PDB Short entry for 1N1X HEADER HYDROLASE 21-OCT-02 1N1X TITLE CRYSTAL STRUCTURE ANALYSIS OF THE MONOMERIC [S- TITLE 2 CARBOXYAMIDOMETHYL-CYS31, S-CARBOXYAMIDOMETHYL-CYS32] TITLE 3 BOVINE SEMINAL RIBONUCLEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE, SEMINAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SEMINAL RNASE, RIBONUCLEASE BS-1; COMPND 5 EC: 3.1.27.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 OTHER_DETAILS: SEMINAL FLUID KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.SICA,A.DI FIORE,A.ZAGARI,L.MAZZARELLA REVDAT 2 24-FEB-09 1N1X 1 VERSN REVDAT 1 26-AUG-03 1N1X 0 JRNL AUTH F.SICA,A.DI FIORE,A.ZAGARI,L.MAZZARELLA JRNL TITL THE UNSWAPPED CHAIN OF BOVINE SEMINAL JRNL TITL 2 RIBONUCLEASE: CRYSTAL STRUCTURE OF THE FREE AND JRNL TITL 3 LIGANDED MONOMERIC DERIVATIVE JRNL REF PROTEINS V. 52 263 2003 JRNL REFN ISSN 0887-3585 JRNL PMID 12833549 JRNL DOI 10.1002/PROT.10407 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.MAZZARELLA,S.CAPASSO,D.DEMASI,G.DI LORENZO, REMARK 1 AUTH 2 C.A.MATTIA,A.ZAGARI REMARK 1 TITL BOVINE SEMINAL RIBONUCLEASE: STRUCTURE AT 1.9 A REMARK 1 TITL 2 RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 49 389 1993 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444993003403 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.MAZZARELLA,L.VITAGLIANO,A.ZAGARI REMARK 1 TITL SWAPPING STRUCTURAL DETERMINANTS OF RIBONUCLEASES: REMARK 1 TITL 2 AN ENERGETIC ANALYSIS OF THE HINGE PEPTIDE 16-22 REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 92 3799 1995 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH F.SICA,S.ADINOLFI,R.BERISIO,C.DE LORENZO, REMARK 1 AUTH 2 L.MAZZARELLA,R.PICCOLI,L.VITAGLIANO,A.ZAGARI REMARK 1 TITL CRYSTALLIZATION OF MULTIPLE FORMS OF BOVINE REMARK 1 TITL 2 SEMINAL RIBONUCLEASE IN THE LIGANDED AND REMARK 1 TITL 3 UNLIGANDED STATE. REMARK 1 REF J.CRYST.GROWTH V. 196 305 1999 REMARK 1 REFN ISSN 0022-0248 REMARK 1 DOI 10.1016/S0022-0248(98)00860-4 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.D'URSI,H.OSCHKINAT,C.CIESLAR,D.PICONE, REMARK 1 AUTH 2 G.D'ALESSIO,P.AMODEO,P.TEMUSSI REMARK 1 TITL ASSIGNMENT AND SECONDARY-STRUCTURE DETERMINATION REMARK 1 TITL 2 OF MONOMERIC BOVINE SEMINAL RIBONUCLEASE EMPLOYING REMARK 1 TITL 3 COMPUTER-ASSISTED EVALUATION OF HOMONUCLEAR REMARK 1 TITL 4 THREE-DIMENSIONAL 1H-NMR SPECTRA REMARK 1 REF EUR.J.BIOCHEM. V. 229 494 1995 REMARK 1 REFN ISSN 0014-2956 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 20831 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) : 0.205 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2044 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.47 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 98 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 : 955 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.80 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 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 1N1X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-02. REMARK 100 THE RCSB ID CODE IS RCSB017416. 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 : 8.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21157 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 17.000 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 1BSR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS-HCL, SODIUM ACETATE, REMARK 280 ACETONITRILE, GLYCEROL (CRYOPROTECTANT), PH 8.7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.0K 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 35.19500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.19500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.36500 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 ASN A 17 REMARK 465 SER A 18 REMARK 465 PRO A 19 REMARK 465 SER A 20 REMARK 465 SER A 21 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 60 -141.43 -101.55 REMARK 500 ASN A 71 34.64 -89.96 REMARK 500 ASN A 94 74.34 -107.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BSR RELATED DB: PDB REMARK 900 THE SWAPPED ISOMER OF THE DIMERIC BOVINE SEMINAL REMARK 900 RIBONUCLEASE DBREF 1N1X A 1 124 UNP P00669 RNS_BOVIN 27 150 SEQADV 1N1X YCM A 31 UNP P00669 CYS 57 MODIFIED RESIDUE SEQADV 1N1X YCM A 32 UNP P00669 CYS 58 MODIFIED RESIDUE SEQRES 1 A 124 LYS GLU SER ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 A 124 ASP SER GLY ASN SER PRO SER SER SER SER ASN TYR CYS SEQRES 3 A 124 ASN LEU MET MET YCM YCM ARG LYS MET THR GLN GLY LYS SEQRES 4 A 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 A 124 ASP VAL LYS ALA VAL CYS SER GLN LYS LYS VAL THR CYS SEQRES 6 A 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER LYS SER THR SEQRES 7 A 124 MET ARG ILE THR ASP CYS ARG GLU THR GLY SER SER LYS SEQRES 8 A 124 TYR PRO ASN CYS ALA TYR LYS THR THR GLN VAL GLU LYS SEQRES 9 A 124 HIS ILE ILE VAL ALA CYS GLY GLY LYS PRO SER VAL PRO SEQRES 10 A 124 VAL HIS PHE ASP ALA SER VAL MODRES 1N1X YCM A 31 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE MODRES 1N1X YCM A 32 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HET YCM A 31 10 HET YCM A 32 10 HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETSYN YCM CYSTEINE-S-ACETAMIDE FORMUL 1 YCM 2(C5 H10 N2 O3 S) FORMUL 2 HOH *146(H2 O) HELIX 1 1 SER A 3 MET A 13 1 11 HELIX 2 2 ASN A 24 ARG A 33 1 10 HELIX 3 3 SER A 50 ALA A 56 1 7 HELIX 4 4 VAL A 57 GLN A 60 5 4 SHEET 1 A 4 VAL A 116 VAL A 124 0 SHEET 2 A 4 TYR A 97 GLY A 111 -1 N ALA A 109 O VAL A 118 SHEET 3 A 4 CYS A 72 GLN A 74 -1 N TYR A 73 O VAL A 108 SHEET 4 A 4 LYS A 61 VAL A 63 -1 N LYS A 61 O GLN A 74 SHEET 1 B 4 VAL A 116 VAL A 124 0 SHEET 2 B 4 TYR A 97 GLY A 111 -1 N ALA A 109 O VAL A 118 SHEET 3 B 4 MET A 79 GLU A 86 -1 N ARG A 85 O LYS A 98 SHEET 4 B 4 VAL A 43 VAL A 47 -1 N ASN A 44 O CYS A 84 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.04 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.03 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.04 SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.03 LINK C MET A 30 N YCM A 31 1555 1555 1.33 LINK C YCM A 31 N YCM A 32 1555 1555 1.33 LINK C YCM A 32 N ARG A 33 1555 1555 1.34 CISPEP 1 TYR A 92 PRO A 93 0 0.49 CISPEP 2 LYS A 113 PRO A 114 0 0.06 CRYST1 70.390 28.730 67.410 90.00 119.00 90.00 C 1 2 1 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 0.014210 0.000000 0.007880 0.00000 SCALE2 0.000000 0.034810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016970 0.00000