HEADER HYDROLASE 17-MAR-04 1VCZ TITLE CRYSTAL STRUCTURE OF THE RNASE NT IN COMPLEX WITH 5'-GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE NGR3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEASE NT, RNASE NT; COMPND 5 EC: 3.1.27.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NICOTIANA GLUTINOSA; SOURCE 3 ORGANISM_TAXID: 35889; SOURCE 4 TISSUE: LEAVES; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPIC9K KEYWDS HYDROLASE, RIBONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KAWANO,Y.KAKUTA,M.KIMURA REVDAT 4 06-NOV-24 1VCZ 1 REMARK REVDAT 3 25-OCT-23 1VCZ 1 REMARK SEQADV REVDAT 2 24-FEB-09 1VCZ 1 VERSN REVDAT 1 26-APR-05 1VCZ 0 JRNL AUTH S.KAWANO,Y.KAKUTA,M.KIMURA JRNL TITL CRYSTAL STRUCTURE OF THE NICOTIANA GLUTINOSA RIBONUCLEASE NT JRNL TITL 2 IN COMPLEX WITH NUCLEOTIDE MONOPHOSPHATES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 405119.610 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 18069 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) : 0.217 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 880 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2715 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1648 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.13000 REMARK 3 B22 (A**2) : -2.49000 REMARK 3 B33 (A**2) : -2.64000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.070 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) : 2.970 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.360 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.810 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 44.95 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : 5GMP_XPLOR.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : 5GMP_XPLOR.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000006477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL40B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18278 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.17400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.0000 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.700 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 1IYB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20%(V/V) 1,4-BUTANEDIOL, 0.1M ACETATE, REMARK 280 PH 4.5, 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 18.64000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.98450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.77350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.98450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.64000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.77350 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 TYR A -3 REMARK 465 VAL A -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 REMARK 465 SER A 205 REMARK 465 SER A 206 REMARK 465 GLU A 207 REMARK 465 SER A 208 REMARK 465 ASP A 209 REMARK 465 HIS A 210 REMARK 465 ASP A 211 REMARK 465 GLU A 212 REMARK 465 PHE A 213 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 THR A 20 -168.66 -106.88 REMARK 500 TRP A 76 50.14 -141.90 REMARK 500 ASN A 120 55.09 36.04 REMARK 500 ASP A 162 -173.12 -69.75 REMARK 500 ARG A 193 103.38 -13.42 REMARK 500 CYS A 195 111.56 81.51 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 5GP A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 296 DBREF 1VCZ A 1 213 UNP Q9SSV1 Q9SSV1_NICGU 24 236 SEQADV 1VCZ TYR A -3 UNP Q9SSV1 CLONING ARTIFACT SEQADV 1VCZ VAL A -2 UNP Q9SSV1 CLONING ARTIFACT SEQADV 1VCZ GLU A -1 UNP Q9SSV1 CLONING ARTIFACT SEQADV 1VCZ PHE A 0 UNP Q9SSV1 CLONING ARTIFACT SEQRES 1 A 217 TYR VAL GLU PHE ALA GLN ASP PHE ASP PHE PHE TYR PHE SEQRES 2 A 217 VAL GLN GLN TRP PRO ALA SER TYR CYS ASP THR ARG ARG SEQRES 3 A 217 SER CYS CYS TYR PRO THR THR GLY LYS PRO ASP GLU ASP SEQRES 4 A 217 PHE SER ILE HIS GLY LEU TRP PRO ASN TYR GLU ASN GLY SEQRES 5 A 217 LYS TRP PRO GLN ASN CYS ASP ARG GLU SER SER LEU ASP SEQRES 6 A 217 GLU SER GLU ILE SER ASP LEU ILE SER THR MET GLU LYS SEQRES 7 A 217 ASN TRP PRO SER LEU ALA CYS PRO SER SER ASP GLY VAL SEQRES 8 A 217 ARG PHE TRP SER HIS GLU TRP LEU LYS HIS GLY THR CYS SEQRES 9 A 217 SER ALA LEU GLY GLU ARG ALA TYR PHE GLN ALA ALA LEU SEQRES 10 A 217 ASP PHE ARG LYS LYS SER ASN LEU LEU GLU ASN LEU LYS SEQRES 11 A 217 ASN ALA GLU ILE THR PRO ARG ASN GLY GLU HIS TYR THR SEQRES 12 A 217 LEU GLU SER ILE LYS LYS ALA ILE GLU GLU GLY VAL GLY SEQRES 13 A 217 HIS SER PRO TYR ILE GLU CYS ASN VAL ASP THR GLN GLY SEQRES 14 A 217 ASN HIS GLN ILE TYR GLN VAL TYR LEU CYS VAL ASP LYS SEQRES 15 A 217 THR ALA THR ASP PHE ILE ASP CYS PRO ILE PHE PRO HIS SEQRES 16 A 217 GLY ARG GLY CYS GLY SER LYS ILE GLU PHE PRO PRO PHE SEQRES 17 A 217 SER SER GLU SER ASP HIS ASP GLU PHE HET 5GP A 295 24 HET 5GP A 296 24 HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 5GP 2(C10 H14 N5 O8 P) FORMUL 4 HOH *92(H2 O) HELIX 1 1 TRP A 13 CYS A 18 1 6 HELIX 2 2 ASP A 61 ASP A 67 5 7 HELIX 3 3 LEU A 68 TRP A 76 1 9 HELIX 4 4 GLY A 86 HIS A 97 1 12 HELIX 5 5 GLY A 98 SER A 101 5 4 HELIX 6 6 GLY A 104 ASN A 120 1 17 HELIX 7 7 ASN A 120 ALA A 128 1 9 HELIX 8 8 LEU A 140 GLY A 152 1 13 SHEET 1 A 4 SER A 37 ASN A 44 0 SHEET 2 A 4 PHE A 6 GLN A 12 -1 N TYR A 8 O TRP A 42 SHEET 3 A 4 HIS A 167 ASP A 177 -1 O LEU A 174 N PHE A 9 SHEET 4 A 4 TYR A 156 VAL A 161 -1 N TYR A 156 O TYR A 173 SHEET 1 B 4 SER A 37 ASN A 44 0 SHEET 2 B 4 PHE A 6 GLN A 12 -1 N TYR A 8 O TRP A 42 SHEET 3 B 4 HIS A 167 ASP A 177 -1 O LEU A 174 N PHE A 9 SHEET 4 B 4 PHE A 183 ILE A 184 -1 O ILE A 184 N CYS A 175 SHEET 1 C 2 ARG A 133 THR A 139 0 SHEET 2 C 2 LYS A 198 PHE A 201 -1 O ILE A 199 N TYR A 138 SSBOND 1 CYS A 18 CYS A 24 1555 1555 2.03 SSBOND 2 CYS A 25 CYS A 81 1555 1555 2.03 SSBOND 3 CYS A 54 CYS A 100 1555 1555 2.04 SSBOND 4 CYS A 159 CYS A 195 1555 1555 2.03 SSBOND 5 CYS A 175 CYS A 186 1555 1555 2.02 CISPEP 1 CYS A 81 PRO A 82 0 0.02 SITE 1 AC1 10 TYR A 8 TRP A 42 PRO A 43 ASN A 44 SITE 2 AC1 10 TRP A 50 LYS A 96 HIS A 97 5GP A 296 SITE 3 AC1 10 HOH A 317 HOH A 382 SITE 1 AC2 18 GLN A 12 TYR A 17 HIS A 39 TRP A 42 SITE 2 AC2 18 PRO A 77 SER A 78 LEU A 79 ALA A 80 SITE 3 AC2 18 PHE A 89 HIS A 92 GLU A 93 LYS A 96 SITE 4 AC2 18 HIS A 97 ASN A 127 TYR A 170 5GP A 295 SITE 5 AC2 18 HOH A 381 HOH A 384 CRYST1 37.280 69.547 73.969 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 0.026824 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013519 0.00000