HEADER HYDROLASE 04-SEP-10 3OQZ TITLE SEMI-SYNTHETIC RIBONUCLEASE S: META-CYANO-PHENYLALANINE AT POSITION 8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE PANCREATIC; COMPND 3 CHAIN: a, b; COMPND 4 FRAGMENT: UNP RESIDUES 27-41; COMPND 5 SYNONYM: RNASE 1, RNASE A; COMPND 6 EC: 3.1.27.5; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RIBONUCLEASE PANCREATIC; COMPND 10 CHAIN: A, B; COMPND 11 FRAGMENT: UNP RESIDUES 47-150; COMPND 12 SYNONYM: RNASE 1, RNASE A; COMPND 13 EC: 3.1.27.5 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 4 ORGANISM_COMMON: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW; SOURCE 5 ORGANISM_TAXID: 9913; SOURCE 6 OTHER_DETAILS: MADE BY SOLID PHASE PEPTIDE SYNTHESIS; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 9 ORGANISM_COMMON: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW; SOURCE 10 ORGANISM_TAXID: 9913 KEYWDS ARTIFICIAL, NON-NATURAL, VIBRATIONAL, PROBE, NITRILE, CYANO, KEYWDS 2 CYANOPHENYLALANINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.T.FAFARMAN,S.G.BOXER REVDAT 5 06-NOV-24 3OQZ 1 REMARK REVDAT 4 06-DEC-23 3OQZ 1 REMARK REVDAT 3 06-SEP-23 3OQZ 1 LINK REVDAT 2 10-NOV-10 3OQZ 1 JRNL REVDAT 1 20-OCT-10 3OQZ 0 JRNL AUTH A.T.FAFARMAN,S.G.BOXER JRNL TITL NITRILE BONDS AS INFRARED PROBES OF ELECTROSTATICS IN JRNL TITL 2 RIBONUCLEASE S. JRNL REF J.PHYS.CHEM.B V. 114 13536 2010 JRNL REFN ISSN 1089-5647 JRNL PMID 20883003 JRNL DOI 10.1021/JP106406P REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7753 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 356 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.7976 - 3.6051 1.00 2525 117 0.1795 0.2259 REMARK 3 2 3.6051 - 2.8617 1.00 2446 117 0.2111 0.3174 REMARK 3 3 2.8617 - 2.5000 1.00 2426 122 0.2363 0.2756 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 28.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.85170 REMARK 3 B22 (A**2) : 11.54540 REMARK 3 B33 (A**2) : -7.69370 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.35240 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1900 REMARK 3 ANGLE : 1.045 2560 REMARK 3 CHIRALITY : 0.069 278 REMARK 3 PLANARITY : 0.012 340 REMARK 3 DIHEDRAL : 18.095 704 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3OQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7757 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 69.171 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1RNV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 0.08M AMMONIUM ACETATE, REMARK 280 0.1 M SODIUM CITRATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 279K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 49.92500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.83950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.92500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.83950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: a, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: b, B 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 SER A 21 REMARK 465 SER A 22 REMARK 465 SER B 21 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 28 CD REMARK 480 LYS A 98 CD 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 GLU a 2 108.95 84.11 REMARK 500 ALA a 4 -27.94 -39.19 REMARK 500 GLN A 60 -140.85 -112.99 REMARK 500 ALA A 122 173.06 178.99 REMARK 500 GLN B 60 -141.13 -98.48 REMARK 500 ASN B 71 40.09 -85.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OQY RELATED DB: PDB REMARK 900 SEMI-SYNTHETIC RIBONUCLEASE S: PARA-CYANO-PHENYLALANINE AT POSITION REMARK 900 8 REMARK 900 RELATED ID: 3OR0 RELATED DB: PDB REMARK 900 SEMI-SYNTHETIC RIBONUCLEASE S: CYANYLATED HOMOCYSTEINE AT POSITION REMARK 900 13 DBREF 3OQZ a 1 15 UNP P61823 RNAS1_BOVIN 27 41 DBREF 3OQZ A 21 124 UNP P61823 RNAS1_BOVIN 47 150 DBREF 3OQZ b 1 15 UNP P61823 RNAS1_BOVIN 27 41 DBREF 3OQZ B 21 124 UNP P61823 RNAS1_BOVIN 47 150 SEQRES 1 a 15 LYS GLU THR ALA ALA ALA LYS 3CF GLU ARG GLN HIS MET SEQRES 2 a 15 ASP SER SEQRES 1 A 104 SER SER SER ASN TYR CYS ASN GLN MET MET LYS SER ARG SEQRES 2 A 104 ASN LEU THR LYS ASP ARG CYS LYS PRO VAL ASN THR PHE SEQRES 3 A 104 VAL HIS GLU SER LEU ALA ASP VAL GLN ALA VAL CYS SER SEQRES 4 A 104 GLN LYS ASN VAL ALA CYS LYS ASN GLY GLN THR ASN CYS SEQRES 5 A 104 TYR GLN SER TYR SER THR MET SER ILE THR ASP CYS ARG SEQRES 6 A 104 GLU THR GLY SER SER LYS TYR PRO ASN CYS ALA TYR LYS SEQRES 7 A 104 THR THR GLN ALA ASN LYS HIS ILE ILE VAL ALA CYS GLU SEQRES 8 A 104 GLY ASN PRO TYR VAL PRO VAL HIS PHE ASP ALA SER VAL SEQRES 1 b 15 LYS GLU THR ALA ALA ALA LYS 3CF GLU ARG GLN HIS MET SEQRES 2 b 15 ASP SER SEQRES 1 B 104 SER SER SER ASN TYR CYS ASN GLN MET MET LYS SER ARG SEQRES 2 B 104 ASN LEU THR LYS ASP ARG CYS LYS PRO VAL ASN THR PHE SEQRES 3 B 104 VAL HIS GLU SER LEU ALA ASP VAL GLN ALA VAL CYS SER SEQRES 4 B 104 GLN LYS ASN VAL ALA CYS LYS ASN GLY GLN THR ASN CYS SEQRES 5 B 104 TYR GLN SER TYR SER THR MET SER ILE THR ASP CYS ARG SEQRES 6 B 104 GLU THR GLY SER SER LYS TYR PRO ASN CYS ALA TYR LYS SEQRES 7 B 104 THR THR GLN ALA ASN LYS HIS ILE ILE VAL ALA CYS GLU SEQRES 8 B 104 GLY ASN PRO TYR VAL PRO VAL HIS PHE ASP ALA SER VAL MODRES 3OQZ 3CF a 8 PHE 3-CYANO-L-PHENYLALANINE MODRES 3OQZ 3CF b 8 PHE 3-CYANO-L-PHENYLALANINE HET 3CF a 8 13 HET 3CF b 8 13 HETNAM 3CF 3-CYANO-L-PHENYLALANINE FORMUL 1 3CF 2(C10 H10 N2 O2) FORMUL 5 HOH *14(H2 O) HELIX 1 1 THR a 3 MET a 13 1 11 HELIX 2 2 ASN A 24 ARG A 33 1 10 HELIX 3 3 SER A 50 VAL A 57 1 8 HELIX 4 4 CYS A 58 GLN A 60 5 3 HELIX 5 5 THR b 3 MET b 13 1 11 HELIX 6 6 ASN B 24 ARG B 33 1 10 HELIX 7 7 SER B 50 ALA B 56 1 7 HELIX 8 8 VAL B 57 GLN B 60 5 4 SHEET 1 A 3 VAL A 43 VAL A 47 0 SHEET 2 A 3 MET A 79 GLU A 86 -1 O CYS A 84 N ASN A 44 SHEET 3 A 3 TYR A 97 LYS A 104 -1 O THR A 100 N ASP A 83 SHEET 1 B 4 LYS A 61 VAL A 63 0 SHEET 2 B 4 CYS A 72 GLN A 74 -1 O CYS A 72 N VAL A 63 SHEET 3 B 4 ILE A 106 GLU A 111 -1 O VAL A 108 N TYR A 73 SHEET 4 B 4 VAL A 116 SER A 123 -1 O VAL A 118 N ALA A 109 SHEET 1 C 3 VAL B 43 VAL B 47 0 SHEET 2 C 3 MET B 79 GLU B 86 -1 O CYS B 84 N ASN B 44 SHEET 3 C 3 TYR B 97 LYS B 104 -1 O LYS B 98 N ARG B 85 SHEET 1 D 4 LYS B 61 VAL B 63 0 SHEET 2 D 4 CYS B 72 GLN B 74 -1 O GLN B 74 N LYS B 61 SHEET 3 D 4 ILE B 106 GLU B 111 -1 O VAL B 108 N TYR B 73 SHEET 4 D 4 VAL B 116 SER B 123 -1 O VAL B 118 N ALA B 109 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.05 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.03 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.01 SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.04 SSBOND 5 CYS B 26 CYS B 84 1555 1555 2.05 SSBOND 6 CYS B 40 CYS B 95 1555 1555 2.03 SSBOND 7 CYS B 58 CYS B 110 1555 1555 2.05 SSBOND 8 CYS B 65 CYS B 72 1555 1555 2.03 LINK C LYS a 7 N 3CF a 8 1555 1555 1.33 LINK C 3CF a 8 N GLU a 9 1555 1555 1.33 LINK C LYS b 7 N 3CF b 8 1555 1555 1.33 LINK C 3CF b 8 N GLU b 9 1555 1555 1.32 CISPEP 1 TYR A 92 PRO A 93 0 1.48 CISPEP 2 ASN A 113 PRO A 114 0 12.46 CISPEP 3 TYR B 92 PRO B 93 0 3.70 CISPEP 4 ASN B 113 PRO B 114 0 3.83 CRYST1 99.850 31.679 69.171 90.00 90.93 90.00 C 1 2 1 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 0.010015 0.000000 0.000163 0.00000 SCALE2 0.000000 0.031567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014459 0.00000