HEADER HYDROLASE 07-MAY-02 1LOY TITLE X-RAY STRUCTURE OF THE H40A/E58A MUTANT OF RIBONUCLEASE T1 COMPLEXED TITLE 2 WITH 3'-GUANOSINE MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYL-SPECIFIC RIBONUCLEASE T1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE T1; COMPND 5 EC: 3.1.27.3; COMPND 6 ENGINEERED: YES; COMPND 7 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMC KEYWDS RNASE, CATALYTIC DYAD, NUCLEOPHILE ACTIVATION, AB INITIO KEYWDS 2 CALCULATIONS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.MIGNON,J.STEYAERT,R.LORIS,P.GEERLINGS,S.LOVERIX REVDAT 6 16-AUG-23 1LOY 1 REMARK REVDAT 5 27-OCT-21 1LOY 1 REMARK SEQADV LINK REVDAT 4 24-FEB-09 1LOY 1 VERSN REVDAT 3 01-APR-03 1LOY 1 JRNL REVDAT 2 06-NOV-02 1LOY 1 JRNL REVDAT 1 21-AUG-02 1LOY 0 JRNL AUTH P.MIGNON,J.STEYAERT,R.LORIS,P.GEERLINGS,S.LOVERIX JRNL TITL A NUCLEOPHILE ACTIVATION DYAD IN RIBONUCLEASES. A COMBINED JRNL TITL 2 X-RAY CRYSTALLOGRAPHIC/AB INITIO QUANTUM CHEMICAL STUDY JRNL REF J.BIOL.CHEM. V. 277 36770 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12122018 JRNL DOI 10.1074/JBC.M206461200 REMARK 2 REMARK 2 RESOLUTION. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.001 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 : 12848 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 SET) : 0.189 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2682 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 : 772 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.90 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL 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 1LOY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000016147. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-00 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL 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 : 12848 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 33.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05900 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) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45700 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1RGA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD,CACL2,SODIUM ACETATE, PH 4.2, REMARK 280 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 20.01150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.05250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.40600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.05250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.01150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.40600 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 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 LYS A 25 CD CE NZ REMARK 480 ASN A 36 CB CG OD1 ND2 REMARK 480 LYS A 41 CE NZ 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 105 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD1 REMARK 620 2 ASP A 15 OD2 51.8 REMARK 620 3 HOH A 216 O 134.5 83.4 REMARK 620 4 HOH A 217 O 141.2 146.6 80.1 REMARK 620 5 HOH A 218 O 73.7 125.2 151.4 75.4 REMARK 620 6 HOH A 219 O 81.5 83.3 86.7 124.2 95.0 REMARK 620 7 HOH A 222 O 80.8 76.6 97.4 77.0 91.2 158.8 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 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3GP A 106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RGA RELATED DB: PDB REMARK 900 RNASE T1 H40A COMPLEXED WITH 3'-GMP REMARK 900 RELATED ID: 1RLS RELATED DB: PDB REMARK 900 RNASE T1 H40A/E58A COMPLEXED WITH 3'-GMP REMARK 900 RELATED ID: 1LOV RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE E58A MUTANT OF RIBONUCLEASE T1 COMPLEXED REMARK 900 WITH 3'-GUANOSINE MONOPHOSPHATE REMARK 900 RELATED ID: 1LOW RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE H40A MUTANT OF RIBONUCLEASE T1 COMPLEXED REMARK 900 WITH 3'-GUANOSINE MONOPHOSPHATE REMARK 999 REMARK 999 THE ISOZYME OF RNASE T1 USED HERE CONTAINS A LYSINE AT POSITION REMARK 999 25. DBREF 1LOY A 1 104 UNP P00651 RNT1_ASPOR 27 130 SEQADV 1LOY LYS A 25 UNP P00651 GLN 51 SEE REMARK 999 SEQADV 1LOY ALA A 40 UNP P00651 HIS 66 ENGINEERED MUTATION SEQADV 1LOY ALA A 58 UNP P00651 GLU 84 ENGINEERED MUTATION 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 ALA LYS TYR ASN ASN TYR GLU GLY PHE ASP PHE SER VAL SEQRES 5 A 104 SER SER PRO TYR TYR ALA 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 CA A 105 1 HET 3GP A 106 24 HETNAM CA CALCIUM ION HETNAM 3GP GUANOSINE-3'-MONOPHOSPHATE FORMUL 2 CA CA 2+ FORMUL 3 3GP C10 H14 N5 O8 P FORMUL 4 HOH *71(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 TYR A 11 N TYR A 4 SHEET 1 B 5 ALA A 40 TYR A 42 0 SHEET 2 B 5 TYR A 56 PRO A 60 -1 O ALA A 58 N ALA A 40 SHEET 3 B 5 ASP A 76 ASN A 81 -1 O VAL A 78 N TRP A 59 SHEET 4 B 5 LEU A 86 THR A 91 -1 O ALA A 87 N 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 2.03 SSBOND 2 CYS A 6 CYS A 103 1555 1555 2.03 LINK OD1 ASP A 15 CA CA A 105 1555 1555 2.59 LINK OD2 ASP A 15 CA CA A 105 1555 1555 2.42 LINK CA CA A 105 O HOH A 216 1555 1555 2.33 LINK CA CA A 105 O HOH A 217 1555 1555 2.52 LINK CA CA A 105 O HOH A 218 1555 1555 2.41 LINK CA CA A 105 O HOH A 219 1555 1555 2.58 LINK CA CA A 105 O HOH A 222 1555 1555 2.45 CISPEP 1 TYR A 38 PRO A 39 0 -0.28 CISPEP 2 SER A 54 PRO A 55 0 -0.17 SITE 1 AC1 6 ASP A 15 HOH A 216 HOH A 217 HOH A 218 SITE 2 AC1 6 HOH A 219 HOH A 222 SITE 1 AC2 12 LYS A 41 TYR A 42 ASN A 43 ASN A 44 SITE 2 AC2 12 TYR A 45 GLU A 46 ASP A 49 HIS A 92 SITE 3 AC2 12 ASN A 98 PHE A 100 HOH A 203 HOH A 244 CRYST1 40.023 44.812 50.105 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 0.024986 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019958 0.00000