HEADER TRANSFERASE 15-NOV-23 8X44 TITLE CRYSTAL STRUCTURE OF DIMT1 IN COMPLEX WITH 5'-METHYLTHIOADENOSINE FROM TITLE 2 PYROCOCCUS HORIKOSHII (FORMI) 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 8X44 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21905 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1163 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1589 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4360 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.20000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : 1.13000 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): 0.658 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.333 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.252 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.121 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4555 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4458 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6121 ; 1.585 ; 1.644 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10388 ; 0.538 ; 1.566 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 542 ; 7.923 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 34 ; 8.712 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 884 ;18.735 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 691 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4974 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 860 ; 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): 2150 ; 2.163 ; 2.298 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2150 ; 2.162 ; 2.298 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2686 ; 3.485 ; 3.438 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2687 ; 3.485 ; 3.440 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2405 ; 3.247 ; 2.768 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2406 ; 3.246 ; 2.769 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3432 ; 4.998 ; 3.943 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5134 ; 7.744 ;35.615 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5110 ; 7.720 ;35.540 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 23 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): -16.0125 -6.8307 32.3333 REMARK 3 T TENSOR REMARK 3 T11: 0.0203 T22: 0.0327 REMARK 3 T33: 0.2229 T12: 0.0154 REMARK 3 T13: 0.0401 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 1.9082 L22: 1.9101 REMARK 3 L33: 1.5016 L12: 1.0851 REMARK 3 L13: -0.4401 L23: -1.3419 REMARK 3 S TENSOR REMARK 3 S11: 0.0549 S12: -0.0915 S13: 0.2073 REMARK 3 S21: 0.0000 S22: 0.0295 S23: -0.0244 REMARK 3 S31: -0.0301 S32: -0.0958 S33: -0.0844 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 23 B 290 REMARK 3 ORIGIN FOR THE GROUP (A): -23.8297 23.3664 32.3039 REMARK 3 T TENSOR REMARK 3 T11: 0.0173 T22: 0.0316 REMARK 3 T33: 0.1813 T12: 0.0089 REMARK 3 T13: -0.0362 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 2.1814 L22: 1.9424 REMARK 3 L33: 1.4361 L12: 1.0720 REMARK 3 L13: 0.1746 L23: 1.2055 REMARK 3 S TENSOR REMARK 3 S11: 0.0480 S12: -0.0828 S13: -0.1705 REMARK 3 S21: -0.0553 S22: 0.0407 S23: -0.0154 REMARK 3 S31: -0.0017 S32: 0.1459 S33: -0.0886 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 8X44 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-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 : 23103 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 85.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.56300 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 ORTHORHOMBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.64 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, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.40500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.67000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.40500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 465 LIES ON A SPECIAL POSITION. 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 LYS A 22 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 465 LYS B 22 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 NZ LYS A 84 O HOH A 401 1.56 REMARK 500 NE2 HIS B 286 O4 PEG B 309 1.80 REMARK 500 OE1 GLU B 105 O HOH B 401 1.94 REMARK 500 NE2 HIS A 231 NE2 HIS B 231 1.98 REMARK 500 OE1 GLU A 253 O1 SO3 B 305 2.08 REMARK 500 O HOH B 480 O HOH B 494 2.14 REMARK 500 O HOH B 407 O HOH B 449 2.16 REMARK 500 O4 PEG B 309 O HOH B 402 2.17 REMARK 500 OE1 GLU A 105 O HOH A 402 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 OE1 GLU B 188 O4 PEG B 309 3455 1.52 REMARK 500 OE2 GLU B 64 OE2 GLU B 64 2566 1.77 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 39 143.34 -171.24 REMARK 500 SER A 131 138.55 -170.69 REMARK 500 SER B 131 140.37 -170.85 REMARK 500 ILE B 288 -70.33 -66.75 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 267 0.08 SIDE CHAIN REMARK 500 ARG B 24 0.08 SIDE CHAIN REMARK 500 ARG B 85 0.08 SIDE CHAIN REMARK 500 ARG B 238 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 493 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 494 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A 495 DISTANCE = 6.91 ANGSTROMS 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 B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 25 OD1 REMARK 620 2 HIS B 263 ND1 73.4 REMARK 620 3 GLU B 275 OE1 72.2 1.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 160 OE1 REMARK 620 2 HIS B 245 NE2 95.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 307 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE1 REMARK 620 2 HIS A 286 NE2 57.2 REMARK 620 3 PEG A 311 O1 136.9 79.7 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 HIS A 245 NE2 REMARK 620 2 GLU B 160 OE1 95.9 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 HIS A 263 ND1 REMARK 620 2 GLU A 275 OE1 92.1 REMARK 620 3 ASP B 25 OD1 28.6 115.4 REMARK 620 N 1 2 DBREF 8X44 A 23 290 UNP O59487 RSMA_PYRHO 1 268 DBREF 8X44 B 23 290 UNP O59487 RSMA_PYRHO 1 268 SEQADV 8X44 MET A 1 UNP O59487 INITIATING METHIONINE SEQADV 8X44 SER A 2 UNP O59487 EXPRESSION TAG SEQADV 8X44 SER A 3 UNP O59487 EXPRESSION TAG SEQADV 8X44 ARG A 4 UNP O59487 EXPRESSION TAG SEQADV 8X44 ILE A 5 UNP O59487 EXPRESSION TAG SEQADV 8X44 ARG A 6 UNP O59487 EXPRESSION TAG SEQADV 8X44 ILE A 7 UNP O59487 EXPRESSION TAG SEQADV 8X44 ASN A 8 UNP O59487 EXPRESSION TAG SEQADV 8X44 THR A 9 UNP O59487 EXPRESSION TAG SEQADV 8X44 LYS A 10 UNP O59487 EXPRESSION TAG SEQADV 8X44 SER A 11 UNP O59487 EXPRESSION TAG SEQADV 8X44 LEU A 12 UNP O59487 EXPRESSION TAG SEQADV 8X44 LEU A 13 UNP O59487 EXPRESSION TAG SEQADV 8X44 VAL A 14 UNP O59487 EXPRESSION TAG SEQADV 8X44 GLN A 15 UNP O59487 EXPRESSION TAG SEQADV 8X44 PRO A 16 UNP O59487 EXPRESSION TAG SEQADV 8X44 GLY A 17 UNP O59487 EXPRESSION TAG SEQADV 8X44 TYR A 18 UNP O59487 EXPRESSION TAG SEQADV 8X44 SER A 19 UNP O59487 EXPRESSION TAG SEQADV 8X44 GLY A 20 UNP O59487 EXPRESSION TAG SEQADV 8X44 SER A 21 UNP O59487 EXPRESSION TAG SEQADV 8X44 LYS A 22 UNP O59487 EXPRESSION TAG SEQADV 8X44 MET B 1 UNP O59487 INITIATING METHIONINE SEQADV 8X44 SER B 2 UNP O59487 EXPRESSION TAG SEQADV 8X44 SER B 3 UNP O59487 EXPRESSION TAG SEQADV 8X44 ARG B 4 UNP O59487 EXPRESSION TAG SEQADV 8X44 ILE B 5 UNP O59487 EXPRESSION TAG SEQADV 8X44 ARG B 6 UNP O59487 EXPRESSION TAG SEQADV 8X44 ILE B 7 UNP O59487 EXPRESSION TAG SEQADV 8X44 ASN B 8 UNP O59487 EXPRESSION TAG SEQADV 8X44 THR B 9 UNP O59487 EXPRESSION TAG SEQADV 8X44 LYS B 10 UNP O59487 EXPRESSION TAG SEQADV 8X44 SER B 11 UNP O59487 EXPRESSION TAG SEQADV 8X44 LEU B 12 UNP O59487 EXPRESSION TAG SEQADV 8X44 LEU B 13 UNP O59487 EXPRESSION TAG SEQADV 8X44 VAL B 14 UNP O59487 EXPRESSION TAG SEQADV 8X44 GLN B 15 UNP O59487 EXPRESSION TAG SEQADV 8X44 PRO B 16 UNP O59487 EXPRESSION TAG SEQADV 8X44 GLY B 17 UNP O59487 EXPRESSION TAG SEQADV 8X44 TYR B 18 UNP O59487 EXPRESSION TAG SEQADV 8X44 SER B 19 UNP O59487 EXPRESSION TAG SEQADV 8X44 GLY B 20 UNP O59487 EXPRESSION TAG SEQADV 8X44 SER B 21 UNP O59487 EXPRESSION TAG SEQADV 8X44 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 MTA A 301 20 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 ZN A 307 1 HET SO3 A 308 4 HET SO3 A 309 4 HET PEG A 310 7 HET PEG A 311 7 HET MTA B 301 20 HET ZN B 302 1 HET ZN B 303 1 HET CL B 304 1 HET SO3 B 305 4 HET SO3 B 306 4 HET GOL B 307 6 HET EDO B 308 4 HET PEG B 309 7 HET PEG B 310 7 HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM ZN ZINC ION HETNAM SO3 SULFITE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 MTA 2(C11 H15 N5 O3 S) FORMUL 4 ZN 8(ZN 2+) FORMUL 10 SO3 4(O3 S 2-) FORMUL 12 PEG 4(C4 H10 O3) FORMUL 17 CL CL 1- FORMUL 20 GOL C3 H8 O3 FORMUL 21 EDO C2 H6 O2 FORMUL 24 HOH *197(H2 O) HELIX 1 AA1 MET A 23 TYR A 34 1 12 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 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 LEU A 247 1 13 HELIX 12 AB3 ILE A 254 ASN A 259 1 6 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 ARG B 24 TYR B 34 1 11 HELIX 16 AB7 ILE B 49 ASN B 61 1 13 HELIX 17 AB8 GLY B 76 LYS B 84 1 9 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 GLN B 230 1 10 HELIX 25 AC7 THR B 235 LEU B 247 1 13 HELIX 26 AC8 ILE B 254 ASN B 259 1 6 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 THR A 91 O ILE A 114 SHEET 3 AA2 7 VAL A 67 VAL A 71 1 N GLU A 70 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 VAL A 209 N VAL A 155 SHEET 7 AA2 7 GLY A 185 ILE A 193 -1 N VAL A 190 O LEU A 208 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 GLU B 70 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 VAL B 209 N VAL B 155 SHEET 7 AA4 7 GLY B 185 ILE B 193 -1 N VAL B 190 O LEU B 208 LINK OD1 ASP A 25 ZN ZN B 302 1555 3445 2.20 LINK OD1 ASP A 80 ZN ZN A 305 1555 1555 2.14 LINK OE1 GLU A 160 ZN ZN A 304 1555 1555 2.30 LINK OE1 GLU A 188 ZN ZN A 307 1555 1555 1.75 LINK NE2 HIS A 245 ZN ZN A 303 1555 1555 2.15 LINK ND1 HIS A 263 ZN ZN A 302 1555 1555 2.09 LINK OE1 GLU A 275 ZN ZN A 302 1555 1555 2.22 LINK OD2 ASP A 278 ZN ZN A 306 1555 1555 2.19 LINK NE2 HIS A 286 ZN ZN A 307 1555 3555 2.06 LINK ZN ZN A 302 OD1 ASP B 25 3555 1555 2.15 LINK ZN ZN A 303 OE1 GLU B 160 1555 1555 2.08 LINK ZN ZN A 304 NE2 HIS B 245 1555 1555 2.10 LINK ZN ZN A 307 O1 PEG A 311 1555 1555 2.08 LINK ND1 HIS B 263 ZN ZN B 302 1555 1555 2.11 LINK OE1 GLU B 275 ZN ZN B 302 1555 1555 2.23 LINK OD2 ASP B 278 ZN ZN B 303 1555 1555 2.32 CISPEP 1 TYR A 199 PRO A 200 0 -7.17 CISPEP 2 TYR B 199 PRO B 200 0 -5.86 CRYST1 79.780 85.340 106.810 90.00 90.00 90.00 P 2 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 0.012534 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009362 0.00000