 8 HET MSE B 234 8 HET MSE B 273 8 HET CO A 301 1 HET CO A 302 1 HET SO4 A 303 5 HET SAM A 304 27 HET CO B 301 1 HET CO B 302 1 HET SO4 B 303 5 HET SAM B 304 27 HETNAM MSE SELENOMETHIONINE HETNAM CO COBALT (II) ION HETNAM SO4 SULFATE ION HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 3 CO 4(CO 2+) FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 SAM 2(C15 H22 N6 O5 S) HELIX 1 AA1 PRO A 27 ALA A 34 1 8 HELIX 2 AA2 GLN A 37 GLU A 43 1 7 HELIX 3 AA3 GLY A 51 LEU A 61 1 11 HELIX 4 AA4 GLN A 79 ARG A 90 1 12 HELIX 5 AA5 ASN A 98 ARG A 107 1 10 HELIX 6 AA6 PRO A 124 ILE A 128 5 5 HELIX 7 AA7 ASP A 144 ALA A 158 1 15 HELIX 8 AA8 SER A 174 THR A 181 1 8 HELIX 9 AA9 MSE A 182 ALA A 187 5 6 HELIX 10 AB1 ASN A 194 ALA A 205 1 12 HELIX 11 AB2 ARG A 221 ILE A 223 5 3 HELIX 12 AB3 PRO A 242 ARG A 247 1 6 HELIX 13 AB4 ASN A 265 ARG A 278 1 14 HELIX 14 AB5 ARG A 279 LEU A 282 5 4 HELIX 15 AB6 ASN B 26 ASP B 31 1 6 HELIX 16 AB7 ILE B 32 THR B 36 5 5 HELIX 17 AB8 GLN B 37 THR B 44 1 8 HELIX 18 AB9 GLY B 51 LEU B 61 1 11 HELIX 19 AC1 GLN B 79 ARG B 90 1 12 HELIX 20 AC2 ASN B 98 ARG B 107 1 10 HELIX 21 AC3 PRO B 124 ILE B 128 5 5 HELIX 22 AC4 ASP B 144 GLY B 159 1 16 HELIX 23 AC5 SER B 174 MSE B 182 1 9 HELIX 24 AC6 GLY B 183 ALA B 187 5 5 HELIX 25 AC7 ASN B 194 GLY B 206 1 13 HELIX 26 AC8 ARG B 221 ILE B 223 5 3 HELIX 27 AC9 PRO B 242 ARG B 247 1 6 HELIX 28 AD1 ASN B 265 ARG B 278 1 14 SHEET 1 AA1 5 LYS A 19 GLU A 20 0 SHEET 2 AA1 5 LEU A 93 GLU A 96 1 O VAL A 94 N LYS A 19 SHEET 3 AA1 5 ILE A 65 VAL A 69 1 N LEU A 68 O LEU A 95 SHEET 4 AA1 5 VAL A 115 GLU A 119 -1 O ILE A 117 N LYS A 66 SHEET 5 AA1 5 SER A 46 GLU A 50 -1 N PHE A 47 O PHE A 118 SHEET 1 AA2 7 ILE A 190 ALA A 193 0 SHEET 2 AA2 7 GLY A 162 VAL A 166 1 N LEU A 165 O ALA A 191 SHEET 3 AA2 7 THR A 135 ASP A 140 1 N VAL A 137 O ILE A 164 SHEET 4 AA2 7 VAL A 230 MSE A 234 1 O LEU A 232 N TYR A 136 SHEET 5 AA2 7 GLN A 208 THR A 212 1 N VAL A 210 O VAL A 231 SHEET 6 AA2 7 ALA A 251 ARG A 254 1 O ALA A 253 N ALA A 211 SHEET 7 AA2 7 VAL A 218 ASP A 219 1 N VAL A 218 O ARG A 254 SHEET 1 AA3 5 VAL B 18 GLU B 20 0 SHEET 2 AA3 5 LEU B 93 GLU B 96 1 O GLU B 96 N LYS B 19 SHEET 3 AA3 5 ILE B 65 VAL B 69 1 N LEU B 68 O LEU B 95 SHEET 4 AA3 5 VAL B 115 GLU B 119 -1 O ILE B 117 N LYS B 66 SHEET 5 AA3 5 SER B 46 GLU B 50 -1 N ALA B 49 O GLY B 116 SHEET 1 AA4 7 ILE B 190 ALA B 193 0 SHEET 2 AA4 7 GLY B 162 VAL B 166 1 N ILE B 163 O ALA B 191 SHEET 3 AA4 7 THR B 135 ASP B 140 1 N LEU B 139 O VAL B 166 SHEET 4 AA4 7 VAL B 230 MSE B 234 1 O LEU B 232 N ALA B 138 SHEET 5 AA4 7 GLN B 208 THR B 212 1 N GLN B 208 O VAL B 231 SHEET 6 AA4 7 ALA B 251 ARG B 254 1 O ALA B 253 N ALA B 211 SHEET 7 AA4 7 VAL B 218 ASP B 219 1 N VAL B 218 O LEU B 252 LINK ND1 HIS A 40 CO CO A 301 1555 1555 2.35 LINK OE2 GLU A 43 CO CO A 301 1555 1555 2.49 LINK C PHE A 47 N AMSE A 48 1555 1555 1.33 LINK C PHE A 47 N BMSE A 48 1555 1555 1.33 LINK C AMSE A 48 N ALA A 49 1555 1555 1.34 LINK C BMSE A 48 N ALA A 49 1555 1555 1.33 LINK C GLN A 112 N MSE A 113 1555 1555 1.33 LINK C MSE A 113 N VAL A 114 1555 1555 1.33 LINK C THR A 181 N MSE A 182 1555 1555 1.33 LINK C MSE A 182 N GLY A 183 1555 1555 1.34 LINK C LEU A 233 N MSE A 234 1555 1555 1.32 LINK C MSE A 234 N GLY A 235 1555 1555 1.32 LINK C AILE A 272 N MSE A 273 1555 1555 1.33 LINK C BILE A 272 N MSE A 273 1555 1555 1.34 LINK C MSE A 273 N LEU A 274 1555 1555 1.33 LINK ND1 HIS B 40 CO CO B 301 1555 1555 2.70 LINK C PHE B 47 N MSE B 48 1555 1555 1.32 LINK C MSE B 48 N ALA B 49 1555 1555 1.34 LINK C GLN B 112 N MSE B 113 1555 1555 1.33 LINK C MSE B 113 N VAL B 114 1555 1555 1.33 LINK C THR B 181 N MSE B 182 1555 1555 1.33 LINK C MSE B 182 N GLY B 183 1555 1555 1.33 LINK C LEU B 233 N MSE B 234 1555 1555 1.33 LINK C MSE B 234 N GLY B 235 1555 1555 1.33 LINK C ILE B 272 N MSE B 273 1555 1555 1.31 LINK C MSE B 273 N LEU B 274 1555 1555 1.33 LINK CO CO A 302 OXT SAM A 304 1555 1555 2.14 LINK CO CO B 302 O SAM B 304 1555 1555 1.92 LINK NE2 HIS A 129 CO CO B 301 1555 1655 2.72 LINK NE2 HIS B 129 CO CO A 301 1555 2565 2.72 SITE 1 AC1 3 HIS A 40 GLU A 43 HIS B 129 SITE 1 AC2 1 SAM A 304 SITE 1 AC3 7 ASN A 147 GLU A 237 ASN A 265 LEU A 266 SITE 2 AC3 7 SAM A 304 ARG B 153 MSE B 182 SITE 1 AC4 18 THR A 212 LEU A 214 MSE A 234 GLY A 235 SITE 2 AC4 18 ASN A 236 GLU A 237 GLN A 238 ALA A 239 SITE 3 AC4 18 GLY A 240 ARG A 254 ILE A 255 GLN A 257 SITE 4 AC4 18 ASP A 262 SER A 263 LEU A 264 ALA A 269 SITE 5 AC4 18 CO A 302 SO4 A 303 SITE 1 AC5 3 HIS A 129 HIS B 40 GLU B 43 SITE 1 AC6 1 SAM B 304 SITE 1 AC7 6 ARG A 153 ASN B 147 GLU B 237 ASN B 265 SITE 2 AC7 6 LEU B 266 SAM B 304 SITE 1 AC8 16 THR B 212 LEU B 214 MSE B 234 GLY B 235 SITE 2 AC8 16 ASN B 236 GLU B 237 GLN B 238 GLY B 240 SITE 3 AC8 16 ILE B 255 GLN B 257 SER B 263 LEU B 264 SITE 4 AC8 16 LEU B 266 ALA B 269 CO B 302 SO4 B 303 CRYST1 64.855 82.896 108.806 90.00 90.00 90.00 P 21 21 21 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 0.015419 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009191 0.00000