PDB Short entry for 2LFJ HEADER HYDROLASE 06-JUL-11 2LFJ TITLE SOLUTION STRUCTURE OF THE MONOMERIC DERIVATIVE OF BS-RNASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEMINAL RIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S-RNASE, SEMINAL RNASE, RIBONUCLEASE BS-1; COMPND 5 EC: 3.1.27.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: COW; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: SRN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET22B(+) KEYWDS HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.SPADACCINI,D.PICONE REVDAT 2 14-JUN-23 2LFJ 1 REMARK SEQADV REVDAT 1 08-FEB-12 2LFJ 0 JRNL AUTH R.SPADACCINI,C.ERCOLE,M.A.GENTILE,D.SANFELICE,R.BOELENS, JRNL AUTH 2 R.WECHSELBERGER,G.BATTA,A.BERNINI,N.NICCOLAI,D.PICONE JRNL TITL NMR STUDIES ON STRUCTURE AND DYNAMICS OF THE MONOMERIC JRNL TITL 2 DERIVATIVE OF BS-RNASE: NEW INSIGHTS FOR 3D DOMAIN SWAPPING. JRNL REF PLOS ONE V. 7 29076 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22253705 JRNL DOI 10.1371/JOURNAL.PONE.0029076 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, CYANA REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM (AMBER), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000102329. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 MBS, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 15N] MBS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 2D 1H- REMARK 210 15N HSQC; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, CYANA, NMRPIPE REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 VAL A 124 O 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 1 SER A 3 36.80 -80.28 REMARK 500 1 ALA A 4 -60.79 62.23 REMARK 500 1 HIS A 12 -58.64 -137.11 REMARK 500 1 SER A 15 162.74 94.34 REMARK 500 1 SER A 18 92.39 -166.86 REMARK 500 1 SER A 21 -133.76 49.00 REMARK 500 1 SER A 22 -78.72 153.46 REMARK 500 1 LYS A 34 52.43 39.03 REMARK 500 1 THR A 36 49.54 -75.15 REMARK 500 1 SER A 50 102.52 -57.11 REMARK 500 1 GLN A 60 -87.03 -114.79 REMARK 500 1 CYS A 65 175.73 -58.53 REMARK 500 1 LYS A 66 33.77 -68.65 REMARK 500 1 ASP A 67 -41.94 -163.45 REMARK 500 1 THR A 70 -112.99 57.79 REMARK 500 1 ASN A 71 51.41 -178.96 REMARK 500 1 SER A 89 -34.58 -163.53 REMARK 500 1 LYS A 113 131.51 -37.39 REMARK 500 1 ALA A 122 -177.22 -176.04 REMARK 500 2 ALA A 4 -63.65 66.99 REMARK 500 2 SER A 20 69.77 -66.70 REMARK 500 2 SER A 23 -63.80 -105.61 REMARK 500 2 ASN A 24 -104.50 -18.71 REMARK 500 2 TYR A 25 -37.14 -37.03 REMARK 500 2 LYS A 34 52.90 70.89 REMARK 500 2 GLN A 37 -110.78 -76.10 REMARK 500 2 GLU A 49 -164.78 166.69 REMARK 500 2 SER A 59 41.79 -98.20 REMARK 500 2 GLN A 60 -119.58 -119.68 REMARK 500 2 CYS A 65 152.88 -48.46 REMARK 500 2 ASP A 67 -35.59 170.11 REMARK 500 2 GLN A 69 -50.94 -137.94 REMARK 500 2 SER A 89 -33.22 -167.69 REMARK 500 2 LYS A 113 119.73 -22.90 REMARK 500 2 SER A 115 96.71 -60.36 REMARK 500 2 ASP A 121 -61.20 -107.85 REMARK 500 3 ALA A 4 -67.25 63.64 REMARK 500 3 GLU A 9 -71.60 -46.95 REMARK 500 3 HIS A 12 -44.86 -141.80 REMARK 500 3 PRO A 19 -178.64 -68.03 REMARK 500 3 SER A 21 -47.85 163.94 REMARK 500 3 SER A 22 -56.50 73.67 REMARK 500 3 LYS A 39 147.69 -172.77 REMARK 500 3 ASN A 44 115.58 -168.20 REMARK 500 3 GLU A 49 -136.48 -154.01 REMARK 500 3 LEU A 51 -77.73 15.21 REMARK 500 3 CYS A 58 -39.52 -35.88 REMARK 500 3 GLN A 60 -71.31 -90.90 REMARK 500 3 ASP A 67 -71.95 177.84 REMARK 500 3 SER A 90 97.02 -65.62 REMARK 500 REMARK 500 THIS ENTRY HAS 163 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 33 0.10 SIDE CHAIN REMARK 500 1 TYR A 97 0.13 SIDE CHAIN REMARK 500 1 PHE A 120 0.08 SIDE CHAIN REMARK 500 2 TYR A 25 0.08 SIDE CHAIN REMARK 500 2 HIS A 48 0.12 SIDE CHAIN REMARK 500 2 ARG A 85 0.12 SIDE CHAIN REMARK 500 3 ARG A 10 0.14 SIDE CHAIN REMARK 500 3 ARG A 33 0.10 SIDE CHAIN REMARK 500 3 TYR A 73 0.12 SIDE CHAIN REMARK 500 4 TYR A 25 0.09 SIDE CHAIN REMARK 500 4 TYR A 97 0.12 SIDE CHAIN REMARK 500 5 PHE A 8 0.07 SIDE CHAIN REMARK 500 5 TYR A 97 0.11 SIDE CHAIN REMARK 500 6 TYR A 25 0.14 SIDE CHAIN REMARK 500 6 ARG A 33 0.09 SIDE CHAIN REMARK 500 6 TYR A 92 0.07 SIDE CHAIN REMARK 500 6 TYR A 97 0.08 SIDE CHAIN REMARK 500 7 ARG A 33 0.12 SIDE CHAIN REMARK 500 7 ARG A 80 0.10 SIDE CHAIN REMARK 500 7 TYR A 92 0.07 SIDE CHAIN REMARK 500 7 TYR A 97 0.15 SIDE CHAIN REMARK 500 8 PHE A 8 0.07 SIDE CHAIN REMARK 500 8 TYR A 92 0.08 SIDE CHAIN REMARK 500 8 TYR A 97 0.12 SIDE CHAIN REMARK 500 9 PHE A 46 0.11 SIDE CHAIN REMARK 500 9 TYR A 73 0.14 SIDE CHAIN REMARK 500 9 TYR A 92 0.09 SIDE CHAIN REMARK 500 9 TYR A 97 0.08 SIDE CHAIN REMARK 500 10 TYR A 25 0.10 SIDE CHAIN REMARK 500 10 TYR A 92 0.08 SIDE CHAIN REMARK 500 10 TYR A 97 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17762 RELATED DB: BMRB DBREF 2LFJ A 1 124 UNP P00669 RNS_BOVIN 27 150 SEQADV 2LFJ ASP A 67 UNP P00669 ASN 93 ENGINEERED MUTATION 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 CYS CYS 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 ASP 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 HELIX 1 1 ALA A 4 MET A 13 1 10 HELIX 2 2 SER A 22 ARG A 33 1 12 HELIX 3 3 SER A 50 SER A 59 1 10 SHEET 1 A 3 VAL A 43 VAL A 47 0 SHEET 2 A 3 MET A 79 GLU A 86 -1 O THR A 82 N PHE A 46 SHEET 3 A 3 TYR A 97 LYS A 104 -1 O VAL A 102 N ILE A 81 SHEET 1 B 4 LYS A 61 LYS A 62 0 SHEET 2 B 4 TYR A 73 GLN A 74 -1 O GLN A 74 N LYS A 61 SHEET 3 B 4 ILE A 106 GLY A 111 -1 O VAL A 108 N TYR A 73 SHEET 4 B 4 VAL A 116 SER A 123 -1 O ASP A 121 N ILE A 107 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.08 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.09 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.06 SSBOND 4 CYS A 65 CYS A 72 1555 1555 2.07 CISPEP 1 TYR A 92 PRO A 93 1 7.52 CISPEP 2 LYS A 113 PRO A 114 1 -5.37 CISPEP 3 TYR A 92 PRO A 93 2 10.97 CISPEP 4 LYS A 113 PRO A 114 2 5.70 CISPEP 5 TYR A 92 PRO A 93 3 5.44 CISPEP 6 LYS A 113 PRO A 114 3 7.20 CISPEP 7 TYR A 92 PRO A 93 4 6.24 CISPEP 8 LYS A 113 PRO A 114 4 3.02 CISPEP 9 TYR A 92 PRO A 93 5 0.99 CISPEP 10 LYS A 113 PRO A 114 5 5.28 CISPEP 11 TYR A 92 PRO A 93 6 10.16 CISPEP 12 LYS A 113 PRO A 114 6 9.64 CISPEP 13 TYR A 92 PRO A 93 7 10.26 CISPEP 14 LYS A 113 PRO A 114 7 7.30 CISPEP 15 TYR A 92 PRO A 93 8 8.61 CISPEP 16 LYS A 113 PRO A 114 8 10.12 CISPEP 17 TYR A 92 PRO A 93 9 9.76 CISPEP 18 LYS A 113 PRO A 114 9 8.13 CISPEP 19 TYR A 92 PRO A 93 10 8.38 CISPEP 20 LYS A 113 PRO A 114 10 8.78 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000