HEADER TRANSFERASE 29-AUG-23 8QDI TITLE COMPOUND 1B BOUND KMT9 CRYSTAL STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLTRANSFERASE N6AMT1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEMK METHYLTRANSFERASE FAMILY MEMBER 2,M.HSAHEMK2P,LYSINE N- COMPND 5 METHYLTRANSFERASE 9,METHYLARSONITE METHYLTRANSFERASE N6AMT1,PROTEIN COMPND 6 N(5)-GLUTAMINE METHYLTRANSFERASE; COMPND 7 EC: 2.1.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: MULTIFUNCTIONAL METHYLTRANSFERASE SUBUNIT TRM112-LIKE COMPND 11 PROTEIN; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: TRNA METHYLTRANSFERASE 112 HOMOLOG; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: N6AMT1, C21ORF127, HEMK2, KMT9, PRED28; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: TRMT112, AD-001, HSPC152, HSPC170; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN TRANSFERASE, GENE REGULATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.SHENG,M.ERIC,S.ROLAND REVDAT 1 11-SEP-24 8QDI 0 JRNL AUTH W.SHENG,M.ERIC,S.ROLAND JRNL TITL COMPOUND 1A BOUND KMT9 CRYSTAL STRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.47 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 80029 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.039 REMARK 3 FREE R VALUE TEST SET COUNT : 4033 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5409 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.3550 REMARK 3 BIN FREE R VALUE SET COUNT : 272 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2407 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 184 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 0.97500 REMARK 3 B12 (A**2) : -0.15000 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): 0.054 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.045 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2570 ; 0.016 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2438 ; 0.008 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3510 ; 1.736 ; 1.646 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5711 ; 0.606 ; 1.551 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 6.639 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 17 ; 8.481 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 444 ;14.381 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 410 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2915 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 468 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 406 ; 0.233 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 77 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1235 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 127 ; 0.121 ; 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): 1283 ; 6.123 ; 2.236 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1283 ; 6.114 ; 2.235 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1610 ; 6.649 ; 3.346 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1611 ; 6.652 ; 3.348 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1287 ;10.385 ; 2.826 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1288 ;10.381 ; 2.826 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1891 ;10.284 ; 3.986 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1892 ;10.281 ; 3.987 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): 5008 ;13.962 ; 3.000 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 20 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): -42.4116 -6.9182 -16.5154 REMARK 3 T TENSOR REMARK 3 T11: 0.0108 T22: 0.0110 REMARK 3 T33: 0.0012 T12: -0.0011 REMARK 3 T13: 0.0008 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.0149 L22: 0.0518 REMARK 3 L33: 0.0334 L12: -0.0157 REMARK 3 L13: 0.0005 L23: 0.0337 REMARK 3 S TENSOR REMARK 3 S11: 0.0014 S12: -0.0014 S13: -0.0031 REMARK 3 S21: -0.0016 S22: -0.0015 S23: 0.0034 REMARK 3 S31: 0.0005 S32: -0.0026 S33: 0.0001 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -47.3507 -26.8381 -2.4533 REMARK 3 T TENSOR REMARK 3 T11: 0.0105 T22: 0.0100 REMARK 3 T33: 0.0001 T12: 0.0003 REMARK 3 T13: -0.0002 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.0202 L22: 0.0080 REMARK 3 L33: 0.0262 L12: 0.0027 REMARK 3 L13: -0.0098 L23: 0.0114 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: 0.0010 S13: 0.0011 REMARK 3 S21: 0.0000 S22: -0.0007 S23: 0.0003 REMARK 3 S31: -0.0013 S32: -0.0020 S33: -0.0003 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 8QDI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292133039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80097 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.467 REMARK 200 RESOLUTION RANGE LOW (A) : 47.901 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 39.40 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 47.85 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 34.30 REMARK 200 R MERGE FOR SHELL (I) : 0.03100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1 M NA3CITRATE, 0.1M HEPES 7.25, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 43.27900 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 86.55800 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 64.91850 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 108.19750 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 21.63950 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.27900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 86.55800 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 108.19750 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 64.91850 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 21.63950 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: 2310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 B 277 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 SER A 12 REMARK 465 HIS A 13 REMARK 465 VAL A 14 REMARK 465 GLY A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 17 REMARK 465 ALA A 18 REMARK 465 PHE A 19 REMARK 465 MET B 1 REMARK 465 SER B 120 REMARK 465 GLU B 121 REMARK 465 GLU B 122 REMARK 465 GLU B 123 REMARK 465 THR B 124 REMARK 465 GLU B 125 REMARK 465 SER B 126 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 GLN A 203 CG GLN A 203 CD 0.150 REMARK 500 GLN A 203 CD GLN A 203 OE1 0.153 REMARK 500 GLN A 203 CD GLN A 203 NE2 0.168 REMARK 500 GLU B 51 CD GLU B 51 OE1 -0.118 REMARK 500 GLU B 57 CD GLU B 57 OE1 0.083 REMARK 500 GLU B 76 CG GLU B 76 CD 0.340 REMARK 500 GLU B 76 CD GLU B 76 OE1 0.177 REMARK 500 GLU B 76 CD GLU B 76 OE2 0.326 REMARK 500 GLU B 93 CD GLU B 93 OE1 -0.091 REMARK 500 GLU B 96 CD GLU B 96 OE1 -0.109 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 154 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 GLU B 76 OE1 - CD - OE2 ANGL. DEV. = 13.8 DEGREES REMARK 500 GLU B 76 CG - CD - OE2 ANGL. DEV. = -16.1 DEGREES REMARK 500 ARG B 106 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 106 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 MET B 107 CG - SD - CE ANGL. DEV. = -17.2 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 LEU A 104 -104.91 62.23 REMARK 500 SER A 135 171.39 -59.10 REMARK 500 ASN A 147 16.40 57.28 REMARK 500 ARG A 166 11.34 57.87 REMARK 500 ASN A 178 67.34 67.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 134 SER A 135 147.16 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 B 25 0.07 SIDE CHAIN REMARK 500 ARG B 32 0.09 SIDE CHAIN REMARK 500 GLU B 76 0.07 SIDE CHAIN REMARK 500 ARG B 106 0.08 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 B 283 DISTANCE = 6.06 ANGSTROMS DBREF 8QDI A 13 214 UNP Q9Y5N5 N6MT1_HUMAN 13 214 DBREF 8QDI B 3 126 UNP Q9UI30 TR112_HUMAN 2 125 SEQADV 8QDI SER A 12 UNP Q9Y5N5 EXPRESSION TAG SEQADV 8QDI MET B 1 UNP Q9UI30 INITIATING METHIONINE SEQADV 8QDI GLY B 2 UNP Q9UI30 EXPRESSION TAG SEQRES 1 A 203 SER HIS VAL GLY ARG GLY ALA PHE SER ASP VAL TYR GLU SEQRES 2 A 203 PRO ALA GLU ASP THR PHE LEU LEU LEU ASP ALA LEU GLU SEQRES 3 A 203 ALA ALA ALA ALA GLU LEU ALA GLY VAL GLU ILE CYS LEU SEQRES 4 A 203 GLU VAL GLY SER GLY SER GLY VAL VAL SER ALA PHE LEU SEQRES 5 A 203 ALA SER MET ILE GLY PRO GLN ALA LEU TYR MET CYS THR SEQRES 6 A 203 ASP ILE ASN PRO GLU ALA ALA ALA CYS THR LEU GLU THR SEQRES 7 A 203 ALA ARG CYS ASN LYS VAL HIS ILE GLN PRO VAL ILE THR SEQRES 8 A 203 ASP LEU VAL LYS GLY LEU LEU PRO ARG LEU THR GLU LYS SEQRES 9 A 203 VAL ASP LEU LEU VAL PHE ASN PRO PRO TYR VAL VAL THR SEQRES 10 A 203 PRO PRO GLN GLU VAL GLY SER HIS GLY ILE GLU ALA ALA SEQRES 11 A 203 TRP ALA GLY GLY ARG ASN GLY ARG GLU VAL MET ASP ARG SEQRES 12 A 203 PHE PHE PRO LEU VAL PRO ASP LEU LEU SER PRO ARG GLY SEQRES 13 A 203 LEU PHE TYR LEU VAL THR ILE LYS GLU ASN ASN PRO GLU SEQRES 14 A 203 GLU ILE LEU LYS ILE MET LYS THR LYS GLY LEU GLN GLY SEQRES 15 A 203 THR THR ALA LEU SER ARG GLN ALA GLY GLN GLU THR LEU SEQRES 16 A 203 SER VAL LEU LYS PHE THR LYS SER SEQRES 1 B 126 MET GLY LYS LEU LEU THR HIS ASN LEU LEU SER SER HIS SEQRES 2 B 126 VAL ARG GLY VAL GLY SER ARG GLY PHE PRO LEU ARG LEU SEQRES 3 B 126 GLN ALA THR GLU VAL ARG ILE CYS PRO VAL GLU PHE ASN SEQRES 4 B 126 PRO ASN PHE VAL ALA ARG MET ILE PRO LYS VAL GLU TRP SEQRES 5 B 126 SER ALA PHE LEU GLU ALA ALA ASP ASN LEU ARG LEU ILE SEQRES 6 B 126 GLN VAL PRO LYS GLY PRO VAL GLU GLY TYR GLU GLU ASN SEQRES 7 B 126 GLU GLU PHE LEU ARG THR MET HIS HIS LEU LEU LEU GLU SEQRES 8 B 126 VAL GLU VAL ILE GLU GLY THR LEU GLN CYS PRO GLU SER SEQRES 9 B 126 GLY ARG MET PHE PRO ILE SER ARG GLY ILE PRO ASN MET SEQRES 10 B 126 LEU LEU SER GLU GLU GLU THR GLU SER HET QII A 301 65 HETNAM QII (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN- HETNAM 2 QII 9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL-[2-[(2~{R})- HETNAM 3 QII PYRROLIDIN-2-YL]ETHYL]AMINO]-2-AZANYL-BUTANOIC ACID FORMUL 3 QII C20 H32 N8 O5 FORMUL 4 HOH *184(H2 O) HELIX 1 AA1 ALA A 26 ALA A 39 1 14 HELIX 2 AA2 ALA A 40 ALA A 44 5 5 HELIX 3 AA3 GLY A 57 GLY A 68 1 12 HELIX 4 AA4 ASN A 79 ASN A 93 1 15 HELIX 5 AA5 PRO A 129 VAL A 133 5 5 HELIX 6 AA6 GLY A 137 ALA A 143 1 7 HELIX 7 AA7 GLY A 145 GLY A 148 5 4 HELIX 8 AA8 ARG A 149 PHE A 156 1 8 HELIX 9 AA9 LEU A 158 LEU A 162 1 5 HELIX 10 AB1 ASN A 178 LYS A 189 1 12 HELIX 11 AB2 LYS B 3 ASN B 8 1 6 HELIX 12 AB3 VAL B 17 PHE B 22 5 6 HELIX 13 AB4 ASN B 39 ILE B 47 1 9 HELIX 14 AB5 PRO B 48 VAL B 50 5 3 HELIX 15 AB6 GLU B 51 LEU B 62 1 12 HELIX 16 AB7 GLY B 74 GLU B 77 5 4 HELIX 17 AB8 ASN B 78 GLU B 91 1 14 SHEET 1 AA1 7 GLN A 98 ILE A 101 0 SHEET 2 AA1 7 LEU A 72 ASP A 77 1 N TYR A 73 O GLN A 98 SHEET 3 AA1 7 ILE A 48 VAL A 52 1 N CYS A 49 O MET A 74 SHEET 4 AA1 7 VAL A 116 PHE A 121 1 O LEU A 118 N LEU A 50 SHEET 5 AA1 7 LEU A 163 ILE A 174 1 O LEU A 168 N LEU A 119 SHEET 6 AA1 7 GLU A 204 LYS A 213 -1 O LEU A 209 N LEU A 171 SHEET 7 AA1 7 LEU A 191 ALA A 201 -1 N ALA A 201 O GLU A 204 SHEET 1 AA2 4 ARG B 25 ILE B 33 0 SHEET 2 AA2 4 VAL B 92 GLN B 100 -1 O GLU B 93 N ARG B 32 SHEET 3 AA2 4 MET B 107 SER B 111 -1 O PHE B 108 N LEU B 99 SHEET 4 AA2 4 ILE B 114 PRO B 115 -1 O ILE B 114 N SER B 111 CISPEP 1 LEU A 109 PRO A 110 0 5.08 CISPEP 2 PHE B 22 PRO B 23 0 -8.02 CRYST1 110.516 110.516 129.837 90.00 90.00 120.00 P 61 2 2 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 0.009048 0.005224 0.000000 0.00000 SCALE2 0.000000 0.010448 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007702 0.00000