PDB Short entry for 1RC9 HEADER TOXIN 03-NOV-03 1RC9 TITLE CRYSTAL STRUCTURE OF STECRISP, A MEMBER OF CRISP FAMILY FROM TITLE 2 TRIMERESURUS STEJNEGERI REFINED AT 1.6 ANGSTROMS RESOLUTION: TITLE 3 STRUCTUAL RELATIONSHIP OF THE TWO DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE-RICH SECRETORY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUE 13-233; COMPND 5 SYNONYM: STECRISP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIRIDOVIPERA STEJNEGERI; SOURCE 3 ORGANISM_COMMON: STEJNEGER'S PIT VIPER; SOURCE 4 ORGANISM_TAXID: 39682; SOURCE 5 ORGAN: VENOM GLAND KEYWDS BETA-ALPHA SANDWICH, DOUBLE DOMAINS, SHORT HELIXS MOTIF, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR M.GUO,M.TENG,L.NIU REVDAT 5 11-OCT-17 1RC9 1 REMARK REVDAT 4 16-NOV-11 1RC9 1 VERSN HETATM REVDAT 3 24-FEB-09 1RC9 1 VERSN REVDAT 2 05-APR-05 1RC9 1 JRNL REVDAT 1 11-JAN-05 1RC9 0 JRNL AUTH M.GUO,M.TENG,L.NIU,Q.LIU,Q.HUANG,Q.HAO JRNL TITL CRYSTAL STRUCTURE OF CYSTEINE-RICH SECRETORY PROTEIN JRNL TITL 2 STECRISP REVEALS THE CYSTEINE-RICH DOMAIN HAS A K+-CHANNEL JRNL TITL 3 INHIBITOR-LIKE FOLD. JRNL REF J.BIOL.CHEM. V. 280 12405 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15596436 JRNL DOI 10.1074/JBC.M413566200 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2655338.290 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 34039 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 : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3399 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2918 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 328 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1756 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 33.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 51.06 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RC9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-NOV-03. REMARK 100 THE DEPOSITION ID IS D_1000020649. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-03; 01-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.75 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : CHESS; BSRF REMARK 200 BEAMLINE : A1; 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9363; 1.7500 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, AUTOMAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34039 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 33.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.280 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL; SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, SHARP, DM, SOLOMON REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, TRIS-HCL, PH REMARK 280 7.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.69050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.21050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.30500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.69050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.21050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.30500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.69050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.21050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.30500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.69050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.21050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.30500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 398 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 411 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 444 LIES ON A SPECIAL POSITION. 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 PRO A 9 6.08 -69.21 REMARK 500 ASP A 95 -9.24 -57.97 REMARK 500 CYS A 170 59.75 -149.49 REMARK 500 ASP A 173 59.46 -143.56 REMARK 500 ASN A 181 66.57 -113.79 REMARK 500 SER A 199 -142.26 -125.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 1RC9 A 1 221 UNP P60623 CRVP_TRIST 13 233 SEQRES 1 A 221 ASN VAL ASP PHE ASP SER GLU SER PRO ARG LYS PRO GLU SEQRES 2 A 221 ILE GLN ASN GLU ILE VAL ASP LEU HIS ASN SER LEU ARG SEQRES 3 A 221 ARG SER VAL ASN PRO THR ALA SER ASN MET LEU ARG MET SEQRES 4 A 221 GLU TRP TYR PRO GLU ALA ALA ASP ASN ALA GLU ARG TRP SEQRES 5 A 221 ALA TYR ARG CYS ILE GLU SER HIS SER SER TYR GLU SER SEQRES 6 A 221 ARG VAL ILE GLU GLY ILE LYS CYS GLY GLU ASN ILE TYR SEQRES 7 A 221 MET SER PRO TYR PRO MET LYS TRP THR ASP ILE ILE HIS SEQRES 8 A 221 ALA TRP HIS ASP GLU TYR LYS ASP PHE LYS TYR GLY VAL SEQRES 9 A 221 GLY ALA ASP PRO PRO ASN ALA VAL THR GLY HIS TYR THR SEQRES 10 A 221 GLN ILE VAL TRP TYR LYS SER TYR ARG ILE GLY CYS ALA SEQRES 11 A 221 ALA ALA TYR CYS PRO SER SER PRO TYR SER TYR PHE PHE SEQRES 12 A 221 VAL CYS GLN TYR CYS PRO ALA GLY ASN PHE ILE GLY LYS SEQRES 13 A 221 THR ALA THR PRO TYR THR SER GLY THR PRO CYS GLY ASP SEQRES 14 A 221 CYS PRO SER ASP CYS ASP ASN GLY LEU CYS THR ASN PRO SEQRES 15 A 221 CYS THR ARG GLU ASN LYS PHE THR ASN CYS ASN THR MET SEQRES 16 A 221 VAL GLN GLN SER SER CYS GLN ASP ASN TYR MET LYS THR SEQRES 17 A 221 ASN CYS PRO ALA SER CYS PHE CYS GLN ASN LYS ILE ILE FORMUL 2 HOH *225(H2 O) HELIX 1 1 PHE A 4 SER A 8 5 5 HELIX 2 2 LYS A 11 SER A 28 1 18 HELIX 3 3 TYR A 42 TYR A 54 1 13 HELIX 4 4 SER A 62 SER A 65 5 4 HELIX 5 5 LYS A 85 ASP A 95 1 11 HELIX 6 6 GLU A 96 LYS A 98 5 3 HELIX 7 7 THR A 113 VAL A 120 1 8 HELIX 8 8 ASN A 191 GLN A 198 1 8 HELIX 9 9 ASP A 203 CYS A 210 1 8 HELIX 10 10 CYS A 210 CYS A 216 1 7 SHEET 1 A 4 GLU A 40 TRP A 41 0 SHEET 2 A 4 ARG A 126 TYR A 133 1 O ILE A 127 N GLU A 40 SHEET 3 A 4 TYR A 141 CYS A 148 -1 O GLN A 146 N GLY A 128 SHEET 4 A 4 GLY A 74 SER A 80 -1 N TYR A 78 O PHE A 143 SHEET 1 B 2 VAL A 67 ILE A 68 0 SHEET 2 B 2 ILE A 71 LYS A 72 -1 O ILE A 71 N ILE A 68 SHEET 1 C 2 PHE A 100 LYS A 101 0 SHEET 2 C 2 GLY A 105 ALA A 106 -1 O GLY A 105 N LYS A 101 SHEET 1 D 2 CYS A 174 ASP A 175 0 SHEET 2 D 2 LEU A 178 CYS A 179 -1 O LEU A 178 N ASP A 175 SSBOND 1 CYS A 56 CYS A 134 1555 1555 2.04 SSBOND 2 CYS A 73 CYS A 148 1555 1555 2.03 SSBOND 3 CYS A 129 CYS A 145 1555 1555 2.05 SSBOND 4 CYS A 167 CYS A 174 1555 1555 2.04 SSBOND 5 CYS A 170 CYS A 179 1555 1555 2.03 SSBOND 6 CYS A 183 CYS A 216 1555 1555 2.05 SSBOND 7 CYS A 192 CYS A 210 1555 1555 2.04 SSBOND 8 CYS A 201 CYS A 214 1555 1555 2.04 CISPEP 1 ASN A 30 PRO A 31 0 0.17 CISPEP 2 ASP A 107 PRO A 108 0 0.13 CISPEP 3 CYS A 148 PRO A 149 0 -0.83 CRYST1 61.381 78.421 106.610 90.00 90.00 90.00 I 2 2 2 8 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 0.016292 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009380 0.00000