HEADER HYDROLASE 15-JUL-98 1BK7 TITLE RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RIBONUCLEASE MC1); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE MC1; COMPND 5 EC: 3.1.27.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MOMORDICA CHARANTIA; SOURCE 3 ORGANISM_COMMON: BALSAM PEAR; SOURCE 4 ORGANISM_TAXID: 3673; SOURCE 5 TISSUE: SEED KEYWDS HYDROLASE (NUCLEIC ACID, RNA), HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.NAKAGAWA,I.TANAKA REVDAT 8 20-NOV-24 1BK7 1 REMARK REVDAT 7 27-DEC-23 1BK7 1 SEQADV REVDAT 6 04-APR-18 1BK7 1 REMARK REVDAT 5 24-FEB-09 1BK7 1 VERSN REVDAT 4 01-APR-03 1BK7 1 JRNL REVDAT 3 26-SEP-01 1BK7 1 HELIX REVDAT 2 26-JAN-00 1BK7 1 JRNL REVDAT 1 23-JUL-99 1BK7 0 JRNL AUTH A.NAKAGAWA,I.TANAKA,R.SAKAI,T.NAKASHIMA,G.FUNATSU,M.KIMURA JRNL TITL CRYSTAL STRUCTURE OF A RIBONUCLEASE FROM THE SEEDS OF BITTER JRNL TITL 2 GOURD (MOMORDICA CHARANTIA) AT 1.75 A RESOLUTION. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1433 253 1999 JRNL REFN ISSN 0006-3002 JRNL PMID 10446375 JRNL DOI 10.1016/S0167-4838(99)00126-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.DE,G.FUNATSU REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF A PLANT RIBONUCLEASE FROM THE SEEDS OF THE BITTER GOURD REMARK 1 TITL 3 MOMORDICA CHARANTIA REMARK 1 REF J.MOL.BIOL. V. 228 1271 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.IDE,M.KIMURA,M.ARAI,G.FUNATSU REMARK 1 TITL THE COMPLETE AMINO ACID SEQUENCE OF RIBONUCLEASE FROM THE REMARK 1 TITL 2 SEEDS OF BITTER GOURD REMARK 1 REF FEBS LETT. V. 284 161 1991 REMARK 1 REFN ISSN 0014-5793 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.IDE,M.KIMURA,M.ARAI,G.FUNATSU REMARK 1 TITL THE COMPLETE AMINO ACID SEQUENCE OF RIBONUCLEASE FROM THE REMARK 1 TITL 2 SEEDS OF BITTER GOURD REMARK 1 REF FEBS LETT. V. 289 126 1991 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 20257 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) : 0.192 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1031 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3042 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 168 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1496 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.620 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.510 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.270 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.830 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.380 ; 2.500 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : WAT.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BK7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007000. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 283 REMARK 200 PH : 6.7 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 : MACSCIENCE M18X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69704 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEN WAS CRYSTALLIZED FROM THE 1:1 REMARK 280 MIXTURE OF 10MG/ML PROTEIN SOLUTION IN 5MM TRIS-HCL PH7.2 AND 30% REMARK 280 PEG 6000, 0.2M NA-ACETATE, 0.1M NA-CACODYLATE PH 6.7 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 19.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.71500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.98500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.71500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.98500 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 GLN A 40 110.91 -160.24 REMARK 500 ALA A 75 27.18 -79.73 REMARK 500 ASN A 126 18.47 -153.72 REMARK 500 SER A 174 -25.08 -141.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BK7 A 1 190 UNP P23540 RNMC_MOMCH 1 191 SEQADV 1BK7 GLN A 40 UNP P23540 GLY 40 CONFLICT SEQADV 1BK7 A UNP P23540 GLN 50 DELETION SEQRES 1 A 190 PHE ASP SER PHE TRP PHE VAL GLN GLN TRP PRO PRO ALA SEQRES 2 A 190 VAL CYS SER PHE GLN LYS SER GLY SER CYS PRO GLY SER SEQRES 3 A 190 GLY LEU ARG THR PHE THR ILE HIS GLY LEU TRP PRO GLN SEQRES 4 A 190 GLN SER GLY THR SER LEU THR ASN CYS PRO GLY SER PRO SEQRES 5 A 190 PHE ASP ILE THR LYS ILE SER HIS LEU GLN SER GLN LEU SEQRES 6 A 190 ASN THR LEU TRP PRO ASN VAL LEU ARG ALA ASN ASN GLN SEQRES 7 A 190 GLN PHE TRP SER HIS GLU TRP THR LYS HIS GLY THR CYS SEQRES 8 A 190 SER GLU SER THR PHE ASN GLN ALA ALA TYR PHE LYS LEU SEQRES 9 A 190 ALA VAL ASP MET ARG ASN ASN TYR ASP ILE ILE GLY ALA SEQRES 10 A 190 LEU ARG PRO HIS ALA ALA GLY PRO ASN GLY ARG THR LYS SEQRES 11 A 190 SER ARG GLN ALA ILE LYS GLY PHE LEU LYS ALA LYS PHE SEQRES 12 A 190 GLY LYS PHE PRO GLY LEU ARG CYS ARG THR ASP PRO GLN SEQRES 13 A 190 THR LYS VAL SER TYR LEU VAL GLN VAL VAL ALA CYS PHE SEQRES 14 A 190 ALA GLN ASP GLY SER THR LEU ILE ASP CYS THR ARG ASP SEQRES 15 A 190 THR CYS GLY ALA ASN PHE ILE PHE FORMUL 2 HOH *187(H2 O) HELIX 1 H1 PRO A 11 SER A 16 1 6 HELIX 2 H2 PRO A 24 GLY A 27 5 4 HELIX 3 H3 ILE A 55 LEU A 61 5 7 HELIX 4 H4 GLN A 62 LEU A 68 1 7 HELIX 5 H5 ASN A 77 LYS A 87 1 11 HELIX 6 H6 GLY A 89 SER A 92 5 4 HELIX 7 H7 GLN A 98 ASN A 111 1 14 HELIX 8 H8 ILE A 114 LEU A 118 1 5 HELIX 9 H9 ARG A 119 HIS A 121 5 3 HELIX 10 H10 ARG A 132 PHE A 143 5 12 SHEET 1 S1 1 SER A 3 GLN A 9 0 SHEET 1 S2 1 THR A 32 GLN A 40 0 SHEET 1 S3 1 THR A 43 SER A 44 0 SHEET 1 S4 1 THR A 129 SER A 131 0 SHEET 1 S5 1 GLY A 148 THR A 153 0 SHEET 1 S6 1 SER A 160 ALA A 170 0 SHEET 1 S7 1 LEU A 176 ILE A 177 0 SHEET 1 S8 1 ASN A 187 ILE A 189 0 SSBOND 1 CYS A 15 CYS A 23 1555 1555 2.02 SSBOND 2 CYS A 48 CYS A 91 1555 1555 2.03 SSBOND 3 CYS A 151 CYS A 184 1555 1555 2.03 SSBOND 4 CYS A 168 CYS A 179 1555 1555 2.03 CRYST1 38.800 67.970 75.430 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 0.025773 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013257 0.00000