HEADER ENDORIBONUCLEASE 09-DEC-97 5GSP TITLE RIBONUCLEASE T1/3'-GMP, 9 WEEKS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE T1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE T1; COMPND 5 EC: 3.1.27.3; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: COMPLEXED WITH 3'GMP IN TWO DIFFERENT CONFORMATIONS 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 HYDROLASE, ENDORIBONUCLEASE, RIBONUCLEASE, ENDONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR I.ZEGERS,L.WYNS REVDAT 4 30-OCT-24 5GSP 1 REMARK REVDAT 3 09-AUG-23 5GSP 1 REMARK LINK REVDAT 2 24-FEB-09 5GSP 1 VERSN REVDAT 1 18-MAR-98 5GSP 0 JRNL AUTH I.ZEGERS,R.LORIS,G.DEHOLLANDER,A.FATTAH HAIKAL,F.POORTMANS, JRNL AUTH 2 J.STEYAERT,L.WYNS JRNL TITL HYDROLYSIS OF A SLOW CYCLIC THIOPHOSPHATE SUBSTRATE OF RNASE JRNL TITL 2 T1 ANALYZED BY TIME-RESOLVED CRYSTALLOGRAPHY. JRNL REF NAT.STRUCT.BIOL. V. 5 280 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9546218 JRNL DOI 10.1038/NSB0498-280 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 9313 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) : 0.170 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 964 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 972 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 122 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 : 781 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 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) : 0.060 REMARK 3 BOND ANGLES (DEGREES) : 1.488 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.44 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.034 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 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GSP 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_1000179718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-97 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(002) 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 : 9454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37100 REMARK 200 FOR SHELL : 6.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1RGA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM NAAC PH 4.2 2 MM CACL2 55 % MPD 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 24.11500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.26500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.26500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.11500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.54500 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 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 76.76 50.95 REMARK 500 ASN A 81 -169.86 -112.04 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 107 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD2 REMARK 620 2 ASP A 15 OD1 54.6 REMARK 620 3 HOH A 131 O 87.8 142.3 REMARK 620 4 HOH A 137 O 84.0 80.8 93.1 REMARK 620 5 HOH A 146 O 79.9 73.5 106.0 154.3 REMARK 620 6 HOH A 166 O 123.6 69.0 148.2 86.0 86.5 REMARK 620 7 HOH A 174 O 147.6 139.9 73.8 122.6 80.0 80.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: BI1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: CAL REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3GP A 105 DBREF 5GSP A 1 104 UNP P00651 RNT1_ASPOR 22 125 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 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 107 1 HET 3GP A 105 48 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 *128(H2 O) HELIX 1 1 SER A 13 ASP A 29 1 17 SHEET 1 S1 2 TYR A 4 CYS A 6 0 SHEET 2 S1 2 ASN A 9 SER A 12 -1 O TYR A 11 N TYR A 4 SHEET 1 S2 5 PRO A 39 TYR A 42 0 SHEET 2 S2 5 PRO A 55 LEU A 62 -1 O GLU A 58 N HIS A 40 SHEET 3 S2 5 ASP A 76 ASN A 81 -1 O VAL A 78 N TRP A 59 SHEET 4 S2 5 GLN A 85 THR A 91 -1 O ILE A 90 N ARG A 77 SHEET 5 S2 5 PHE A 100 CYS A 103 -1 N VAL A 101 O 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 CA CA A 107 1555 1555 2.25 LINK OD1 ASP A 15 CA CA A 107 1555 1555 2.52 LINK CA CA A 107 O HOH A 131 1555 1555 2.47 LINK CA CA A 107 O HOH A 137 1555 1555 2.78 LINK CA CA A 107 O HOH A 146 1555 1555 3.06 LINK CA CA A 107 O HOH A 166 1555 1555 2.59 LINK CA CA A 107 O HOH A 174 1555 1555 2.79 CISPEP 1 TYR A 38 PRO A 39 0 -0.14 CISPEP 2 SER A 54 PRO A 55 0 -0.25 SITE 1 CAT 5 TYR A 38 HIS A 40 GLU A 58 ARG A 77 SITE 2 CAT 5 HIS A 92 SITE 1 BI1 5 TYR A 42 ASN A 43 ASN A 44 TYR A 45 SITE 2 BI1 5 GLU A 46 SITE 1 CAL 1 ASP A 15 SITE 1 AC1 6 ASP A 15 HOH A 131 HOH A 137 HOH A 146 SITE 2 AC1 6 HOH A 166 HOH A 174 SITE 1 AC2 14 ASN A 36 TYR A 38 HIS A 40 LYS A 41 SITE 2 AC2 14 TYR A 42 ASN A 43 ASN A 44 TYR A 45 SITE 3 AC2 14 GLU A 46 GLU A 58 ARG A 77 HIS A 92 SITE 4 AC2 14 ASN A 98 PHE A 100 CRYST1 48.230 51.090 40.530 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 0.020734 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024673 0.00000