HEADER HYDROLASE 14-SEP-98 3BU4 TITLE RIBONUCLEASE T1 COMPLEX WITH 2'GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RIBONUCLEASE T1); COMPND 3 CHAIN: A; 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; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PMC5-RT1; SOURCE 7 EXPRESSION_SYSTEM_GENE: SYNTHETIC GENE KEYWDS ENDORIBONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.LORIS,S.DEVOS,U.LANGHORST,K.DECANNIERE,J.BOUCKAERT,D.MAES, AUTHOR 2 T.R.TRANSUE,J.STEYAERT REVDAT 5 30-AUG-23 3BU4 1 REMARK SEQADV LINK REVDAT 4 24-FEB-09 3BU4 1 VERSN REVDAT 3 01-APR-03 3BU4 1 JRNL REVDAT 2 22-DEC-99 3BU4 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 23-SEP-98 3BU4 0 JRNL AUTH R.LORIS,U.LANGHORST,S.DE VOS,K.DECANNIERE,J.BOUCKAERT, JRNL AUTH 2 D.MAES,T.R.TRANSUE,J.STEYAERT JRNL TITL CONSERVED WATER MOLECULES IN A LARGE FAMILY OF MICROBIAL JRNL TITL 2 RIBONUCLEASES. JRNL REF PROTEINS V. 36 117 1999 JRNL REFN ISSN 0887-3585 JRNL PMID 10373011 JRNL DOI 10.1002/(SICI)1097-0134(19990701)36:1<117::AID-PROT10>3.0.CO JRNL DOI 2 ;2-H REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 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) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 9670 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) : 0.199 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 967 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 : 781 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.732 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 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 3BU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-98 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 : 9718 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 3.950 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 22.9600 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1LRA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM NA-ACETATE PH 4.2 2 MM CACL2 55 REMARK 280 % 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 20.24000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.38500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.38500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.24000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.05000 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 CA A 106 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD1 REMARK 620 2 ASP A 15 OD2 51.4 REMARK 620 3 HOH A 113 O 120.0 69.0 REMARK 620 4 HOH A 115 O 140.0 141.5 83.7 REMARK 620 5 HOH A 117 O 72.8 72.0 84.3 78.9 REMARK 620 6 HOH A 128 O 81.0 82.5 99.1 129.8 151.2 REMARK 620 7 HOH A 146 O 79.9 131.2 159.7 77.4 99.0 87.6 REMARK 620 8 HOH A 148 O 133.3 146.1 99.2 62.4 140.3 67.7 65.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: CAL REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CALCIUM BINDING SITE REMARK 800 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 2GP A 105 DBREF 3BU4 A 1 104 UNP P00651 RNT1_ASPOR 27 130 SEQADV 3BU4 LYS A 25 UNP P00651 GLN 51 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 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 106 1 HET 2GP A 105 24 HETNAM CA CALCIUM ION HETNAM 2GP GUANOSINE-2'-MONOPHOSPHATE FORMUL 2 CA CA 2+ FORMUL 3 2GP C10 H14 N5 O8 P FORMUL 4 HOH *66(H2 O) HELIX 1 A 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 2.03 SSBOND 2 CYS A 6 CYS A 103 1555 1555 2.03 LINK OD1 ASP A 15 CA CA A 106 4556 1555 2.58 LINK OD2 ASP A 15 CA CA A 106 4556 1555 2.45 LINK CA CA A 106 O HOH A 113 1555 1555 2.74 LINK CA CA A 106 O HOH A 115 1555 4556 2.97 LINK CA CA A 106 O HOH A 117 1555 1555 2.88 LINK CA CA A 106 O HOH A 128 1555 4556 2.63 LINK CA CA A 106 O HOH A 146 1555 4556 2.72 LINK CA CA A 106 O HOH A 148 1555 4556 3.19 CISPEP 1 TYR A 38 PRO A 39 0 -0.19 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 CAL 1 ASP A 15 SITE 1 AC1 6 ASP A 15 HOH A 113 HOH A 115 HOH A 117 SITE 2 AC1 6 HOH A 128 HOH A 146 SITE 1 AC2 13 TYR A 38 HIS A 40 LYS A 41 TYR A 42 SITE 2 AC2 13 ASN A 43 ASN A 44 TYR A 45 GLU A 46 SITE 3 AC2 13 GLU A 58 HIS A 92 ASN A 98 PHE A 100 SITE 4 AC2 13 HOH A 137 CRYST1 40.480 48.100 50.770 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 0.024703 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019697 0.00000