HEADER TRANSFERASE 15-NOV-23 8X4I TITLE CRYSTAL STRUCTURE OF THE D117A MUTANT OF DIMT1 IN COMPLEX WITH 5'- TITLE 2 METHYLTHIOADENOSINE FROM PYROCOCCUS HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.182; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII OT3; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 GENE: DIMT1; 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: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ARCHAEA, KSGA/DIMT1, RRNA METHYLTRANSFERASE, SAM, SAH, SFG, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SAHA,A.DUTTA,S.P.KANAUJIA REVDAT 1 28-AUG-24 8X4I 0 JRNL AUTH S.SAHA,S.P.KANAUJIA JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF ARCHAEAL DIMT1 JRNL TITL 2 UNVEILS DISTINCT PROTEIN DYNAMICS ESSENTIAL FOR EFFICIENT JRNL TITL 3 CATALYSIS. JRNL REF STRUCTURE 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 39146930 JRNL DOI 10.1016/J.STR.2024.07.013 REMARK 2 REMARK 2 RESOLUTION. 3.30 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 4330 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 448 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) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 349 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.4680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2186 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 128.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.50000 REMARK 3 B22 (A**2) : -1.50000 REMARK 3 B33 (A**2) : 4.85000 REMARK 3 B12 (A**2) : -0.75000 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): 0.717 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.591 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 78.995 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2249 ; 0.004 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2208 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3029 ; 1.211 ; 1.645 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5142 ; 0.384 ; 1.566 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 9.511 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 17 ; 6.044 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 441 ;17.478 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 342 ; 0.048 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2472 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 429 ; 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): 1075 ; 5.395 ; 8.398 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1075 ; 5.395 ; 8.398 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1342 ; 8.928 ;12.585 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1343 ; 8.925 ;12.588 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1174 ; 4.947 ; 8.732 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1174 ; 4.948 ; 8.732 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1688 ; 8.465 ;12.973 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2581 ;14.003 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2582 ;14.001 ; 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 : 1 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 22 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): 34.2839 -26.5389 8.1813 REMARK 3 T TENSOR REMARK 3 T11: 0.3799 T22: 0.3031 REMARK 3 T33: 0.3938 T12: 0.2923 REMARK 3 T13: 0.0334 T23: 0.1559 REMARK 3 L TENSOR REMARK 3 L11: 1.4174 L22: 3.5205 REMARK 3 L33: 3.1752 L12: -0.6227 REMARK 3 L13: -0.9858 L23: 1.4667 REMARK 3 S TENSOR REMARK 3 S11: -0.0327 S12: -0.2489 S13: -0.3741 REMARK 3 S21: -0.1549 S22: -0.1738 S23: -0.3573 REMARK 3 S31: 0.5662 S32: 0.3766 S33: 0.2066 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 8X4I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 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 : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NICKEL FILTER REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.4.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.13 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9013 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 62.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.57 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.51300 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 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: PRIMITIVE HEXAGONAL 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: 0.2 M ZINC ACETATE DIHYDRATE, 20% REMARK 280 (W/V) PEG 3350, PH 6.4, MICROBATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 80 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 ILE A 5 REMARK 465 ARG A 6 REMARK 465 ILE A 7 REMARK 465 ASN A 8 REMARK 465 THR A 9 REMARK 465 LYS A 10 REMARK 465 SER A 11 REMARK 465 LEU A 12 REMARK 465 LEU A 13 REMARK 465 VAL A 14 REMARK 465 GLN A 15 REMARK 465 PRO A 16 REMARK 465 GLY A 17 REMARK 465 TYR A 18 REMARK 465 SER A 19 REMARK 465 GLY A 20 REMARK 465 SER A 21 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 ARG A 233 NH1 ARG A 267 2.11 REMARK 500 OE2 GLU A 93 O2' MTA A 301 2.18 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 CZ ARG A 172 OD2 ASP A 278 5555 1.71 REMARK 500 NH1 ARG A 172 OD2 ASP A 278 5555 1.95 REMARK 500 NH2 ARG A 172 OD2 ASP A 278 5555 1.98 REMARK 500 OD2 ASP A 25 OD2 ASP A 25 4545 2.09 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 LEU A 75 CB - CA - C ANGL. DEV. = -13.2 DEGREES REMARK 500 PHE A 150 CB - CA - C ANGL. DEV. = 14.4 DEGREES REMARK 500 HIS A 245 CB - CA - C ANGL. DEV. = 15.4 DEGREES REMARK 500 HIS A 245 N - CA - C ANGL. DEV. = -21.2 DEGREES REMARK 500 ILE A 288 CB - CA - C ANGL. DEV. = -14.3 DEGREES REMARK 500 ILE A 288 N - CA - C ANGL. DEV. = 20.1 DEGREES REMARK 500 ILE A 289 N - CA - CB ANGL. DEV. = 18.0 DEGREES REMARK 500 ILE A 289 N - CA - C ANGL. DEV. = -23.0 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 ARG A 85 -65.08 -137.74 REMARK 500 PRO A 124 -161.75 -76.42 REMARK 500 VAL A 190 -60.56 -96.06 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 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 231 ND1 REMARK 620 2 HIS A 286 NE2 71.9 REMARK 620 N 1 DBREF 8X4I A 23 290 UNP O59487 RSMA_PYRHO 1 268 SEQADV 8X4I MET A 1 UNP O59487 INITIATING METHIONINE SEQADV 8X4I SER A 2 UNP O59487 EXPRESSION TAG SEQADV 8X4I SER A 3 UNP O59487 EXPRESSION TAG SEQADV 8X4I ARG A 4 UNP O59487 EXPRESSION TAG SEQADV 8X4I ILE A 5 UNP O59487 EXPRESSION TAG SEQADV 8X4I ARG A 6 UNP O59487 EXPRESSION TAG SEQADV 8X4I ILE A 7 UNP O59487 EXPRESSION TAG SEQADV 8X4I ASN A 8 UNP O59487 EXPRESSION TAG SEQADV 8X4I THR A 9 UNP O59487 EXPRESSION TAG SEQADV 8X4I LYS A 10 UNP O59487 EXPRESSION TAG SEQADV 8X4I SER A 11 UNP O59487 EXPRESSION TAG SEQADV 8X4I LEU A 12 UNP O59487 EXPRESSION TAG SEQADV 8X4I LEU A 13 UNP O59487 EXPRESSION TAG SEQADV 8X4I VAL A 14 UNP O59487 EXPRESSION TAG SEQADV 8X4I GLN A 15 UNP O59487 EXPRESSION TAG SEQADV 8X4I PRO A 16 UNP O59487 EXPRESSION TAG SEQADV 8X4I GLY A 17 UNP O59487 EXPRESSION TAG SEQADV 8X4I TYR A 18 UNP O59487 EXPRESSION TAG SEQADV 8X4I SER A 19 UNP O59487 EXPRESSION TAG SEQADV 8X4I GLY A 20 UNP O59487 EXPRESSION TAG SEQADV 8X4I SER A 21 UNP O59487 EXPRESSION TAG SEQADV 8X4I LYS A 22 UNP O59487 EXPRESSION TAG SEQADV 8X4I ALA A 117 UNP O59487 ASP 95 ENGINEERED MUTATION SEQRES 1 A 290 MET SER SER ARG ILE ARG ILE ASN THR LYS SER LEU LEU SEQRES 2 A 290 VAL GLN PRO GLY TYR SER GLY SER LYS MET ARG ASP ARG SEQRES 3 A 290 LEU PHE PHE LEU LEU SER LYS TYR GLY ILE ARG PRO ARG SEQRES 4 A 290 ASP SER ILE GLY GLN HIS PHE LEU ILE ILE GLU ASP VAL SEQRES 5 A 290 ILE GLU LYS ALA ILE GLU THR ALA ASN VAL ASN GLU ASN SEQRES 6 A 290 ASP VAL ILE LEU GLU VAL GLY PRO GLY LEU GLY PHE LEU SEQRES 7 A 290 THR ASP GLU LEU ALA LYS ARG ALA LYS LYS VAL TYR THR SEQRES 8 A 290 ILE GLU ILE ASP GLN LYS ILE ILE GLU ILE LEU LYS LYS SEQRES 9 A 290 GLU TYR SER TRP ASN ASN VAL LYS ILE ILE GLN GLY ALA SEQRES 10 A 290 ALA VAL ARG VAL GLU TRP PRO LYS PHE ASN LYS VAL VAL SEQRES 11 A 290 SER ASN ILE PRO TYR LYS ILE SER SER PRO PHE THR PHE SEQRES 12 A 290 LYS LEU LEU LYS THR ASP PHE GLU ARG ALA VAL VAL MET SEQRES 13 A 290 TYR GLN LEU GLU PHE ALA LEU ARG MET VAL ALA LYS PRO SEQRES 14 A 290 GLY SER ARG ASN TYR SER ARG LEU SER LEU MET ALA GLN SEQRES 15 A 290 ALA LEU GLY ASN VAL GLU ILE VAL MET LYS ILE GLY LYS SEQRES 16 A 290 GLY ALA PHE TYR PRO ARG PRO LYS VAL ASP SER ALA LEU SEQRES 17 A 290 VAL LEU ILE GLU PRO ARG LYS ASP LYS ILE VAL LEU ASN SEQRES 18 A 290 GLU ASN LEU VAL LYS ALA LEU PHE GLN HIS ARG ARG LYS SEQRES 19 A 290 THR VAL PRO ARG ALA LEU LYS ASP SER ILE HIS MET LEU SEQRES 20 A 290 GLY VAL SER LYS ASP GLU ILE ARG GLY ILE ILE ASN ASN SEQRES 21 A 290 VAL PRO HIS SER ASN LYS ARG VAL PHE GLN LEU TYR PRO SEQRES 22 A 290 GLU GLU VAL LYS ASP ILE GLU GLU TYR LEU LYS LYS HIS SEQRES 23 A 290 GLY ILE ILE SER HET MTA A 301 20 HET ZN A 302 1 HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM ZN ZINC ION FORMUL 2 MTA C11 H15 N5 O3 S FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *6(H2 O) HELIX 1 AA1 LYS A 22 GLY A 35 1 14 HELIX 2 AA2 ILE A 49 ASN A 61 1 13 HELIX 3 AA3 GLY A 76 LYS A 84 1 9 HELIX 4 AA4 ASP A 95 TYR A 106 1 12 HELIX 5 AA5 PRO A 134 LYS A 136 5 3 HELIX 6 AA6 ILE A 137 LYS A 147 1 11 HELIX 7 AA7 LEU A 159 ALA A 167 1 9 HELIX 8 AA8 SER A 175 LEU A 184 1 10 HELIX 9 AA9 GLY A 194 PHE A 198 5 5 HELIX 10 AB1 ASN A 221 PHE A 229 1 9 HELIX 11 AB2 GLN A 230 ARG A 232 5 3 HELIX 12 AB3 THR A 235 SER A 243 1 9 HELIX 13 AB4 SER A 250 VAL A 261 1 12 HELIX 14 AB5 ARG A 267 LEU A 271 5 5 HELIX 15 AB6 TYR A 272 LYS A 285 1 14 SHEET 1 AA1 3 VAL A 67 VAL A 71 0 SHEET 2 AA1 3 LYS A 88 GLU A 93 1 O LYS A 88 N ILE A 68 SHEET 3 AA1 3 LYS A 112 GLN A 115 1 O LYS A 112 N THR A 91 SHEET 1 AA2 4 LYS A 128 ASN A 132 0 SHEET 2 AA2 4 ARG A 152 GLN A 158 1 O VAL A 154 N VAL A 129 SHEET 3 AA2 4 SER A 206 PRO A 213 -1 O VAL A 209 N VAL A 155 SHEET 4 AA2 4 GLY A 185 ILE A 193 -1 N VAL A 190 O LEU A 208 LINK ND1 HIS A 231 ZN ZN A 302 1555 1555 2.30 LINK NE2 HIS A 286 ZN ZN A 302 1555 6555 2.16 CISPEP 1 TYR A 199 PRO A 200 0 -10.05 CRYST1 124.920 124.920 36.810 90.00 90.00 120.00 P 6 6 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 0.008005 0.004622 0.000000 0.00000 SCALE2 0.000000 0.009244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027167 0.00000