HEADER HYDROLASE 18-MAR-05 1Z5F TITLE SOLUTION STRUCTURE OF THE CYTOTOXIC RC-RNASE 3 WITH A PYROGLUTAMATE TITLE 2 RESIDUE AT THE N-TERMINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RC-RNASE 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RC-RNASE3 RIBONUCLEASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RANA CATESBEIANA; SOURCE 3 ORGANISM_COMMON: BULLFROG; SOURCE 4 ORGANISM_TAXID: 8400; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TISSUE: OOCYTE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS RIBONUCLEASE, PYROGLUTAMATE, CYTOTOXICITY, BULLFROG, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.C.LOU,Y.C.HUANG,Y.R.PAN,C.CHEN,Y.D.LIAO REVDAT 4 23-OCT-24 1Z5F 1 REMARK REVDAT 3 25-DEC-19 1Z5F 1 JRNL REMARK SEQADV SEQRES REVDAT 3 2 1 LINK REVDAT 2 24-FEB-09 1Z5F 1 VERSN REVDAT 1 28-FEB-06 1Z5F 0 JRNL AUTH Y.C.LOU,Y.C.HUANG,Y.R.PAN,C.CHEN,Y.D.LIAO JRNL TITL ROLES OF N-TERMINAL PYROGLUTAMATE IN MAINTAINING STRUCTURAL JRNL TITL 2 INTEGRITY AND PKA VALUES OF CATALYTIC HISTIDINE RESIDUES IN JRNL TITL 3 BULLFROG RIBONUCLEASE 3 JRNL REF J.MOL.BIOL. V. 355 409 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16309702 JRNL DOI 10.1016/J.JMB.2005.10.069 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.H.HSU,Y.D.LIAO,L.W.CHEN,S.H.WU,Y.J.LEU,C.CHEN REMARK 1 TITL SOLUTION STRUCTURE OF THE CYTOTOXIC RNASE 4 FROM OOCYTES OF REMARK 1 TITL 2 BULLFROG RANA CATESBEIANA REMARK 1 REF J.MOL.BIOL. V. 326 1189 2003 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12589762 REMARK 1 DOI 10.1016/S0022-2836(02)01472-9 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Z5F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032320. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 3.5 REMARK 210 IONIC STRENGTH : 20 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM RC-RNASE 3, U-15N,13C; 20MM REMARK 210 PHOSPHATE BUFFER; 90% H2O, 10% REMARK 210 D2O; 2MM RC-RNASE 3, U-15N,13C; REMARK 210 20MM PHOSPHATE BUFFER; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; IPAP_1H, 15N_ REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 5.0, X-PLOR REMARK 210 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 4 -79.17 -62.29 REMARK 500 1 LYS A 16 64.36 -116.17 REMARK 500 1 LYS A 25 -131.72 -60.68 REMARK 500 1 ASP A 29 37.89 86.11 REMARK 500 1 CYS A 30 70.53 54.40 REMARK 500 1 LYS A 31 -129.72 -77.55 REMARK 500 1 LYS A 32 -32.61 -142.51 REMARK 500 1 LEU A 47 0.01 -69.95 REMARK 500 1 ASN A 50 -10.91 75.21 REMARK 500 1 ASP A 53 -148.68 -60.51 REMARK 500 1 ASP A 61 -94.91 -160.48 REMARK 500 1 LEU A 73 174.95 52.90 REMARK 500 1 VAL A 91 -147.27 -91.40 REMARK 500 1 GLN A 93 42.58 179.79 REMARK 500 1 ILE A 96 -7.31 -142.62 REMARK 500 1 ALA A 99 -74.66 -57.96 REMARK 500 2 GLU A 4 -79.31 -62.54 REMARK 500 2 VAL A 17 173.98 -51.99 REMARK 500 2 CYS A 19 -43.42 -29.57 REMARK 500 2 GLU A 22 -6.46 -55.40 REMARK 500 2 LYS A 25 -171.01 -51.44 REMARK 500 2 ASP A 29 35.71 71.22 REMARK 500 2 LYS A 31 -139.45 -68.54 REMARK 500 2 LYS A 32 -33.62 -133.76 REMARK 500 2 ASN A 50 -1.73 59.80 REMARK 500 2 ASP A 53 -147.75 -59.81 REMARK 500 2 ASP A 61 -69.25 -151.92 REMARK 500 2 LEU A 73 174.69 61.00 REMARK 500 2 VAL A 91 -148.58 -84.14 REMARK 500 2 GLN A 93 48.21 -179.99 REMARK 500 2 ILE A 96 -7.16 -142.38 REMARK 500 2 ALA A 99 -72.86 -62.12 REMARK 500 2 SER A 103 144.61 -171.13 REMARK 500 3 GLU A 4 -76.27 -60.25 REMARK 500 3 VAL A 17 170.37 -51.93 REMARK 500 3 GLU A 22 -3.47 -55.19 REMARK 500 3 LYS A 25 -163.71 -55.46 REMARK 500 3 ASP A 29 36.12 84.67 REMARK 500 3 LYS A 31 -142.76 -70.06 REMARK 500 3 LYS A 32 -32.44 -137.67 REMARK 500 3 ASN A 50 -12.39 73.98 REMARK 500 3 ARG A 52 -162.65 -100.19 REMARK 500 3 ASP A 53 -151.68 -58.89 REMARK 500 3 ASP A 61 -74.71 -118.28 REMARK 500 3 ILE A 71 -35.90 -138.60 REMARK 500 3 LEU A 73 174.27 53.17 REMARK 500 3 VAL A 91 -152.32 -83.03 REMARK 500 3 GLN A 93 47.36 -177.50 REMARK 500 3 ILE A 96 -25.32 -143.66 REMARK 500 3 ALA A 99 -72.25 -63.51 REMARK 500 REMARK 500 THIS ENTRY HAS 383 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KVZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF CYTOTOXIC RC-RNASE4 DBREF 1Z5F A 1 105 GB 15111749 AAG31440 24 128 SEQRES 1 A 105 PCA ASP TRP GLU THR PHE GLN LYS LYS HIS LEU THR ASP SEQRES 2 A 105 THR LYS LYS VAL LYS CYS ASP VAL GLU MET ALA LYS ALA SEQRES 3 A 105 LEU PHE ASP CYS LYS LYS THR ASN THR PHE ILE TYR ALA SEQRES 4 A 105 LEU PRO GLY ARG VAL LYS ALA LEU CYS LYS ASN ILE ARG SEQRES 5 A 105 ASP ASN THR ASP VAL LEU SER ARG ASP ALA PHE LEU LEU SEQRES 6 A 105 PRO GLN CYS ASP ARG ILE LYS LEU PRO CYS HIS TYR LYS SEQRES 7 A 105 LEU SER SER SER THR ASN THR ILE CYS ILE THR CYS VAL SEQRES 8 A 105 ASN GLN LEU PRO ILE HIS PHE ALA GLY VAL GLY SER CYS SEQRES 9 A 105 PRO MODRES 1Z5F PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 14 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA C5 H7 N O3 HELIX 1 1 ASP A 2 LYS A 9 1 8 HELIX 2 2 LYS A 18 LYS A 25 1 8 HELIX 3 3 LEU A 40 LEU A 47 1 8 SHEET 1 A 3 THR A 33 THR A 35 0 SHEET 2 A 3 PHE A 63 ASP A 69 -1 O CYS A 68 N ASN A 34 SHEET 3 A 3 LYS A 78 ASN A 84 -1 O SER A 80 N GLN A 67 SHEET 1 B 3 THR A 55 LEU A 58 0 SHEET 2 B 3 CYS A 87 CYS A 90 -1 O ILE A 88 N VAL A 57 SHEET 3 B 3 PRO A 95 GLY A 100 -1 O HIS A 97 N THR A 89 SSBOND 1 CYS A 19 CYS A 68 1555 1555 2.01 SSBOND 2 CYS A 30 CYS A 75 1555 1555 2.03 SSBOND 3 CYS A 48 CYS A 90 1555 1555 2.02 SSBOND 4 CYS A 87 CYS A 104 1555 1555 2.02 LINK C PCA A 1 N ASP A 2 1555 1555 1.30 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 MODEL 1 HETATM 1 N PCA A 1 -6.198 9.583 1.693 1.00 1.00 N HETATM 2 CA PCA A 1 -6.691 10.955 1.551 1.00 1.00 C HETATM 3 CB PCA A 1 -5.591 11.831 2.037 1.00 1.00 C HETATM 4 CG PCA A 1 -4.743 10.922 2.671 1.00 1.00 C HETATM 5 CD PCA A 1 -4.964 9.541 2.341 1.00 1.00 C HETATM 6 OE PCA A 1 -4.274 8.480 2.544 1.00 1.00 O HETATM 7 C PCA A 1 -7.038 11.262 0.103 1.00 1.00 C HETATM 8 O PCA A 1 -7.765 12.193 -0.178 1.00 1.00 O HETATM 9 H PCA A 1 -6.583 8.818 1.216 1.00 1.00 H HETATM 10 HA PCA A 1 -7.588 11.116 2.124 1.00 1.00 H HETATM 11 HB2 PCA A 1 -5.954 12.581 2.722 1.00 1.00 H HETATM 12 HB3 PCA A 1 -5.106 12.345 1.211 1.00 1.00 H HETATM 13 HG2 PCA A 1 -4.875 11.033 3.742 1.00 1.00 H HETATM 14 HG3 PCA A 1 -3.729 11.151 2.388 1.00 1.00 H