HEADER HYDROLASE 19-JAN-01 1HYF TITLE RIBONUCLEASE T1 V16A MUTANT IN COMPLEX WITH SR2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYL-SPECIFIC RIBONUCLEASE T1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.27.3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS ORYZAE; SOURCE 3 ORGANISM_TAXID: 5062; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBONUCLEASE, STABILITY, METAL BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.DE SWARTE,S.DE VOS,U.LANGHORST,J.STEYAERT,R.LORIS REVDAT 6 09-OCT-24 1HYF 1 REMARK REVDAT 5 10-NOV-21 1HYF 1 REMARK SEQADV LINK REVDAT 4 21-MAR-18 1HYF 1 REMARK REVDAT 3 24-FEB-09 1HYF 1 VERSN REVDAT 2 31-DEC-02 1HYF 1 REMARK REVDAT 1 14-FEB-01 1HYF 0 JRNL AUTH J.DESWARTE,S.DE VOS,U.LANGHORST,J.STEYAERT,R.LORIS JRNL TITL THE CONTRIBUTION OF METAL IONS TO THE CONFORMATIONAL JRNL TITL 2 STABILITY OF RIBONUCLEASE T1: CRYSTAL VERSUS SOLUTION. JRNL REF EUR.J.BIOCHEM. V. 268 3993 2001 JRNL REFN ISSN 0014-2956 JRNL PMID 11453993 JRNL DOI 10.1046/J.1432-1327.2001.02310.X REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 833 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 779 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.478 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000012685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.2 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : GRAPHITE MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10427 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 7.770 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.48600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.180 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, CALCIUM CHLORIDE, ACETATE, PH REMARK 280 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.22250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.04650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.58300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.04650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.22250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.58300 REMARK 290 SMTRY3 4 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 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 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 SR A 105 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD2 REMARK 620 2 ASP A 15 OD1 48.7 REMARK 620 3 HOH A 201 O 78.8 127.0 REMARK 620 4 HOH A 202 O 134.2 138.4 81.0 REMARK 620 5 HOH A 203 O 140.9 135.2 79.5 72.9 REMARK 620 6 HOH A 204 O 122.7 74.9 158.1 80.1 84.4 REMARK 620 7 HOH A 205 O 78.5 76.9 87.4 140.9 68.3 100.4 REMARK 620 8 HOH A 207 O 71.4 78.0 93.5 69.3 142.2 90.2 149.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2GP A 106 DBREF 1HYF A 1 104 UNP P00651 RNT1_ASPOR 27 130 SEQADV 1HYF ALA A 16 UNP P00651 VAL 42 ENGINEERED MUTATION SEQADV 1HYF LYS A 25 UNP P00651 GLN 51 SEE REMARK 999 SEQRES 1 A 104 ALA CYS ASP TYR THR CYS GLY SER ASN CYS TYR SER SER SEQRES 2 A 104 SER ASP ALA 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 TRP 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 HET SR A 105 1 HET 2GP A 106 24 HETNAM SR STRONTIUM ION HETNAM 2GP GUANOSINE-2'-MONOPHOSPHATE FORMUL 2 SR SR 2+ FORMUL 3 2GP C10 H14 N5 O8 P FORMUL 4 HOH *95(H2 O) HELIX 1 1 SER A 12 GLY A 30 1 19 SHEET 1 A 2 TYR A 4 CYS A 6 0 SHEET 2 A 2 ASN A 9 TYR A 11 -1 O ASN A 9 N CYS A 6 SHEET 1 B 5 HIS A 40 TYR A 42 0 SHEET 2 B 5 TYR A 56 PRO A 60 -1 O TYR A 56 N TYR A 42 SHEET 3 B 5 ASP A 76 ASN A 81 -1 N VAL A 78 O TRP A 59 SHEET 4 B 5 LEU A 86 THR A 91 -1 N ALA A 87 O VAL A 79 SHEET 5 B 5 VAL A 101 GLU A 102 -1 O VAL A 101 N THR A 91 SSBOND 1 CYS A 2 CYS A 10 1555 1555 2.02 SSBOND 2 CYS A 6 CYS A 103 1555 1555 2.03 LINK OD2 ASP A 15 SR SR A 105 1555 1555 2.66 LINK OD1 ASP A 15 SR SR A 105 1555 1555 2.66 LINK SR SR A 105 O HOH A 201 1555 1555 2.53 LINK SR SR A 105 O HOH A 202 1555 1555 2.60 LINK SR SR A 105 O HOH A 203 1555 1555 2.64 LINK SR SR A 105 O HOH A 204 1555 1555 2.51 LINK SR SR A 105 O HOH A 205 1555 1555 2.62 LINK SR SR A 105 O HOH A 207 1555 1555 2.64 CISPEP 1 TYR A 38 PRO A 39 0 -0.59 CISPEP 2 SER A 54 PRO A 55 0 -0.02 SITE 1 AC1 7 ASP A 15 HOH A 201 HOH A 202 HOH A 203 SITE 2 AC1 7 HOH A 204 HOH A 205 HOH A 207 SITE 1 AC2 14 TYR A 38 HIS A 40 LYS A 41 TYR A 42 SITE 2 AC2 14 ASN A 43 ASN A 44 TYR A 45 GLU A 46 SITE 3 AC2 14 GLU A 58 ASN A 98 PHE A 100 HOH A 244 SITE 4 AC2 14 HOH A 245 HOH A 264 CRYST1 40.445 47.166 50.093 90.00 90.00 90.00 P 21 21 21 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 0.024725 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021202 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019963 0.00000