HEADER HYDROLASE(ENDORIBONUCLEASE) 06-JUL-93 1TRQ TITLE X-RAY CRYSTALLOGRAPHIC AND CALORIMERIC STUDIES OF THE EFFECTS OF THE TITLE 2 MUTATION TRP 59 TYR IN RIBONUCLEASE T1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE T1 ISOZYME; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.27.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS ORYZAE; SOURCE 3 ORGANISM_TAXID: 5062 KEYWDS HYDROLASE(ENDORIBONUCLEASE) EXPDTA X-RAY DIFFRACTION AUTHOR W.-D.SCHUBERT,W.SAENGER REVDAT 4 29-NOV-17 1TRQ 1 HELIX REVDAT 3 24-FEB-09 1TRQ 1 VERSN REVDAT 2 01-APR-03 1TRQ 1 JRNL REVDAT 1 30-APR-94 1TRQ 0 JRNL AUTH W.D.SCHUBERT,G.SCHLUCKEBIER,J.BACKMANN,J.GRANZIN,C.KISKER, JRNL AUTH 2 H.W.CHOE,U.HAHN,W.PFEIL,W.SAENGER JRNL TITL X-RAY CRYSTALLOGRAPHIC AND CALORIMETRIC STUDIES OF THE JRNL TITL 2 EFFECTS OF THE MUTATION TRP59-->TYR IN RIBONUCLEASE T1. JRNL REF EUR.J.BIOCHEM. V. 220 527 1994 JRNL REFN ISSN 0014-2956 JRNL PMID 8125111 JRNL DOI 10.1111/J.1432-1033.1994.TB18652.X REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6908 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1556 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.005 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.160 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TRQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL 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 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.10000 REMARK 290 SMTRY3 2 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 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 O HOH A 477 O HOH B 493 2756 2.19 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 SER A 37 70.19 52.66 REMARK 500 ASN A 44 41.81 88.19 REMARK 500 SER A 69 15.61 -142.65 REMARK 500 GLU A 82 -16.69 -49.50 REMARK 500 SER B 237 74.31 52.21 REMARK 500 ASN B 244 44.89 75.67 REMARK 500 ASN B 284 34.36 76.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 106 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD2 REMARK 620 2 ASP A 15 OD1 49.6 REMARK 620 3 HOH A 468 O 75.2 95.4 REMARK 620 4 HOH A 499 O 143.7 141.2 69.6 REMARK 620 5 HOH A 506 O 151.7 120.4 132.5 63.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 306 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 444 O REMARK 620 2 HOH B 487 O 88.5 REMARK 620 3 HOH B 479 O 95.5 86.2 REMARK 620 4 ASP B 215 OD1 77.1 131.5 140.5 REMARK 620 5 HOH B 414 O 161.6 108.5 92.6 86.2 REMARK 620 6 ASP B 215 OD2 88.5 175.7 91.0 50.6 74.9 REMARK 620 7 HOH B 456 O 98.0 61.7 144.6 74.7 84.6 121.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2GP A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2GP B 305 DBREF 1TRQ A 1 104 UNP P00651 RNT1_ASPOR 27 130 DBREF 1TRQ B 201 304 UNP P00651 RNT1_ASPOR 27 130 SEQADV 1TRQ LYS A 25 UNP P00651 GLN 51 CONFLICT SEQADV 1TRQ TYR A 59 UNP P00651 TRP 85 CONFLICT SEQADV 1TRQ LYS B 225 UNP P00651 GLN 51 CONFLICT SEQADV 1TRQ TYR B 259 UNP P00651 TRP 85 CONFLICT SEQRES 1 A 104 ALA CYS ASP TYR THR CYS GLY SER ASN CYS TYR SER SER SEQRES 2 A 104 SER ASP VAL SER THR ALA GLN ALA ALA GLY TYR LYS LEU SEQRES 3 A 104 HIS GLU ASP GLY GLU THR VAL GLY SER ASN SER TYR PRO SEQRES 4 A 104 HIS LYS TYR ASN ASN TYR GLU GLY PHE ASP PHE SER VAL SEQRES 5 A 104 SER SER PRO TYR TYR GLU TYR PRO ILE LEU SER SER GLY SEQRES 6 A 104 ASP VAL TYR SER GLY GLY SER PRO GLY ALA ASP ARG VAL SEQRES 7 A 104 VAL PHE ASN GLU ASN ASN GLN LEU ALA GLY VAL ILE THR SEQRES 8 A 104 HIS THR GLY ALA SER GLY ASN ASN PHE VAL GLU CYS THR SEQRES 1 B 104 ALA CYS ASP TYR THR CYS GLY SER ASN CYS TYR SER SER SEQRES 2 B 104 SER ASP VAL SER THR ALA GLN ALA ALA GLY TYR LYS LEU SEQRES 3 B 104 HIS GLU ASP GLY GLU THR VAL GLY SER ASN SER TYR PRO SEQRES 4 B 104 HIS LYS TYR ASN ASN TYR GLU GLY PHE ASP PHE SER VAL SEQRES 5 B 104 SER SER PRO TYR TYR GLU TYR PRO ILE LEU SER SER GLY SEQRES 6 B 104 ASP VAL TYR SER GLY GLY SER PRO GLY ALA ASP ARG VAL SEQRES 7 B 104 VAL PHE ASN GLU ASN ASN GLN LEU ALA GLY VAL ILE THR SEQRES 8 B 104 HIS THR GLY ALA SER GLY ASN ASN PHE VAL GLU CYS THR HET CA A 106 1 HET 2GP A 105 24 HET CA B 306 1 HET 2GP B 305 24 HETNAM CA CALCIUM ION HETNAM 2GP GUANOSINE-2'-MONOPHOSPHATE FORMUL 3 CA 2(CA 2+) FORMUL 4 2GP 2(C10 H14 N5 O8 P) FORMUL 7 HOH *119(H2 O) HELIX 1 A SER A 13 ASP A 29 1 17 HELIX 2 B SER B 213 ASP B 229 1 17 SHEET 1 1A 2 TYR A 4 CYS A 6 0 SHEET 2 1A 2 ASN A 9 SER A 12 -1 O TYR A 11 N TYR A 4 SHEET 1 2A 5 PRO A 39 TYR A 42 0 SHEET 2 2A 5 PRO A 55 LEU A 62 -1 O GLU A 58 N HIS A 40 SHEET 3 2A 5 ASP A 76 ASN A 81 -1 O VAL A 78 N TYR A 59 SHEET 4 2A 5 GLN A 85 THR A 91 -1 O ILE A 90 N ARG A 77 SHEET 5 2A 5 PHE A 100 CYS A 103 -1 N VAL A 101 O THR A 91 SHEET 1 3B 2 TYR B 204 CYS B 206 0 SHEET 2 3B 2 ASN B 209 SER B 212 -1 O TYR B 211 N TYR B 204 SHEET 1 4B 5 PRO B 239 TYR B 242 0 SHEET 2 4B 5 PRO B 255 LEU B 262 -1 O GLU B 258 N HIS B 240 SHEET 3 4B 5 ASP B 276 ASN B 281 -1 O VAL B 278 N TYR B 259 SHEET 4 4B 5 GLN B 285 THR B 291 -1 O ILE B 290 N ARG B 277 SHEET 5 4B 5 PHE B 300 CYS B 303 -1 N VAL B 301 O THR B 291 SSBOND 1 CYS A 2 CYS A 10 1555 1555 2.01 SSBOND 2 CYS A 6 CYS A 103 1555 1555 1.97 SSBOND 3 CYS B 202 CYS B 210 1555 1555 2.01 SSBOND 4 CYS B 206 CYS B 303 1555 1555 2.01 LINK CA CA A 106 OD2 ASP A 15 1555 1555 2.37 LINK CA CA A 106 OD1 ASP A 15 1555 1555 2.77 LINK CA CA A 106 O HOH A 468 1555 1555 2.27 LINK CA CA A 106 O HOH A 499 1555 1555 2.46 LINK CA CA A 106 O HOH A 506 1555 1555 3.22 LINK CA CA B 306 O HOH B 444 1555 1555 2.41 LINK CA CA B 306 O HOH B 487 1555 1555 3.15 LINK CA CA B 306 O HOH B 479 1555 1555 2.67 LINK CA CA B 306 OD1 ASP B 215 1555 1555 2.81 LINK CA CA B 306 O HOH B 414 1555 1555 2.65 LINK CA CA B 306 OD2 ASP B 215 1555 1555 2.09 LINK CA CA B 306 O HOH B 456 1555 1555 2.80 CISPEP 1 TYR A 38 PRO A 39 0 3.62 CISPEP 2 SER A 54 PRO A 55 0 3.92 CISPEP 3 TYR B 238 PRO B 239 0 2.18 CISPEP 4 SER B 254 PRO B 255 0 -0.09 SITE 1 AC1 3 ASP A 15 HOH A 468 HOH A 499 SITE 1 AC2 5 ASP B 215 HOH B 414 HOH B 444 HOH B 456 SITE 2 AC2 5 HOH B 479 SITE 1 AC3 13 TYR A 38 HIS A 40 LYS A 41 TYR A 42 SITE 2 AC3 13 ASN A 43 ASN A 44 TYR A 45 GLU A 46 SITE 3 AC3 13 GLU A 58 ARG A 77 HIS A 92 ASN A 98 SITE 4 AC3 13 PHE A 100 SITE 1 AC4 13 TYR B 238 HIS B 240 TYR B 242 ASN B 243 SITE 2 AC4 13 ASN B 244 TYR B 245 GLU B 246 GLU B 258 SITE 3 AC4 13 ARG B 277 HIS B 292 ASN B 298 ASN B 299 SITE 4 AC4 13 PHE B 300 CRYST1 49.340 48.200 40.150 90.00 90.29 90.00 P 1 21 1 4 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 0.020268 0.000000 0.000103 0.00000 SCALE2 0.000000 0.020747 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024907 0.00000