PDB Short entry for 1T4O HEADER HYDROLASE 30-APR-04 1T4O TITLE CRYSTAL STRUCTURE OF RNT1P DSRBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE III; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DSRBD; COMPND 5 SYNONYM: RNASE III, RNT1P; COMPND 6 EC: 3.1.26.3; 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: RNT1, YMR239C, YM9408.01C, YM9959.21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNT1P, DSRBD, RNA-BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.LEULLIOT,S.QUEVILLON-CHERUEL,M.GRAILLE,H.VAN TILBEURGH,T.C.LEEPER, AUTHOR 2 K.S.GODIN,T.E.EDWARDS,S.T.SIGURDSSON,N.ROZENKRANTS,R.J.NAGEL,M.ARES AUTHOR 3 JR.,G.VARANI REVDAT 4 23-AUG-23 1T4O 1 SEQADV REVDAT 3 24-FEB-09 1T4O 1 VERSN REVDAT 2 17-AUG-04 1T4O 1 JRNL REVDAT 1 22-JUN-04 1T4O 0 JRNL AUTH N.LEULLIOT,S.QUEVILLON-CHERUEL,M.GRAILLE,H.VAN TILBEURGH, JRNL AUTH 2 T.C.LEEPER,K.S.GODIN,T.E.EDWARDS,S.T.SIGURDSSON, JRNL AUTH 3 N.ROZENKRANTS,R.J.NAGEL,M.ARES,G.VARANI JRNL TITL A NEW ALPHA-HELICAL EXTENSION PROMOTES RNA BINDING BY THE JRNL TITL 2 DSRBD OF RNT1P RNASE III JRNL REF EMBO J. V. 23 2468 2004 JRNL REFN ISSN 0261-4189 JRNL PMID 15192703 JRNL DOI 10.1038/SJ.EMBOJ.7600260 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 7162 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 779 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 398 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1302 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.02000 REMARK 3 B22 (A**2) : 0.91000 REMARK 3 B33 (A**2) : -0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.426 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.311 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.233 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.581 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1278 ; 0.032 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1212 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1714 ; 2.490 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2790 ; 1.200 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 166 ; 8.328 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 198 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1418 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 255 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 274 ; 0.264 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1353 ; 0.258 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 824 ; 0.107 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 43 ; 0.249 ; 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): 10 ; 0.233 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 54 ; 0.291 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.303 ; 0.200 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): 829 ; 1.268 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1319 ; 2.232 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 449 ; 3.149 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 395 ; 5.223 ; 4.500 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1T4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022307. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7943 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 48.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1T4N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 30% PEG 4000, REMARK 280 12% MPD, 0.1M TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K, PH 8.50 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 36.90750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.15600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.90750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.15600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 361 REMARK 465 LYS A 362 REMARK 465 GLN A 444 REMARK 465 ARG A 445 REMARK 465 ALA A 446 REMARK 465 ALA A 447 REMARK 465 ILE A 448 REMARK 465 PRO A 449 REMARK 465 ARG A 450 REMARK 465 SER A 451 REMARK 465 GLU A 452 REMARK 465 SER A 453 REMARK 465 VAL A 454 REMARK 465 LEU A 455 REMARK 465 LYS A 456 REMARK 465 ASP A 457 REMARK 465 PRO A 458 REMARK 465 SER A 459 REMARK 465 GLN A 460 REMARK 465 LYS A 461 REMARK 465 ASN A 462 REMARK 465 LYS A 463 REMARK 465 LYS A 464 REMARK 465 ARG A 465 REMARK 465 LYS A 466 REMARK 465 PHE A 467 REMARK 465 SER A 468 REMARK 465 ASP A 469 REMARK 465 THR A 470 REMARK 465 SER A 471 REMARK 465 HIS A 472 REMARK 465 HIS A 473 REMARK 465 HIS A 474 REMARK 465 HIS A 475 REMARK 465 HIS A 476 REMARK 465 HIS A 477 REMARK 465 PRO B 449 REMARK 465 ARG B 450 REMARK 465 SER B 451 REMARK 465 GLU B 452 REMARK 465 SER B 453 REMARK 465 VAL B 454 REMARK 465 LEU B 455 REMARK 465 LYS B 456 REMARK 465 ASP B 457 REMARK 465 PRO B 458 REMARK 465 SER B 459 REMARK 465 GLN B 460 REMARK 465 LYS B 461 REMARK 465 ASN B 462 REMARK 465 LYS B 463 REMARK 465 LYS B 464 REMARK 465 ARG B 465 REMARK 465 LYS B 466 REMARK 465 PHE B 467 REMARK 465 SER B 468 REMARK 465 ASP B 469 REMARK 465 THR B 470 REMARK 465 SER B 471 REMARK 465 HIS B 472 REMARK 465 HIS B 473 REMARK 465 HIS B 474 REMARK 465 HIS B 475 REMARK 465 HIS B 476 REMARK 465 HIS B 477 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLY B 407 N REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU A 366 CD2 REMARK 480 MET A 368 CE REMARK 480 LYS A 392 CG CD CE NZ REMARK 480 LYS A 421 CD CE REMARK 480 LYS A 436 CD CE NZ REMARK 480 MET A 437 CE REMARK 480 MET B 361 N CA CB REMARK 480 THR B 363 OG1 REMARK 480 ASN B 369 OD1 REMARK 480 LEU B 377 CD1 REMARK 480 LEU B 385 CD2 REMARK 480 LYS B 392 CD CE NZ REMARK 480 VAL B 416 CG1 REMARK 480 ILE B 420 CG2 REMARK 480 ARG B 433 NH1 NH2 REMARK 480 LYS B 435 CG REMARK 480 LYS B 436 CG CD CE REMARK 480 ALA B 442 CB REMARK 480 LYS B 443 CE NZ REMARK 480 GLN B 444 NE2 REMARK 480 ARG B 445 NH1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 23 O HOH A 27 1.81 REMARK 500 NZ LYS A 391 O ASN A 399 2.02 REMARK 500 O HOH B 16 O HOH B 20 2.17 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 GLN A 373 N MET B 361 4546 1.20 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 LEU A 366 CG LEU A 366 CD2 -0.364 REMARK 500 LYS A 421 CE LYS A 421 NZ 0.214 REMARK 500 TYR A 441 CE1 TYR A 441 CZ -0.093 REMARK 500 MET B 361 CB MET B 361 CG -0.928 REMARK 500 THR B 363 CB THR B 363 OG1 -0.299 REMARK 500 ASN B 369 CG ASN B 369 OD1 -0.207 REMARK 500 TYR B 375 CE2 TYR B 375 CD2 0.096 REMARK 500 LEU B 377 CG LEU B 377 CD1 -0.333 REMARK 500 LEU B 385 CG LEU B 385 CD2 -0.302 REMARK 500 ARG B 433 CZ ARG B 433 NH1 0.585 REMARK 500 ARG B 433 CZ ARG B 433 NH2 0.120 REMARK 500 LYS B 435 CB LYS B 435 CG -0.185 REMARK 500 LYS B 435 CG LYS B 435 CD 0.282 REMARK 500 LYS B 436 CE LYS B 436 NZ -0.840 REMARK 500 LYS B 443 CD LYS B 443 CE -0.212 REMARK 500 ARG B 445 CZ ARG B 445 NH1 -0.798 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 ASP A 364 CB - CG - OD2 ANGL. DEV. = 8.0 DEGREES REMARK 500 LEU A 366 CD1 - CG - CD2 ANGL. DEV. = -26.2 DEGREES REMARK 500 LEU A 366 CB - CG - CD2 ANGL. DEV. = 43.9 DEGREES REMARK 500 MET A 368 CG - SD - CE ANGL. DEV. = 13.9 DEGREES REMARK 500 ASP A 408 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 LYS A 421 CD - CE - NZ ANGL. DEV. = 15.7 DEGREES REMARK 500 ARG A 426 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 426 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 MET A 437 CG - SD - CE ANGL. DEV. = 34.5 DEGREES REMARK 500 ASP A 439 CB - CG - OD2 ANGL. DEV. = 8.6 DEGREES REMARK 500 MET B 361 CB - CG - SD ANGL. DEV. = 18.3 DEGREES REMARK 500 MET B 361 CA - C - O ANGL. DEV. = -83.7 DEGREES REMARK 500 MET B 361 CA - C - N ANGL. DEV. = -17.6 DEGREES REMARK 500 ASP B 367 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASN B 369 OD1 - CG - ND2 ANGL. DEV. = -20.8 DEGREES REMARK 500 ARG B 372 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 LEU B 377 CB - CG - CD1 ANGL. DEV. = 30.9 DEGREES REMARK 500 ARG B 384 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 384 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 LEU B 385 CB - CG - CD2 ANGL. DEV. = 25.9 DEGREES REMARK 500 ASP B 397 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ILE B 420 CA - CB - CG2 ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG B 426 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 426 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 433 NH1 - CZ - NH2 ANGL. DEV. = -34.3 DEGREES REMARK 500 ARG B 433 NE - CZ - NH1 ANGL. DEV. = -38.6 DEGREES REMARK 500 ARG B 433 NE - CZ - NH2 ANGL. DEV. = -20.9 DEGREES REMARK 500 ASP B 434 CB - CG - OD2 ANGL. DEV. = 8.0 DEGREES REMARK 500 LYS B 435 CA - CB - CG ANGL. DEV. = 13.2 DEGREES REMARK 500 LYS B 435 CB - CG - CD ANGL. DEV. = 26.1 DEGREES REMARK 500 LYS B 435 CG - CD - CE ANGL. DEV. = -18.9 DEGREES REMARK 500 LYS B 436 CD - CE - NZ ANGL. DEV. = -23.9 DEGREES REMARK 500 GLN B 444 OE1 - CD - NE2 ANGL. DEV. = -22.3 DEGREES REMARK 500 ARG B 445 NH1 - CZ - NH2 ANGL. DEV. = -17.4 DEGREES REMARK 500 ARG B 445 NE - CZ - NH1 ANGL. DEV. = 18.0 DEGREES REMARK 500 ARG B 445 NE - CZ - NH2 ANGL. DEV. = -3.4 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 366 131.08 -173.96 REMARK 500 ALA A 442 26.66 -71.78 REMARK 500 LEU B 366 138.76 -178.98 REMARK 500 LYS B 391 103.98 -170.82 REMARK 500 THR B 394 -176.16 66.56 REMARK 500 VAL B 396 -28.67 -144.96 REMARK 500 ALA B 447 125.18 76.87 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 MET B 361 LYS B 362 125.59 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 ASN B 369 0.10 SIDE CHAIN REMARK 500 ARG B 433 0.33 SIDE CHAIN REMARK 500 GLN B 444 0.21 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MET B 361 -33.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T4N RELATED DB: PDB REMARK 900 SAME PROTEIN SOLVED BY NMR DBREF 1T4O A 362 471 UNP Q02555 RNT1_YEAST 362 471 DBREF 1T4O B 362 471 UNP Q02555 RNT1_YEAST 362 471 SEQADV 1T4O MET A 361 UNP Q02555 INITIATING METHIONINE SEQADV 1T4O HIS A 472 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS A 473 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS A 474 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS A 475 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS A 476 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS A 477 UNP Q02555 EXPRESSION TAG SEQADV 1T4O MET B 361 UNP Q02555 INITIATING METHIONINE SEQADV 1T4O HIS B 472 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS B 473 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS B 474 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS B 475 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS B 476 UNP Q02555 EXPRESSION TAG SEQADV 1T4O HIS B 477 UNP Q02555 EXPRESSION TAG SEQRES 1 A 117 MET LYS THR ASP LYS LEU ASP MET ASN ALA LYS ARG GLN SEQRES 2 A 117 LEU TYR SER LEU ILE GLY TYR ALA SER LEU ARG LEU HIS SEQRES 3 A 117 TYR VAL THR VAL LYS LYS PRO THR ALA VAL ASP PRO ASN SEQRES 4 A 117 SER ILE VAL GLU CYS ARG VAL GLY ASP GLY THR VAL LEU SEQRES 5 A 117 GLY THR GLY VAL GLY ARG ASN ILE LYS ILE ALA GLY ILE SEQRES 6 A 117 ARG ALA ALA GLU ASN ALA LEU ARG ASP LYS LYS MET LEU SEQRES 7 A 117 ASP PHE TYR ALA LYS GLN ARG ALA ALA ILE PRO ARG SER SEQRES 8 A 117 GLU SER VAL LEU LYS ASP PRO SER GLN LYS ASN LYS LYS SEQRES 9 A 117 ARG LYS PHE SER ASP THR SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 117 MET LYS THR ASP LYS LEU ASP MET ASN ALA LYS ARG GLN SEQRES 2 B 117 LEU TYR SER LEU ILE GLY TYR ALA SER LEU ARG LEU HIS SEQRES 3 B 117 TYR VAL THR VAL LYS LYS PRO THR ALA VAL ASP PRO ASN SEQRES 4 B 117 SER ILE VAL GLU CYS ARG VAL GLY ASP GLY THR VAL LEU SEQRES 5 B 117 GLY THR GLY VAL GLY ARG ASN ILE LYS ILE ALA GLY ILE SEQRES 6 B 117 ARG ALA ALA GLU ASN ALA LEU ARG ASP LYS LYS MET LEU SEQRES 7 B 117 ASP PHE TYR ALA LYS GLN ARG ALA ALA ILE PRO ARG SER SEQRES 8 B 117 GLU SER VAL LEU LYS ASP PRO SER GLN LYS ASN LYS LYS SEQRES 9 B 117 ARG LYS PHE SER ASP THR SER HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *33(H2 O) HELIX 1 1 ASN A 369 GLY A 379 1 11 HELIX 2 2 TYR A 380 ARG A 384 5 5 HELIX 3 3 ASN A 419 ASP A 434 1 16 HELIX 4 4 ASP A 434 ALA A 442 1 9 HELIX 5 5 ASN B 369 GLY B 379 1 11 HELIX 6 6 ASN B 419 ASP B 434 1 16 HELIX 7 7 ASP B 434 ALA B 446 1 13 SHEET 1 A 3 HIS A 386 LYS A 391 0 SHEET 2 A 3 SER A 400 ARG A 405 -1 O ARG A 405 N HIS A 386 SHEET 3 A 3 VAL A 411 GLY A 417 -1 O GLY A 415 N VAL A 402 SHEET 1 B 3 HIS B 386 LYS B 391 0 SHEET 2 B 3 SER B 400 ARG B 405 -1 O ARG B 405 N HIS B 386 SHEET 3 B 3 VAL B 411 GLY B 417 -1 O LEU B 412 N CYS B 404 CRYST1 73.815 68.312 57.178 90.00 121.91 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 0.013547 0.000000 0.008436 0.00000 SCALE2 0.000000 0.014639 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020603 0.00000