HEADER TRANSFERASE 21-NOV-23 8X6K TITLE THE X-RAY STRUCTURE OF N-TERMINAL CATALYTIC DOMAIN OF THERMOPLASMA TITLE 2 ACIDOPHILUM TRNA METHYLTRANSFERASE TRM56 (TA0931). COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (CYTIDINE(56)-2'-O)-METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRNA RIBOSE 2'-O-METHYLTRANSFERASE ATRM56; COMPND 5 EC: 2.1.1.206; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM DSM 1728; SOURCE 3 ORGANISM_TAXID: 273075; SOURCE 4 STRAIN: DSM 1728; SOURCE 5 GENE: TA0931; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 KEYWDS 2'-O METHYLATION, SPOUT SUPERFAMILY, ARCHAEA, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FUKUMOTO,T.HASEGAWA,M.OTOTAKE,S.MORIGUCHI,M.NAMBA,R.YAMAGAMI, AUTHOR 2 T.KAWAMURA,A.HIRATA,H.HORI REVDAT 4 15-OCT-25 8X6K 1 JRNL REVDAT 3 08-OCT-25 8X6K 1 JRNL REVDAT 2 02-APR-25 8X6K 1 COMPND SOURCE REMARK SEQRES REVDAT 2 2 1 HET HETNAM FORMUL SHEET REVDAT 2 3 1 LINK SCALE ATOM REVDAT 1 27-NOV-24 8X6K 0 JRNL AUTH S.HIDETAKA,S.FUKUMOTO,T.HASEGAWA,T.KAWAMURA,M.OTOTAKE, JRNL AUTH 2 S.MORIGUCHI,M.NAMBA,C.TOMIKAWA,R.YAMAGAMI,A.HIRATA,H.HORI JRNL TITL TRANSFER RNA RECOGNITION MECHANISM OF THERMOPLASMA JRNL TITL 2 ACIDOPHILUM TRM56, A SPOUT TRNA METHYLTRANSFERASE THAT JRNL TITL 3 POSSESSES AN UNUSUALLY LONG C-TERMINAL REGION. JRNL REF J.MOL.BIOL. V. 437 69328 2025 JRNL REFN ESSN 1089-8638 JRNL PMID 40664129 JRNL DOI 10.1016/J.JMB.2025.169328 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 36939 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1847 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2489 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.2120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2424 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00500 REMARK 3 B22 (A**2) : 0.00500 REMARK 3 B33 (A**2) : -0.01500 REMARK 3 B12 (A**2) : 0.00200 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.920 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2508 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2300 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3394 ; 1.700 ; 1.638 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5345 ; 0.619 ; 1.551 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 312 ; 6.664 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 24 ;18.219 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 441 ;15.024 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 381 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2906 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 534 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 469 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 70 ; 0.160 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1271 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 108 ; 0.217 ; 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): 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): 1212 ; 2.966 ; 3.011 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1212 ; 2.966 ; 3.011 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1515 ; 3.776 ; 4.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1516 ; 3.777 ; 4.504 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1296 ; 4.450 ; 3.515 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1297 ; 4.448 ; 3.516 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1872 ; 6.220 ; 5.073 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1873 ; 6.219 ; 5.074 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8X6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36948 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.4300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38700 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: PHASER REMARK 200 STARTING MODEL: 2YY8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, BIS-TRIS, PH 5.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.48533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.24267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.24267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.48533 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 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 GLU B 150 REMARK 465 PHE B 151 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 NH1 ARG A 84 NH1 ARG B 13 3665 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 ARG A 10 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 84 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 GLU A 92 CB - CA - C ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG B 140 NE - CZ - NH2 ANGL. DEV. = -3.2 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 GLU A 107 -140.57 54.96 REMARK 500 GLU A 107 -144.16 61.11 REMARK 500 ARG B 13 -31.81 -132.70 REMARK 500 LYS B 108 -157.00 63.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 84 0.10 SIDE CHAIN REMARK 500 ARG B 13 0.23 SIDE CHAIN REMARK 500 ARG B 16 0.08 SIDE CHAIN REMARK 500 ARG B 84 0.10 SIDE CHAIN REMARK 500 ARG B 85 0.23 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8X6K A 1 151 UNP Q9HJN6 TRM56_THEAC 1 151 DBREF 8X6K B 1 151 UNP Q9HJN6 TRM56_THEAC 1 151 SEQRES 1 A 151 MET ILE THR VAL LEU ARG ILE ASN HIS ARG PRO TYR ARG SEQRES 2 A 151 ASP LYS ARG ILE THR THR HIS VAL ALA LEU THR ALA ARG SEQRES 3 A 151 ALA PHE GLY ALA SER ALA ILE LEU VAL ASP GLU ARG ASP SEQRES 4 A 151 GLU THR LEU GLU ASN THR ILE ARG GLY VAL ILE SER ASN SEQRES 5 A 151 PHE GLY GLY SER PHE SER ILE LYS THR GLY CME ASN TRP SEQRES 6 A 151 ILE GLN GLU PHE LYS HIS PHE GLN GLY ILE ARG VAL HIS SEQRES 7 A 151 LEU THR MET TYR GLY ARG ARG ILE ASN ASP VAL ILE ASP SEQRES 8 A 151 GLU ILE ARG ASN SER GLY LYS ASP VAL MET VAL LEU VAL SEQRES 9 A 151 GLY SER GLU LYS VAL PRO ILE GLU ALA TYR GLU ILE ALA SEQRES 10 A 151 ASP TYR ASN VAL SER VAL THR ASN GLN PRO ILE SER GLU SEQRES 11 A 151 VAL SER ALA LEU ALA ILE PHE LEU ASP ARG TYR PHE GLN SEQRES 12 A 151 GLY LYS GLU PHE GLU PHE GLU PHE SEQRES 1 B 151 MET ILE THR VAL LEU ARG ILE ASN HIS ARG PRO TYR ARG SEQRES 2 B 151 ASP LYS ARG ILE THR THR HIS VAL ALA LEU THR ALA ARG SEQRES 3 B 151 ALA PHE GLY ALA SER ALA ILE LEU VAL ASP GLU ARG ASP SEQRES 4 B 151 GLU THR LEU GLU ASN THR ILE ARG GLY VAL ILE SER ASN SEQRES 5 B 151 PHE GLY GLY SER PHE SER ILE LYS THR GLY CME ASN TRP SEQRES 6 B 151 ILE GLN GLU PHE LYS HIS PHE GLN GLY ILE ARG VAL HIS SEQRES 7 B 151 LEU THR MET TYR GLY ARG ARG ILE ASN ASP VAL ILE ASP SEQRES 8 B 151 GLU ILE ARG ASN SER GLY LYS ASP VAL MET VAL LEU VAL SEQRES 9 B 151 GLY SER GLU LYS VAL PRO ILE GLU ALA TYR GLU ILE ALA SEQRES 10 B 151 ASP TYR ASN VAL SER VAL THR ASN GLN PRO ILE SER GLU SEQRES 11 B 151 VAL SER ALA LEU ALA ILE PHE LEU ASP ARG TYR PHE GLN SEQRES 12 B 151 GLY LYS GLU PHE GLU PHE GLU PHE MODRES 8X6K CME A 63 CYS MODIFIED RESIDUE MODRES 8X6K CME B 63 CYS MODIFIED RESIDUE HET CME A 63 10 HET CME B 63 10 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 3 HOH *125(H2 O) HELIX 1 AA1 LYS A 15 PHE A 28 1 14 HELIX 2 AA2 ASP A 39 GLY A 54 1 16 HELIX 3 AA3 ASN A 64 HIS A 71 1 8 HELIX 4 AA4 ILE A 86 SER A 96 1 11 HELIX 5 AA5 PRO A 110 ALA A 117 1 8 HELIX 6 AA6 SER A 129 PHE A 142 1 14 HELIX 7 AA7 LYS A 145 PHE A 149 5 5 HELIX 8 AA8 ASP B 14 PHE B 28 1 15 HELIX 9 AA9 ASP B 39 GLY B 54 1 16 HELIX 10 AB1 ASN B 64 PHE B 72 1 9 HELIX 11 AB2 VAL B 89 SER B 96 1 8 HELIX 12 AB3 PRO B 110 ALA B 117 1 8 HELIX 13 AB4 SER B 129 PHE B 142 1 14 SHEET 1 AA1 7 SER A 58 THR A 61 0 SHEET 2 AA1 7 ALA A 32 VAL A 35 1 N ILE A 33 O SER A 58 SHEET 3 AA1 7 ILE A 2 ARG A 6 1 N ARG A 6 O LEU A 34 SHEET 4 AA1 7 VAL A 100 VAL A 104 1 O VAL A 102 N LEU A 5 SHEET 5 AA1 7 ILE A 75 LEU A 79 1 N VAL A 77 O MET A 101 SHEET 6 AA1 7 TYR A 119 SER A 122 1 O VAL A 121 N HIS A 78 SHEET 7 AA1 7 ARG A 84 ARG A 85 1 N ARG A 84 O ASN A 120 SHEET 1 AA2 7 SER B 58 THR B 61 0 SHEET 2 AA2 7 ALA B 32 VAL B 35 1 N ILE B 33 O SER B 58 SHEET 3 AA2 7 ILE B 2 ARG B 6 1 N ARG B 6 O LEU B 34 SHEET 4 AA2 7 VAL B 100 VAL B 104 1 O VAL B 102 N LEU B 5 SHEET 5 AA2 7 ILE B 75 LEU B 79 1 N VAL B 77 O LEU B 103 SHEET 6 AA2 7 TYR B 119 SER B 122 1 O VAL B 121 N HIS B 78 SHEET 7 AA2 7 ARG B 84 ARG B 85 1 N ARG B 84 O SER B 122 LINK C GLY A 62 N CME A 63 1555 1555 1.33 LINK C CME A 63 N ASN A 64 1555 1555 1.34 LINK C GLY B 62 N CME B 63 1555 1555 1.32 LINK C CME B 63 N ASN B 64 1555 1555 1.32 CRYST1 110.074 110.074 57.728 90.00 90.00 120.00 P 32 2 1 12 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 0.009085 0.005245 0.000000 0.00000 SCALE2 0.000000 0.010490 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017323 0.00000 HETATM 499 N CME A 63 41.241 23.760 -6.919 1.00 26.45 N0 HETATM 500 CA CME A 63 40.194 24.723 -6.617 1.00 29.36 C0 HETATM 501 CB CME A 63 39.408 24.326 -5.374 1.00 29.92 C0 HETATM 502 SG CME A 63 38.690 22.660 -5.493 1.00 31.16 S0 HETATM 503 SD CME A 63 36.952 23.110 -6.431 1.00 46.00 S0 HETATM 504 CE CME A 63 37.552 22.707 -8.078 1.00 42.80 C0 HETATM 505 CZ CME A 63 37.294 21.348 -8.650 1.00 51.70 C0 HETATM 506 OH CME A 63 36.183 21.384 -9.512 1.00 59.77 O0 HETATM 507 C CME A 63 40.888 26.059 -6.382 1.00 27.00 C0 HETATM 508 O CME A 63 42.014 26.102 -5.889 1.00 27.95 O0 TER 1243 PHE A 151 HETATM 1728 N CME B 63 65.074 6.230 21.416 1.00 29.07 N0 HETATM 1729 CA CME B 63 64.550 5.573 22.600 1.00 28.42 C0 HETATM 1730 CB CME B 63 63.316 6.290 23.144 1.00 31.39 C0 HETATM 1731 SG CME B 63 63.623 8.053 23.451 1.00 31.79 S0 HETATM 1732 SD CME B 63 64.356 7.979 25.410 1.00 42.34 S0 HETATM 1733 CE CME B 63 66.086 7.885 24.922 1.00 42.56 C0 HETATM 1734 CZ CME B 63 66.662 9.176 24.586 1.00 51.64 C0 HETATM 1735 OH CME B 63 67.011 9.863 25.744 1.00 61.53 O0 HETATM 1736 C CME B 63 64.179 4.130 22.239 1.00 30.68 C0 HETATM 1737 O CME B 63 63.701 3.839 21.169 1.00 32.99 O0 TER 2460 PHE B 149 HETATM 2461 O HOH A 201 28.136 9.885 8.228 1.00 50.21 O0 HETATM 2462 O HOH A 202 38.030 38.962 9.064 1.00 42.99 O0 HETATM 2463 O HOH A 203 32.636 12.038 22.029 1.00 55.14 O0 HETATM 2464 O HOH A 204 47.088 24.954 24.113 1.00 35.97 O0 HETATM 2465 O HOH A 205 25.239 19.343 18.341 1.00 55.98 O0 HETATM 2466 O HOH A 206 49.279 19.592 -8.896 1.00 43.91 O0 HETATM 2467 O HOH A 207 45.889 7.343 -7.827 1.00 53.25 O0 HETATM 2468 O HOH A 208 36.745 18.986 22.064 1.00 41.91 O0 HETATM 2469 O HOH A 209 29.639 24.230 22.744 1.00 50.34 O0 HETATM 2470 O HOH A 210 45.662 29.324 9.096 1.00 39.54 O0 HETATM 2471 O HOH A 211 50.736 23.831 9.677 1.00 49.68 O0 HETATM 2472 O HOH A 212 44.460 26.033 9.548 1.00 35.77 O0 HETATM 2473 O HOH A 213 31.642 12.703 7.105 1.00 28.36 O0 HETATM 2474 O HOH A 214 38.522 35.293 24.505 1.00 56.49 O0 HETATM 2475 O HOH A 215 32.522 28.103 -2.387 1.00 37.73 O0 HETATM 2476 O HOH A 216 50.003 32.635 19.525 1.00 43.31 O0 HETATM 2477 O HOH A 217 57.846 15.058 -5.591 1.00 38.08 O0 HETATM 2478 O HOH A 218 34.080 38.341 4.072 1.00 46.09 O0 HETATM 2479 O HOH A 219 25.954 25.822 11.546 1.00 34.06 O0 HETATM 2480 O HOH A 220 47.458 28.209 13.114 1.00 43.14 O0 HETATM 2481 O HOH A 221 32.308 24.849 -4.716 1.00 52.13 O0 HETATM 2482 O HOH A 222 31.346 11.511 11.716 1.00 35.51 O0 HETATM 2483 O HOH A 223 31.280 7.243 12.843 1.00 37.74 O0 HETATM 2484 O HOH A 224 50.378 17.087 2.612 1.00 30.30 O0 HETATM 2485 O HOH A 225 34.052 18.343 -2.444 1.00 35.15 O0 HETATM 2486 O HOH A 226 32.171 8.916 3.356 1.00 26.48 O0 HETATM 2487 O HOH A 227 56.482 30.746 4.482 1.00 38.42 O0 HETATM 2488 O HOH A 228 29.205 23.169 3.324 1.00 33.02 O0 HETATM 2489 O HOH A 229 28.850 18.151 7.330 1.00 29.37 O0 HETATM 2490 O HOH A 230 30.119 34.492 0.616 1.00 48.09 O0 HETATM 2491 O HOH A 231 44.184 25.513 -7.943 1.00 45.95 O0 HETATM 2492 O HOH A 232 53.794 12.428 0.672 1.00 40.67 O0 HETATM 2493 O HOH A 233 30.369 29.641 21.953 1.00 31.58 O0 HETATM 2494 O HOH A 234 30.733 21.870 -0.637 1.00 45.09 O0 HETATM 2495 O HOH A 235 53.018 13.968 -11.530 1.00 50.96 O0 HETATM 2496 O HOH A 236 50.132 19.962 3.471 1.00 47.40 O0 HETATM 2497 O HOH A 237 52.687 23.072 20.451 1.00 25.85 O0 HETATM 2498 O HOH A 238 38.504 17.161 -8.351 1.00 33.27 O0 HETATM 2499 O HOH A 239 39.846 5.204 -5.682 1.00 44.95 O0 HETATM 2500 O HOH A 240 48.707 12.745 -8.022 1.00 42.10 O0 HETATM 2501 O HOH A 241 34.220 6.481 -3.759 1.00 46.30 O0 HETATM 2502 O HOH A 242 51.444 19.266 1.016 1.00 28.50 O0 HETATM 2503 O HOH A 243 23.973 24.420 20.445 1.00 44.47 O0 HETATM 2504 O HOH A 244 28.218 27.983 -1.401 1.00 37.61 O0 HETATM 2505 O HOH A 245 33.728 8.483 12.745 1.00 29.14 O0 HETATM 2506 O HOH A 246 45.603 38.002 14.676 1.00 26.77 O0 HETATM 2507 O HOH A 247 36.999 36.521 13.397 1.00 39.36 O0 HETATM 2508 O HOH A 248 32.563 1.889 7.846 1.00 37.47 O0 HETATM 2509 O HOH A 249 35.132 36.288 -9.392 1.00 31.96 O0 HETATM 2510 O HOH A 250 37.625 26.884 -7.733 1.00 30.94 O0 HETATM 2511 O HOH A 251 47.624 14.968 -9.579 1.00 38.55 O0 HETATM 2512 O HOH A 252 50.945 8.557 7.309 1.00 41.27 O0 HETATM 2513 O HOH A 253 53.008 22.633 -8.764 1.00 54.23 O0 HETATM 2514 O HOH A 254 43.100 31.504 -4.618 1.00 36.72 O0 HETATM 2515 O HOH A 255 26.477 21.510 9.421 1.00 41.65 O0 HETATM 2516 O HOH A 256 38.720 9.038 -8.499 1.00 51.55 O0 HETATM 2517 O HOH A 257 49.725 37.340 2.976 1.00 41.93 O0 HETATM 2518 O HOH A 258 36.170 37.479 -6.424 1.00 50.93 O0 HETATM 2519 O HOH A 259 33.343 17.524 22.786 1.00 45.38 O0 HETATM 2520 O HOH A 260 28.976 31.560 20.588 1.00 34.71 O0 HETATM 2521 O HOH A 261 42.603 26.745 15.283 1.00 29.19 O0 HETATM 2522 O HOH A 262 46.118 22.855 -9.343 1.00 39.60 O0 HETATM 2523 O HOH A 263 38.285 27.911 23.515 1.00 33.51 O0 HETATM 2524 O HOH A 264 27.268 3.974 3.213 1.00 44.81 O0 HETATM 2525 O HOH A 265 24.259 28.458 4.579 1.00 37.30 O0 HETATM 2526 O HOH A 266 34.704 12.747 -4.378 1.00 31.42 O0 HETATM 2527 O HOH A 267 40.937 28.226 22.379 1.00 44.47 O0 HETATM 2528 O HOH A 268 49.174 26.364 14.496 1.00 40.90 O0 HETATM 2529 O HOH A 269 43.923 28.378 -5.178 1.00 37.72 O0 HETATM 2530 O HOH A 270 27.332 24.065 1.661 1.00 41.33 O0 HETATM 2531 O HOH A 271 34.046 38.987 6.241 1.00 60.96 O0 HETATM 2532 O HOH A 272 38.107 41.479 7.959 1.00 57.50 O0 HETATM 2533 O HOH A 273 41.552 22.558 24.304 1.00 61.43 O0 HETATM 2534 O HOH A 274 30.930 10.666 5.027 1.00 32.66 O0 HETATM 2535 O HOH A 275 45.177 26.409 14.432 1.00 36.69 O0 HETATM 2536 O HOH A 276 26.570 31.989 21.528 1.00 43.34 O0 HETATM 2537 O HOH A 277 29.811 11.730 9.332 1.00 36.26 O0 HETATM 2538 O HOH A 278 36.846 29.398 -8.690 1.00 41.08 O0 HETATM 2539 O HOH B 201 49.890 1.099 9.697 1.00 45.47 O0 HETATM 2540 O HOH B 202 41.585 20.045 23.989 1.00 51.54 O0 HETATM 2541 O HOH B 203 60.827 12.627 1.476 1.00 49.75 O0 HETATM 2542 O HOH B 204 52.957 4.504 12.179 1.00 36.50 O0 HETATM 2543 O HOH B 205 31.686 4.620 11.898 1.00 38.27 O0 HETATM 2544 O HOH B 206 46.881 -4.788 26.552 1.00 36.62 O0 HETATM 2545 O HOH B 207 67.324 12.915 22.621 1.00 39.91 O0 HETATM 2546 O HOH B 208 34.928 7.705 20.479 1.00 49.02 O0 HETATM 2547 O HOH B 209 51.362 16.451 31.230 1.00 30.22 O0 HETATM 2548 O HOH B 210 68.130 7.538 13.470 1.00 40.49 O0 HETATM 2549 O HOH B 211 61.130 13.762 26.742 1.00 31.08 O0 HETATM 2550 O HOH B 212 52.416 20.904 27.382 1.00 33.61 O0 HETATM 2551 O HOH B 213 45.830 9.993 35.322 1.00 37.66 O0 HETATM 2552 O HOH B 214 54.659 -12.289 21.032 1.00 49.23 O0 HETATM 2553 O HOH B 215 59.474 5.012 30.377 1.00 36.84 O0 HETATM 2554 O HOH B 216 56.636 23.813 26.184 1.00 31.16 O0 HETATM 2555 O HOH B 217 54.740 11.060 32.147 1.00 32.85 O0 HETATM 2556 O HOH B 218 62.028 -1.385 21.379 1.00 39.66 O0 HETATM 2557 O HOH B 219 55.462 23.823 30.292 1.00 51.32 O0 HETATM 2558 O HOH B 220 65.298 4.146 25.797 1.00 32.16 O0 HETATM 2559 O HOH B 221 55.642 -0.446 34.346 1.00 44.26 O0 HETATM 2560 O HOH B 222 52.425 7.336 38.022 1.00 41.63 O0 HETATM 2561 O HOH B 223 47.594 -0.027 15.783 1.00 36.88 O0 HETATM 2562 O HOH B 224 58.313 14.536 6.454 1.00 36.01 O0 HETATM 2563 O HOH B 225 37.948 8.960 7.308 1.00 24.06 O0 HETATM 2564 O HOH B 226 67.569 13.112 10.155 1.00 50.69 O0 HETATM 2565 O HOH B 227 36.349 4.821 33.029 1.00 47.54 O0 HETATM 2566 O HOH B 228 58.381 6.129 34.526 1.00 39.53 O0 HETATM 2567 O HOH B 229 62.727 1.520 19.854 1.00 33.56 O0 HETATM 2568 O HOH B 230 40.598 5.172 16.463 1.00 33.70 O0 HETATM 2569 O HOH B 231 42.661 4.958 11.556 1.00 42.48 O0 HETATM 2570 O HOH B 232 50.032 3.308 18.806 1.00 32.93 O0 HETATM 2571 O HOH B 233 36.232 16.901 26.203 1.00 59.21 O0 HETATM 2572 O HOH B 234 67.758 5.392 17.102 1.00 39.26 O0 HETATM 2573 O HOH B 235 48.694 13.873 34.248 1.00 53.49 O0 HETATM 2574 O HOH B 236 60.342 27.743 16.431 1.00 49.64 O0 HETATM 2575 O HOH B 237 61.559 13.335 7.046 1.00 32.07 O0 HETATM 2576 O HOH B 238 64.120 6.919 7.894 1.00 36.54 O0 HETATM 2577 O HOH B 239 53.118 -3.649 18.682 1.00 39.80 O0 HETATM 2578 O HOH B 240 65.475 3.128 18.829 1.00 48.70 O0 HETATM 2579 O HOH B 241 45.667 2.061 14.659 1.00 38.16 O0 HETATM 2580 O HOH B 242 63.753 18.736 24.951 1.00 31.79 O0 HETATM 2581 O HOH B 243 56.364 8.227 35.955 1.00 48.07 O0 HETATM 2582 O HOH B 244 58.969 17.843 30.869 1.00 43.42 O0 HETATM 2583 O HOH B 245 56.102 10.639 34.177 1.00 48.03 O0 HETATM 2584 O HOH B 246 48.404 5.526 16.947 1.00 33.95 O0 HETATM 2585 O HOH B 247 54.619 22.852 27.731 1.00 46.83 O0 CONECT 497 499 CONECT 499 497 500 CONECT 500 499 501 507 CONECT 501 500 502 CONECT 502 501 503 CONECT 503 502 504 CONECT 504 503 505 CONECT 505 504 506 CONECT 506 505 CONECT 507 500 508 509 CONECT 508 507 CONECT 509 507 CONECT 1726 1728 CONECT 1728 1726 1729 CONECT 1729 1728 1730 1736 CONECT 1730 1729 1731 CONECT 1731 1730 1732 CONECT 1732 1731 1733 CONECT 1733 1732 1734 CONECT 1734 1733 1735 CONECT 1735 1734 CONECT 1736 1729 1737 1738 CONECT 1737 1736 CONECT 1738 1736 MASTER 336 0 2 13 14 0 0 6 2549 2 24 24 END