HEADER TRANSFERASE 15-NOV-23 8X46 TITLE CRYSTAL STRUCTURE OF DIMT1 IN COMPLEX WITH ADENOSYLORNITHINE (SFG) TITLE 2 FROM PYROCOCCUS HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.1.182; COMPND 5 ENGINEERED: 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,S.P.KANAUJIA REVDAT 1 28-AUG-24 8X46 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 34748 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1759 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2562 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4378 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 235 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.72000 REMARK 3 B22 (A**2) : -1.75000 REMARK 3 B33 (A**2) : -0.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.260 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.207 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.223 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4564 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4482 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6137 ; 1.420 ; 1.646 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10444 ; 0.518 ; 1.569 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 538 ; 7.497 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 36 ; 9.717 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 891 ;17.543 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 692 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4997 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 865 ; 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): 2164 ; 1.949 ; 2.520 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2164 ; 1.947 ; 2.520 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2695 ; 3.069 ; 3.767 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2696 ; 3.070 ; 3.767 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2400 ; 2.609 ; 2.896 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2401 ; 2.608 ; 2.896 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3442 ; 4.239 ; 4.178 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5233 ; 6.970 ;37.527 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5196 ; 6.900 ;37.164 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 22 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): 19.4869 3.2974 34.7629 REMARK 3 T TENSOR REMARK 3 T11: 0.2369 T22: 0.0072 REMARK 3 T33: 0.0662 T12: -0.0266 REMARK 3 T13: 0.0486 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.1812 L22: 2.1170 REMARK 3 L33: 1.8134 L12: 0.0961 REMARK 3 L13: 0.4794 L23: 1.2057 REMARK 3 S TENSOR REMARK 3 S11: -0.0812 S12: 0.0225 S13: 0.0614 REMARK 3 S21: -0.2861 S22: -0.0339 S23: -0.1799 REMARK 3 S31: -0.2202 S32: 0.0294 S33: 0.1150 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 22 B 290 REMARK 3 ORIGIN FOR THE GROUP (A): 32.2025 10.9269 8.1212 REMARK 3 T TENSOR REMARK 3 T11: 0.1658 T22: 0.0070 REMARK 3 T33: 0.1074 T12: 0.0072 REMARK 3 T13: 0.0691 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 1.5260 L22: 2.3705 REMARK 3 L33: 0.1822 L12: -0.8173 REMARK 3 L13: -0.4474 L23: 0.4794 REMARK 3 S TENSOR REMARK 3 S11: -0.0044 S12: 0.0427 S13: -0.2234 REMARK 3 S21: 0.3088 S22: -0.0565 S23: 0.0424 REMARK 3 S31: 0.0207 S32: -0.0105 S33: 0.0609 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 8X46 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_1300042606. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : 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 : 36508 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 75.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.11100 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.55400 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: C-CENTERED MONOCLINIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M ZINC ACETATE DIHYDRATE, 0.1 M REMARK 280 SODIUM CACODYLATE TRIHYDRATE PH 6.5, 18% (W/V) PEG 8000, REMARK 280 MICROBATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 59.57500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.57500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.17000 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: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -208.0 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 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 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 ARG B 4 REMARK 465 ILE B 5 REMARK 465 ARG B 6 REMARK 465 ILE B 7 REMARK 465 ASN B 8 REMARK 465 THR B 9 REMARK 465 LYS B 10 REMARK 465 SER B 11 REMARK 465 LEU B 12 REMARK 465 LEU B 13 REMARK 465 VAL B 14 REMARK 465 GLN B 15 REMARK 465 PRO B 16 REMARK 465 GLY B 17 REMARK 465 TYR B 18 REMARK 465 SER B 19 REMARK 465 GLY B 20 REMARK 465 SER B 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 OE1 GLU B 253 O HOH B 401 1.45 REMARK 500 OE2 GLU B 188 N ARG B 307 1.56 REMARK 500 O HOH B 403 O HOH B 413 1.60 REMARK 500 OE2 GLU A 188 N ARG A 309 1.66 REMARK 500 OD2 ASP B 40 O HOH B 402 1.92 REMARK 500 O HOH A 402 O HOH A 443 1.92 REMARK 500 O HOH A 414 O HOH A 456 1.94 REMARK 500 OE2 GLU A 222 O HOH A 401 1.95 REMARK 500 O HOH B 401 O HOH B 404 1.96 REMARK 500 OD2 ASP A 278 O HOH A 402 2.00 REMARK 500 NH2 ARG A 309 O HOH A 403 2.10 REMARK 500 OD2 ASP B 278 O HOH B 403 2.11 REMARK 500 OE1 GLU B 253 O HOH B 404 2.11 REMARK 500 OE2 GLU B 212 CZ ARG B 307 2.12 REMARK 500 O HOH A 470 O HOH A 473 2.15 REMARK 500 OE2 GLU A 212 CZ ARG A 309 2.19 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 NE2 HIS A 286 N ARG B 307 4545 1.84 REMARK 500 NE2 HIS B 286 N ARG A 309 4556 1.86 REMARK 500 O HOH B 403 O HOH B 495 4555 1.90 REMARK 500 O HOH A 402 O HOH A 455 4546 2.01 REMARK 500 O HOH B 478 O HOH B 478 2655 2.09 REMARK 500 O HOH B 495 O HOH B 507 4545 2.14 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 HIS B 231 NE2 HIS B 231 CD2 -0.072 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 GLN A 44 45.97 -147.46 REMARK 500 ASP A 205 150.93 -48.75 REMARK 500 ASP A 216 71.38 -110.69 REMARK 500 ASP B 40 1.04 -68.64 REMARK 500 GLN B 44 45.40 -148.06 REMARK 500 ASP B 205 152.22 -49.87 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 152 0.08 SIDE CHAIN REMARK 500 ARG A 172 0.08 SIDE CHAIN REMARK 500 ARG A 233 0.09 SIDE CHAIN REMARK 500 ARG A 238 0.13 SIDE CHAIN REMARK 500 ARG B 152 0.10 SIDE CHAIN REMARK 500 ARG B 238 0.09 SIDE CHAIN 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 306 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 25 OD1 REMARK 620 2 HIS A 263 ND1 21.6 REMARK 620 3 GLU A 275 OE1 20.1 2.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 40 OD2 REMARK 620 2 GLU B 253 OE2 102.7 REMARK 620 N 1 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 GLU A 160 OE1 REMARK 620 2 HIS B 245 NE2 89.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 305 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 245 NE2 REMARK 620 2 GLU B 160 OE1 86.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 25 OD1 REMARK 620 2 HIS B 263 ND1 24.5 REMARK 620 3 GLU B 275 OE1 24.1 2.1 REMARK 620 N 1 2 DBREF 8X46 A 23 290 UNP O59487 RSMA_PYRHO 1 268 DBREF 8X46 B 23 290 UNP O59487 RSMA_PYRHO 1 268 SEQADV 8X46 MET A 1 UNP O59487 INITIATING METHIONINE SEQADV 8X46 SER A 2 UNP O59487 EXPRESSION TAG SEQADV 8X46 SER A 3 UNP O59487 EXPRESSION TAG SEQADV 8X46 ARG A 4 UNP O59487 EXPRESSION TAG SEQADV 8X46 ILE A 5 UNP O59487 EXPRESSION TAG SEQADV 8X46 ARG A 6 UNP O59487 EXPRESSION TAG SEQADV 8X46 ILE A 7 UNP O59487 EXPRESSION TAG SEQADV 8X46 ASN A 8 UNP O59487 EXPRESSION TAG SEQADV 8X46 THR A 9 UNP O59487 EXPRESSION TAG SEQADV 8X46 LYS A 10 UNP O59487 EXPRESSION TAG SEQADV 8X46 SER A 11 UNP O59487 EXPRESSION TAG SEQADV 8X46 LEU A 12 UNP O59487 EXPRESSION TAG SEQADV 8X46 LEU A 13 UNP O59487 EXPRESSION TAG SEQADV 8X46 VAL A 14 UNP O59487 EXPRESSION TAG SEQADV 8X46 GLN A 15 UNP O59487 EXPRESSION TAG SEQADV 8X46 PRO A 16 UNP O59487 EXPRESSION TAG SEQADV 8X46 GLY A 17 UNP O59487 EXPRESSION TAG SEQADV 8X46 TYR A 18 UNP O59487 EXPRESSION TAG SEQADV 8X46 SER A 19 UNP O59487 EXPRESSION TAG SEQADV 8X46 GLY A 20 UNP O59487 EXPRESSION TAG SEQADV 8X46 SER A 21 UNP O59487 EXPRESSION TAG SEQADV 8X46 LYS A 22 UNP O59487 EXPRESSION TAG SEQADV 8X46 MET B 1 UNP O59487 INITIATING METHIONINE SEQADV 8X46 SER B 2 UNP O59487 EXPRESSION TAG SEQADV 8X46 SER B 3 UNP O59487 EXPRESSION TAG SEQADV 8X46 ARG B 4 UNP O59487 EXPRESSION TAG SEQADV 8X46 ILE B 5 UNP O59487 EXPRESSION TAG SEQADV 8X46 ARG B 6 UNP O59487 EXPRESSION TAG SEQADV 8X46 ILE B 7 UNP O59487 EXPRESSION TAG SEQADV 8X46 ASN B 8 UNP O59487 EXPRESSION TAG SEQADV 8X46 THR B 9 UNP O59487 EXPRESSION TAG SEQADV 8X46 LYS B 10 UNP O59487 EXPRESSION TAG SEQADV 8X46 SER B 11 UNP O59487 EXPRESSION TAG SEQADV 8X46 LEU B 12 UNP O59487 EXPRESSION TAG SEQADV 8X46 LEU B 13 UNP O59487 EXPRESSION TAG SEQADV 8X46 VAL B 14 UNP O59487 EXPRESSION TAG SEQADV 8X46 GLN B 15 UNP O59487 EXPRESSION TAG SEQADV 8X46 PRO B 16 UNP O59487 EXPRESSION TAG SEQADV 8X46 GLY B 17 UNP O59487 EXPRESSION TAG SEQADV 8X46 TYR B 18 UNP O59487 EXPRESSION TAG SEQADV 8X46 SER B 19 UNP O59487 EXPRESSION TAG SEQADV 8X46 GLY B 20 UNP O59487 EXPRESSION TAG SEQADV 8X46 SER B 21 UNP O59487 EXPRESSION TAG SEQADV 8X46 LYS B 22 UNP O59487 EXPRESSION TAG 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 ASP 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 SEQRES 1 B 290 MET SER SER ARG ILE ARG ILE ASN THR LYS SER LEU LEU SEQRES 2 B 290 VAL GLN PRO GLY TYR SER GLY SER LYS MET ARG ASP ARG SEQRES 3 B 290 LEU PHE PHE LEU LEU SER LYS TYR GLY ILE ARG PRO ARG SEQRES 4 B 290 ASP SER ILE GLY GLN HIS PHE LEU ILE ILE GLU ASP VAL SEQRES 5 B 290 ILE GLU LYS ALA ILE GLU THR ALA ASN VAL ASN GLU ASN SEQRES 6 B 290 ASP VAL ILE LEU GLU VAL GLY PRO GLY LEU GLY PHE LEU SEQRES 7 B 290 THR ASP GLU LEU ALA LYS ARG ALA LYS LYS VAL TYR THR SEQRES 8 B 290 ILE GLU ILE ASP GLN LYS ILE ILE GLU ILE LEU LYS LYS SEQRES 9 B 290 GLU TYR SER TRP ASN ASN VAL LYS ILE ILE GLN GLY ASP SEQRES 10 B 290 ALA VAL ARG VAL GLU TRP PRO LYS PHE ASN LYS VAL VAL SEQRES 11 B 290 SER ASN ILE PRO TYR LYS ILE SER SER PRO PHE THR PHE SEQRES 12 B 290 LYS LEU LEU LYS THR ASP PHE GLU ARG ALA VAL VAL MET SEQRES 13 B 290 TYR GLN LEU GLU PHE ALA LEU ARG MET VAL ALA LYS PRO SEQRES 14 B 290 GLY SER ARG ASN TYR SER ARG LEU SER LEU MET ALA GLN SEQRES 15 B 290 ALA LEU GLY ASN VAL GLU ILE VAL MET LYS ILE GLY LYS SEQRES 16 B 290 GLY ALA PHE TYR PRO ARG PRO LYS VAL ASP SER ALA LEU SEQRES 17 B 290 VAL LEU ILE GLU PRO ARG LYS ASP LYS ILE VAL LEU ASN SEQRES 18 B 290 GLU ASN LEU VAL LYS ALA LEU PHE GLN HIS ARG ARG LYS SEQRES 19 B 290 THR VAL PRO ARG ALA LEU LYS ASP SER ILE HIS MET LEU SEQRES 20 B 290 GLY VAL SER LYS ASP GLU ILE ARG GLY ILE ILE ASN ASN SEQRES 21 B 290 VAL PRO HIS SER ASN LYS ARG VAL PHE GLN LEU TYR PRO SEQRES 22 B 290 GLU GLU VAL LYS ASP ILE GLU GLU TYR LEU LYS LYS HIS SEQRES 23 B 290 GLY ILE ILE SER HET SFG A 301 27 HET ZN A 302 1 HET ZN A 303 1 HET ZN A 304 1 HET ZN A 305 1 HET ZN A 306 1 HET CL A 307 1 HET PEG A 308 7 HET ARG A 309 12 HET SFG B 301 27 HET ZN B 302 1 HET CL B 303 1 HET SO3 B 304 4 HET EDO B 305 4 HET PEG B 306 7 HET ARG B 307 12 HETNAM SFG SINEFUNGIN HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ARG ARGININE HETNAM SO3 SULFITE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN SFG ADENOSYL-ORNITHINE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 SFG 2(C15 H23 N7 O5) FORMUL 4 ZN 6(ZN 2+) FORMUL 9 CL 2(CL 1-) FORMUL 10 PEG 2(C4 H10 O3) FORMUL 11 ARG 2(C6 H15 N4 O2 1+) FORMUL 15 SO3 O3 S 2- FORMUL 16 EDO C2 H6 O2 FORMUL 19 HOH *235(H2 O) HELIX 1 AA1 LYS A 22 TYR A 34 1 13 HELIX 2 AA2 ILE A 49 ALA A 60 1 12 HELIX 3 AA3 GLY A 76 ALA A 86 1 11 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 VAL A 166 1 8 HELIX 8 AA8 SER A 175 LEU A 184 1 10 HELIX 9 AA9 GLY A 194 GLY A 196 5 3 HELIX 10 AB1 ASN A 221 GLN A 230 1 10 HELIX 11 AB2 THR A 235 GLY A 248 1 14 HELIX 12 AB3 ILE A 254 ASN A 260 1 7 HELIX 13 AB4 ARG A 267 LEU A 271 5 5 HELIX 14 AB5 TYR A 272 HIS A 286 1 15 HELIX 15 AB6 MET B 23 TYR B 34 1 12 HELIX 16 AB7 ILE B 49 ASN B 61 1 13 HELIX 17 AB8 GLY B 76 ALA B 86 1 11 HELIX 18 AB9 ASP B 95 TYR B 106 1 12 HELIX 19 AC1 PRO B 134 LYS B 136 5 3 HELIX 20 AC2 ILE B 137 LYS B 147 1 11 HELIX 21 AC3 LEU B 159 VAL B 166 1 8 HELIX 22 AC4 SER B 175 LEU B 184 1 10 HELIX 23 AC5 GLY B 194 GLY B 196 5 3 HELIX 24 AC6 ASN B 221 HIS B 231 1 11 HELIX 25 AC7 THR B 235 GLY B 248 1 14 HELIX 26 AC8 ILE B 254 ASN B 260 1 7 HELIX 27 AC9 ARG B 267 LEU B 271 5 5 HELIX 28 AD1 TYR B 272 HIS B 286 1 15 SHEET 1 AA1 2 PHE A 46 LEU A 47 0 SHEET 2 AA1 2 PHE A 198 TYR A 199 -1 O TYR A 199 N PHE A 46 SHEET 1 AA2 7 VAL A 111 GLN A 115 0 SHEET 2 AA2 7 LYS A 88 GLU A 93 1 N VAL A 89 O LYS A 112 SHEET 3 AA2 7 VAL A 67 VAL A 71 1 N ILE A 68 O TYR A 90 SHEET 4 AA2 7 LYS A 128 ASN A 132 1 O LYS A 128 N LEU A 69 SHEET 5 AA2 7 ARG A 152 GLN A 158 1 O VAL A 154 N VAL A 129 SHEET 6 AA2 7 SER A 206 PRO A 213 -1 O ALA A 207 N TYR A 157 SHEET 7 AA2 7 GLY A 185 ILE A 193 -1 N ILE A 193 O SER A 206 SHEET 1 AA3 2 PHE B 46 LEU B 47 0 SHEET 2 AA3 2 PHE B 198 TYR B 199 -1 O TYR B 199 N PHE B 46 SHEET 1 AA4 7 VAL B 111 GLN B 115 0 SHEET 2 AA4 7 LYS B 88 GLU B 93 1 N VAL B 89 O LYS B 112 SHEET 3 AA4 7 VAL B 67 VAL B 71 1 N ILE B 68 O TYR B 90 SHEET 4 AA4 7 LYS B 128 ASN B 132 1 O LYS B 128 N LEU B 69 SHEET 5 AA4 7 ARG B 152 GLN B 158 1 O VAL B 154 N VAL B 129 SHEET 6 AA4 7 SER B 206 PRO B 213 -1 O ALA B 207 N TYR B 157 SHEET 7 AA4 7 GLY B 185 ILE B 193 -1 N ILE B 193 O SER B 206 LINK OD1 ASP A 25 ZN ZN A 306 1555 4556 2.13 LINK OD2 ASP A 40 ZN ZN A 303 1555 1555 1.80 LINK OD1 ASP A 80 ZN ZN A 304 1555 1555 2.29 LINK OE1 GLU A 160 ZN ZN A 302 1555 1555 2.04 LINK NE2 HIS A 245 ZN ZN A 305 1555 1555 2.20 LINK ND1 HIS A 263 ZN ZN A 306 1555 1555 1.97 LINK OE1 GLU A 275 ZN ZN A 306 1555 1555 2.66 LINK ZN ZN A 302 NE2 HIS B 245 1555 1555 2.04 LINK ZN ZN A 303 OE2 GLU B 253 1555 1555 2.63 LINK ZN ZN A 305 OE1 GLU B 160 1555 1555 1.96 LINK OD1 ASP B 25 ZN ZN B 302 1555 4545 2.07 LINK ND1 HIS B 263 ZN ZN B 302 1555 1555 1.83 LINK OE1 GLU B 275 ZN ZN B 302 1555 1555 2.54 CISPEP 1 TYR A 199 PRO A 200 0 -8.11 CISPEP 2 TYR B 199 PRO B 200 0 -7.66 CRYST1 119.150 80.340 84.110 90.00 115.46 90.00 C 1 2 1 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 0.008393 0.000000 0.003996 0.00000 SCALE2 0.000000 0.012447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013168 0.00000