HEADER ISOMERASE 24-MAY-21 7MZV TITLE STRUCTURE OF YEAST PSEUDOURIDINE SYNTHASE 7 (PUS7) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTISUBSTRATE PSEUDOURIDINE SYNTHASE 7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNA PSEUDOURIDYLATE SYNTHASE 7,RNA-URIDINE ISOMERASE 7,TRNA COMPND 5 PSEUDOURIDINE(13) SYNTHASE; COMPND 6 EC: 5.4.99.-,5.4.99.27; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: PUS7, YOR243C, O5254; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-PLYS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS PUS7, PSEUDOURIDINE SYNTHASE, RNA BINDING PROTEIN, RBP, MRNA KEYWDS 2 MODIFICATION, PSEUDOURIDINE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PURCHAL,M.KOUTMOS REVDAT 3 15-NOV-23 7MZV 1 REMARK REVDAT 2 18-OCT-23 7MZV 1 REMARK REVDAT 1 09-FEB-22 7MZV 0 JRNL AUTH M.K.PURCHAL,D.E.EYLER,M.TARDU,M.K.FRANCO,M.M.KORN,T.KHAN, JRNL AUTH 2 R.MCNASSOR,R.GILES,K.LEV,H.SHARMA,J.MONROE,L.MALLIK, JRNL AUTH 3 M.KOUTMOS,K.S.KOUTMOU JRNL TITL PSEUDOURIDINE SYNTHASE 7 IS AN OPPORTUNISTIC ENZYME THAT JRNL TITL 2 BINDS AND MODIFIES SUBSTRATES WITH DIVERSE SEQUENCES AND JRNL TITL 3 STRUCTURES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35058356 JRNL DOI 10.1073/PNAS.2109708119 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17136 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 881 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1236 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4679 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 120.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25000 REMARK 3 B22 (A**2) : -2.27000 REMARK 3 B33 (A**2) : 2.03000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.489 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.420 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.620 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4759 ; 0.003 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4636 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6398 ; 1.208 ; 1.654 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10668 ; 1.016 ; 1.589 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 575 ; 6.868 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 266 ;31.414 ;22.331 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 866 ;17.382 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;13.183 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 623 ; 0.038 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5300 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1094 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7MZV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000256820. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18019 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.16200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 9.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 46.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.08100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 5KKP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 10MM NICKEL(II) REMARK 280 CHLORIDE, 100 MM TRIS PH 8.5, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 1.000000 0.000000 0.000000 58.94500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 85.90000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 58.94500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 85.90000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 58.94500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 85.90000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 58.94500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 85.90000 REMARK 290 SMTRY3 8 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 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 MSE A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 GLU A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8 REMARK 465 VAL A 9 REMARK 465 LYS A 10 REMARK 465 ARG A 11 REMARK 465 PRO A 12 REMARK 465 LEU A 13 REMARK 465 ASP A 14 REMARK 465 ALA A 15 REMARK 465 HIS A 16 REMARK 465 VAL A 17 REMARK 465 GLY A 18 REMARK 465 PRO A 19 REMARK 465 SER A 20 REMARK 465 GLU A 21 REMARK 465 ASN A 22 REMARK 465 ALA A 23 REMARK 465 ALA A 24 REMARK 465 LYS A 25 REMARK 465 LYS A 26 REMARK 465 LEU A 27 REMARK 465 LYS A 28 REMARK 465 ILE A 29 REMARK 465 GLU A 30 REMARK 465 GLN A 31 REMARK 465 ARG A 32 REMARK 465 THR A 33 REMARK 465 GLN A 34 REMARK 465 ALA A 35 REMARK 465 ASP A 36 REMARK 465 GLN A 93 REMARK 465 ARG A 94 REMARK 465 ASN A 150 REMARK 465 PHE A 151 REMARK 465 GLU A 152 REMARK 465 ASP A 377 REMARK 465 GLN A 378 REMARK 465 ASP A 379 REMARK 465 ASN A 380 REMARK 465 VAL A 381 REMARK 465 LEU A 382 REMARK 465 PRO A 383 REMARK 465 LYS A 384 REMARK 465 SER A 385 REMARK 465 ARG A 407 REMARK 465 GLN A 408 REMARK 465 CYS A 409 REMARK 465 LEU A 410 REMARK 465 ALA A 414 REMARK 465 ILE A 442 REMARK 465 GLU A 485 REMARK 465 LYS A 486 REMARK 465 SER A 487 REMARK 465 PRO A 488 REMARK 465 LEU A 489 REMARK 465 ILE A 490 REMARK 465 SER A 491 REMARK 465 GLY A 492 REMARK 465 ILE A 493 REMARK 465 ASP A 494 REMARK 465 ASP A 495 REMARK 465 GLU A 496 REMARK 465 ASP A 497 REMARK 465 PHE A 498 REMARK 465 ASP A 499 REMARK 465 GLU A 500 REMARK 465 ASP A 501 REMARK 465 VAL A 502 REMARK 465 ARG A 503 REMARK 465 GLU A 504 REMARK 465 ALA A 505 REMARK 465 GLN A 506 REMARK 465 GLU A 662 REMARK 465 THR A 663 REMARK 465 SER A 664 REMARK 465 ARG A 665 REMARK 465 ARG A 666 REMARK 465 GLY A 667 REMARK 465 ASP A 668 REMARK 465 MSE A 669 REMARK 465 CYS A 670 REMARK 465 ASP A 671 REMARK 465 VAL A 672 REMARK 465 LYS A 673 REMARK 465 GLU A 674 REMARK 465 ASN A 675 REMARK 465 ILE A 676 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 HG1 THR A 202 O GLU A 209 1.41 REMARK 500 OG1 THR A 202 O GLU A 209 2.19 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 MSE A 558 CG - SE - CE ANGL. DEV. = 14.2 DEGREES REMARK 500 MSE A 563 CG - SE - CE ANGL. DEV. = 16.0 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 LYS A 84 40.55 -103.85 REMARK 500 PHE A 127 -64.16 -98.76 REMARK 500 ALA A 142 72.43 -112.59 REMARK 500 THR A 147 162.32 84.28 REMARK 500 ALA A 148 117.10 -163.78 REMARK 500 LEU A 164 -62.11 -90.03 REMARK 500 LYS A 169 -61.28 69.48 REMARK 500 THR A 176 121.35 -38.30 REMARK 500 THR A 177 -119.87 -112.59 REMARK 500 THR A 179 -140.43 64.67 REMARK 500 ASN A 180 55.20 -118.97 REMARK 500 THR A 193 -71.17 -82.41 REMARK 500 LYS A 195 -47.81 82.44 REMARK 500 ASN A 200 -6.04 -52.98 REMARK 500 ARG A 258 63.56 -68.44 REMARK 500 LYS A 283 -75.19 -88.63 REMARK 500 ASN A 318 107.25 -42.03 REMARK 500 ASN A 341 43.65 -73.89 REMARK 500 PHE A 351 76.16 -59.64 REMARK 500 SER A 352 -125.71 -142.46 REMARK 500 THR A 395 -151.65 -92.45 REMARK 500 LYS A 396 15.24 -150.88 REMARK 500 LYS A 403 73.82 -65.68 REMARK 500 GLN A 404 -20.40 -166.30 REMARK 500 ASN A 421 -158.10 -77.33 REMARK 500 GLN A 422 -160.33 60.22 REMARK 500 GLU A 425 -161.72 57.63 REMARK 500 ASP A 427 -3.25 73.51 REMARK 500 LYS A 511 129.19 -174.59 REMARK 500 VAL A 521 44.55 34.92 REMARK 500 ASP A 536 67.47 -110.59 REMARK 500 VAL A 537 119.32 -165.17 REMARK 500 ASN A 562 71.87 -100.64 REMARK 500 ASP A 569 36.74 -70.88 REMARK 500 PHE A 570 -3.79 -55.98 REMARK 500 SER A 571 -2.60 81.39 REMARK 500 LEU A 572 160.88 64.40 REMARK 500 ASP A 594 -68.86 -122.71 REMARK 500 ALA A 613 33.20 -98.59 REMARK 500 LYS A 660 57.69 70.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 7MZV A 1 676 UNP Q08647 PUS7_YEAST 1 676 SEQRES 1 A 676 MSE SER ASP SER SER GLU ALA THR VAL LYS ARG PRO LEU SEQRES 2 A 676 ASP ALA HIS VAL GLY PRO SER GLU ASN ALA ALA LYS LYS SEQRES 3 A 676 LEU LYS ILE GLU GLN ARG THR GLN ALA ASP GLY ILE HIS SEQRES 4 A 676 GLU ALA ASP VAL GLY ILE THR LEU PHE LEU SER PRO GLU SEQRES 5 A 676 LEU PRO GLY PHE ARG GLY GLN ILE LYS GLN ARG TYR THR SEQRES 6 A 676 ASP PHE LEU VAL ASN GLU ILE ASP GLN GLU GLY LYS VAL SEQRES 7 A 676 ILE HIS LEU THR ASP LYS GLY PHE LYS MSE PRO LYS LYS SEQRES 8 A 676 PRO GLN ARG SER LYS GLU GLU VAL ASN ALA GLU LYS GLU SEQRES 9 A 676 SER GLU ALA ALA ARG ARG GLN GLU PHE ASN VAL ASP PRO SEQRES 10 A 676 GLU LEU ARG ASN GLN LEU VAL GLU ILE PHE GLY GLU GLU SEQRES 11 A 676 ASP VAL LEU LYS ILE GLU SER VAL TYR ARG THR ALA ASN SEQRES 12 A 676 LYS MSE GLU THR ALA LYS ASN PHE GLU ASP LYS SER VAL SEQRES 13 A 676 ARG THR LYS ILE HIS GLN LEU LEU ARG GLU ALA PHE LYS SEQRES 14 A 676 ASN GLU LEU GLU SER VAL THR THR ASP THR ASN THR PHE SEQRES 15 A 676 LYS ILE ALA ARG SER ASN ARG ASN SER ARG THR ASN LYS SEQRES 16 A 676 GLN GLU LYS ILE ASN GLN THR ARG ASP ALA ASN GLY VAL SEQRES 17 A 676 GLU ASN TRP GLY TYR GLY PRO SER LYS ASP PHE ILE HIS SEQRES 18 A 676 PHE THR LEU HIS LYS GLU ASN LYS ASP THR MSE GLU ALA SEQRES 19 A 676 VAL ASN VAL ILE THR LYS LEU LEU ARG VAL PRO SER ARG SEQRES 20 A 676 VAL ILE ARG TYR ALA GLY THR LYS ASP ARG ARG ALA VAL SEQRES 21 A 676 THR CYS GLN ARG VAL SER ILE SER LYS ILE GLY LEU ASP SEQRES 22 A 676 ARG LEU ASN ALA LEU ASN ARG THR LEU LYS GLY MSE ILE SEQRES 23 A 676 ILE GLY ASN TYR ASN PHE SER ASP ALA SER LEU ASN LEU SEQRES 24 A 676 GLY ASP LEU LYS GLY ASN GLU PHE VAL VAL VAL ILE ARG SEQRES 25 A 676 ASP VAL THR THR GLY ASN SER GLU VAL SER LEU GLU GLU SEQRES 26 A 676 ILE VAL SER ASN GLY CYS LYS SER LEU SER GLU ASN GLY SEQRES 27 A 676 PHE ILE ASN TYR PHE GLY MSE GLN ARG PHE GLY THR PHE SEQRES 28 A 676 SER ILE SER THR HIS THR ILE GLY ARG GLU LEU LEU LEU SEQRES 29 A 676 SER ASN TRP LYS LYS ALA ALA GLU LEU ILE LEU SER ASP SEQRES 30 A 676 GLN ASP ASN VAL LEU PRO LYS SER LYS GLU ALA ARG LYS SEQRES 31 A 676 ILE TRP ALA GLU THR LYS ASP ALA ALA LEU ALA LEU LYS SEQRES 32 A 676 GLN MSE PRO ARG GLN CYS LEU ALA GLU ASN ALA LEU LEU SEQRES 33 A 676 TYR SER LEU SER ASN GLN ARG LYS GLU GLU ASP GLY THR SEQRES 34 A 676 TYR SER GLU ASN ALA TYR TYR THR ALA ILE MSE LYS ILE SEQRES 35 A 676 PRO ARG ASN LEU ARG THR MSE TYR VAL HIS ALA TYR GLN SEQRES 36 A 676 SER TYR VAL TRP ASN SER ILE ALA SER LYS ARG ILE GLU SEQRES 37 A 676 LEU HIS GLY LEU LYS LEU VAL VAL GLY ASP LEU VAL ILE SEQRES 38 A 676 ASP THR SER GLU LYS SER PRO LEU ILE SER GLY ILE ASP SEQRES 39 A 676 ASP GLU ASP PHE ASP GLU ASP VAL ARG GLU ALA GLN PHE SEQRES 40 A 676 ILE ARG ALA LYS ALA VAL THR GLN GLU ASP ILE ASP SER SEQRES 41 A 676 VAL LYS TYR THR MSE GLU ASP VAL VAL LEU PRO SER PRO SEQRES 42 A 676 GLY PHE ASP VAL LEU TYR PRO SER ASN GLU GLU LEU LYS SEQRES 43 A 676 GLN LEU TYR VAL ASP ILE LEU LYS ALA ASP ASN MSE ASP SEQRES 44 A 676 PRO PHE ASN MSE ARG ARG LYS VAL ARG ASP PHE SER LEU SEQRES 45 A 676 ALA GLY SER TYR ARG THR VAL ILE GLN LYS PRO LYS SER SEQRES 46 A 676 LEU GLU TYR ARG ILE ILE HIS TYR ASP ASP PRO SER GLN SEQRES 47 A 676 GLN LEU VAL ASN THR ASP LEU ASP ILE LEU ASN ASN THR SEQRES 48 A 676 ARG ALA LYS GLU SER GLY GLN LYS TYR MSE LYS ALA LYS SEQRES 49 A 676 LEU ASP ARG TYR MSE PRO ASP LYS GLY GLY GLU LYS THR SEQRES 50 A 676 ALA VAL VAL LEU LYS PHE GLN LEU GLY THR SER ALA TYR SEQRES 51 A 676 ALA THR MSE ALA LEU ARG GLU LEU MSE LYS LEU GLU THR SEQRES 52 A 676 SER ARG ARG GLY ASP MSE CYS ASP VAL LYS GLU ASN ILE MODRES 7MZV MSE A 88 MET MODIFIED RESIDUE MODRES 7MZV MSE A 145 MET MODIFIED RESIDUE MODRES 7MZV MSE A 232 MET MODIFIED RESIDUE MODRES 7MZV MSE A 285 MET MODIFIED RESIDUE MODRES 7MZV MSE A 345 MET MODIFIED RESIDUE MODRES 7MZV MSE A 405 MET MODIFIED RESIDUE MODRES 7MZV MSE A 440 MET MODIFIED RESIDUE MODRES 7MZV MSE A 449 MET MODIFIED RESIDUE MODRES 7MZV MSE A 525 MET MODIFIED RESIDUE MODRES 7MZV MSE A 558 MET MODIFIED RESIDUE MODRES 7MZV MSE A 563 MET MODIFIED RESIDUE MODRES 7MZV MSE A 621 MET MODIFIED RESIDUE MODRES 7MZV MSE A 629 MET MODIFIED RESIDUE MODRES 7MZV MSE A 653 MET MODIFIED RESIDUE MODRES 7MZV MSE A 659 MET MODIFIED RESIDUE HET MSE A 88 17 HET MSE A 145 17 HET MSE A 232 17 HET MSE A 285 17 HET MSE A 345 17 HET MSE A 405 17 HET MSE A 440 17 HET MSE A 449 17 HET MSE A 525 17 HET MSE A 558 17 HET MSE A 563 17 HET MSE A 621 17 HET MSE A 629 17 HET MSE A 653 17 HET MSE A 659 17 HET SO4 A1001 5 HET SO4 A1002 5 HET SO4 A1003 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 15(C5 H11 N O2 SE) FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *12(H2 O) HELIX 1 AA1 GLU A 40 GLY A 44 5 5 HELIX 2 AA2 ARG A 63 THR A 65 5 3 HELIX 3 AA3 LYS A 96 PHE A 113 1 18 HELIX 4 AA4 ASP A 116 PHE A 127 1 12 HELIX 5 AA5 GLY A 128 THR A 141 1 14 HELIX 6 AA6 ASP A 153 ARG A 157 5 5 HELIX 7 AA7 THR A 158 GLU A 166 1 9 HELIX 8 AA8 LYS A 198 ARG A 203 5 6 HELIX 9 AA9 ASP A 230 LEU A 242 1 13 HELIX 10 AB1 GLY A 271 LEU A 278 1 8 HELIX 11 AB2 ASN A 279 THR A 281 5 3 HELIX 12 AB3 SER A 322 ASN A 337 1 16 HELIX 13 AB4 GLY A 344 PHE A 348 5 5 HELIX 14 AB5 SER A 354 LEU A 364 1 11 HELIX 15 AB6 ASN A 366 SER A 376 1 11 HELIX 16 AB7 GLU A 387 THR A 395 1 9 HELIX 17 AB8 ASP A 397 LYS A 403 1 7 HELIX 18 AB9 GLU A 412 ASN A 413 5 2 HELIX 19 AC1 LEU A 415 LEU A 415 5 1 HELIX 20 AC2 LEU A 416 ASN A 421 1 6 HELIX 21 AC3 SER A 431 MSE A 440 1 10 HELIX 22 AC4 ARG A 444 HIS A 470 1 27 HELIX 23 AC5 THR A 514 SER A 520 1 7 HELIX 24 AC6 THR A 524 ASP A 527 5 4 HELIX 25 AC7 ASN A 542 ASP A 556 1 15 HELIX 26 AC8 THR A 603 GLY A 617 1 15 HELIX 27 AC9 MSE A 621 LEU A 625 5 5 HELIX 28 AD1 TYR A 650 LYS A 660 1 11 SHEET 1 AA1 6 ARG A 57 GLN A 59 0 SHEET 2 AA1 6 GLY A 304 THR A 315 -1 O ARG A 312 N GLN A 59 SHEET 3 AA1 6 PHE A 67 ILE A 72 -1 N ASN A 70 O GLU A 306 SHEET 4 AA1 6 VAL A 260 CYS A 262 1 O CYS A 262 N GLU A 71 SHEET 5 AA1 6 PHE A 219 GLU A 227 -1 N LYS A 226 O THR A 261 SHEET 6 AA1 6 MSE A 285 SER A 293 -1 O GLY A 288 N THR A 223 SHEET 1 AA2 8 ILE A 249 TYR A 251 0 SHEET 2 AA2 8 ARG A 264 SER A 268 -1 O SER A 266 N ARG A 250 SHEET 3 AA2 8 PHE A 219 GLU A 227 -1 N PHE A 222 O VAL A 265 SHEET 4 AA2 8 VAL A 260 CYS A 262 -1 O THR A 261 N LYS A 226 SHEET 5 AA2 8 PHE A 67 ILE A 72 1 N GLU A 71 O CYS A 262 SHEET 6 AA2 8 GLY A 304 THR A 315 -1 O GLU A 306 N ASN A 70 SHEET 7 AA2 8 LYS A 636 GLY A 646 -1 O PHE A 643 N PHE A 307 SHEET 8 AA2 8 LYS A 584 TYR A 593 -1 N GLU A 587 O LYS A 642 SHEET 1 AA3 2 PHE A 339 ILE A 340 0 SHEET 2 AA3 2 ILE A 580 GLN A 581 -1 O GLN A 581 N PHE A 339 SHEET 1 AA4 2 LEU A 479 ILE A 481 0 SHEET 2 AA4 2 ALA A 510 ALA A 512 -1 O LYS A 511 N VAL A 480 SHEET 1 AA5 2 VAL A 529 PRO A 531 0 SHEET 2 AA5 2 TYR A 576 THR A 578 -1 O ARG A 577 N LEU A 530 LINK C LYS A 87 N MSE A 88 1555 1555 1.34 LINK C MSE A 88 N PRO A 89 1555 1555 1.36 LINK C LYS A 144 N MSE A 145 1555 1555 1.34 LINK C MSE A 145 N GLU A 146 1555 1555 1.34 LINK C THR A 231 N MSE A 232 1555 1555 1.34 LINK C MSE A 232 N GLU A 233 1555 1555 1.34 LINK C GLY A 284 N MSE A 285 1555 1555 1.34 LINK C MSE A 285 N ILE A 286 1555 1555 1.34 LINK C GLY A 344 N MSE A 345 1555 1555 1.34 LINK C MSE A 345 N GLN A 346 1555 1555 1.34 LINK C GLN A 404 N MSE A 405 1555 1555 1.34 LINK C MSE A 405 N PRO A 406 1555 1555 1.36 LINK C ILE A 439 N MSE A 440 1555 1555 1.34 LINK C MSE A 440 N LYS A 441 1555 1555 1.34 LINK C THR A 448 N MSE A 449 1555 1555 1.34 LINK C MSE A 449 N TYR A 450 1555 1555 1.34 LINK C THR A 524 N MSE A 525 1555 1555 1.34 LINK C MSE A 525 N GLU A 526 1555 1555 1.34 LINK C ASN A 557 N MSE A 558 1555 1555 1.34 LINK C MSE A 558 N ASP A 559 1555 1555 1.34 LINK C ASN A 562 N MSE A 563 1555 1555 1.34 LINK C MSE A 563 N ARG A 564 1555 1555 1.34 LINK C TYR A 620 N MSE A 621 1555 1555 1.34 LINK C MSE A 621 N LYS A 622 1555 1555 1.34 LINK C TYR A 628 N MSE A 629 1555 1555 1.34 LINK C MSE A 629 N PRO A 630 1555 1555 1.35 LINK C THR A 652 N MSE A 653 1555 1555 1.34 LINK C MSE A 653 N ALA A 654 1555 1555 1.34 LINK C LEU A 658 N MSE A 659 1555 1555 1.34 LINK C MSE A 659 N LYS A 660 1555 1555 1.34 CRYST1 117.890 171.800 105.340 90.00 90.00 90.00 C 2 2 2 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 0.008482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009493 0.00000