HEADER HYDROLASE 10-APR-03 1UCD TITLE CRYSTAL STRUCTURE OF RIBONUCLEASE MC1 FROM BITTER GOURD SEEDS TITLE 2 COMPLEXED WITH 5'-UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE MC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEASE 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 ALPHA PLUS BETA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SUZUKI,T.NUMATA,M.YAO,M.KIMURA,I.TANAKA REVDAT 4 06-NOV-24 1UCD 1 REMARK REVDAT 3 25-OCT-23 1UCD 1 REMARK REVDAT 2 24-FEB-09 1UCD 1 VERSN REVDAT 1 18-MAY-04 1UCD 0 JRNL AUTH A.SUZUKI,T.NUMATA,M.YAO,M.KIMURA,I.TANAKA JRNL TITL STRUCTURE OF RNASE MC1 FROM BITTER GOURD SEEDS IN COMPLEX JRNL TITL 2 WITH 5'UMP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 45870 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) : 0.200 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1770 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 1.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 222 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 : 1496 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04500 REMARK 3 B22 (A**2) : -2.37700 REMARK 3 B33 (A**2) : 2.42200 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) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.07 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) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.359 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.819 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1UCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000005672. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45999 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 19.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.23900 REMARK 200 R SYM FOR SHELL (I) : 0.22100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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 1BK7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, SODIUM ACETATE, SODIUM REMARK 280 CACODYLATE, PH 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 19.59000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.87000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.74000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.87000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.59000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.74000 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 300 REMARK: THE BILOGICAL UNIT IS A MONOMER IN THE ASYMMETRIC UNIT. 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 254 O HOH A 431 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 23 99.87 -162.03 REMARK 500 HIS A 88 -51.05 -121.34 REMARK 500 ASN A 126 15.80 -149.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URA A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BK7 RELATED DB: PDB REMARK 900 SUBSTRATE-FREE FORM REMARK 900 RELATED ID: 1UCA RELATED DB: PDB REMARK 900 THE SAME ENZYME IS COMPLEXED WITH 2'-UMP REMARK 900 RELATED ID: 1UCC RELATED DB: PDB REMARK 900 THE SAME ENZYME IS COMPLEXED WITH 3'-UMP DBREF 1UCD A 1 190 UNP P23540 RNMC_MOMCH 1 191 SEQADV 1UCD GLN A 40 UNP P23540 GLY 40 SEE REMARK 999 SEQADV 1UCD A UNP P23540 GLN 50 SEE REMARK 999 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 HET U5P A 500 21 HET URA A 501 8 HETNAM U5P URIDINE-5'-MONOPHOSPHATE HETNAM URA URACIL FORMUL 2 U5P C9 H13 N2 O9 P FORMUL 3 URA C4 H4 N2 O2 FORMUL 4 HOH *239(H2 O) HELIX 1 1 TRP A 10 PHE A 17 1 8 HELIX 2 2 CYS A 23 LEU A 28 5 6 HELIX 3 3 ASP A 54 HIS A 60 5 7 HELIX 4 4 LEU A 61 TRP A 69 1 9 HELIX 5 5 ASN A 76 HIS A 88 1 13 HELIX 6 6 GLY A 89 GLU A 93 5 5 HELIX 7 7 ASN A 97 ASN A 111 1 15 HELIX 8 8 ASP A 113 ARG A 119 1 7 HELIX 9 9 PRO A 120 ALA A 122 5 3 HELIX 10 10 ARG A 132 GLY A 144 1 13 SHEET 1 A 5 THR A 43 SER A 44 0 SHEET 2 A 5 THR A 32 GLN A 40 -1 N GLN A 40 O THR A 43 SHEET 3 A 5 SER A 3 GLN A 9 -1 N TRP A 5 O TRP A 37 SHEET 4 A 5 SER A 160 ALA A 170 -1 O ALA A 167 N PHE A 6 SHEET 5 A 5 GLY A 148 THR A 153 -1 N GLY A 148 O VAL A 166 SHEET 1 B 5 THR A 43 SER A 44 0 SHEET 2 B 5 THR A 32 GLN A 40 -1 N GLN A 40 O THR A 43 SHEET 3 B 5 SER A 3 GLN A 9 -1 N TRP A 5 O TRP A 37 SHEET 4 B 5 SER A 160 ALA A 170 -1 O ALA A 167 N PHE A 6 SHEET 5 B 5 LEU A 176 ILE A 177 -1 O ILE A 177 N CYS A 168 SHEET 1 C 2 ARG A 128 SER A 131 0 SHEET 2 C 2 ASN A 187 PHE A 190 -1 O PHE A 188 N LYS A 130 SSBOND 1 CYS A 15 CYS A 23 1555 1555 2.03 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 2.04 SITE 1 AC1 19 GLN A 9 HIS A 34 ASN A 71 VAL A 72 SITE 2 AC1 19 LEU A 73 ARG A 74 PHE A 80 HIS A 83 SITE 3 AC1 19 GLU A 84 LYS A 87 HIS A 88 HOH A 227 SITE 4 AC1 19 HOH A 260 HOH A 263 HOH A 286 HOH A 309 SITE 5 AC1 19 HOH A 337 HOH A 386 HOH A 426 SITE 1 AC2 7 TRP A 5 TRP A 37 GLN A 39 GLY A 42 SITE 2 AC2 7 SER A 44 HOH A 313 HOH A 412 CRYST1 39.180 63.480 73.740 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 0.025523 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013561 0.00000