HEADER SIGNALING PROTEIN 18-OCT-01 1K76 TITLE SOLUTION STRUCTURE OF THE C-TERMINAL SEM-5 SH3 DOMAIN (MINIMIZED TITLE 2 AVERAGE STRUCTURE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEX MUSCLE ABNORMAL PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN (RESIDUES 155-214); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: SEM-5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET19B KEYWDS ALL BETA PROTEIN, SIGNALING PROTEIN EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR J.FERREON,D.VOLK,B.LUXON,D.GORENSTEIN,V.HILSER REVDAT 3 27-OCT-21 1K76 1 REMARK SEQADV REVDAT 2 24-FEB-09 1K76 1 VERSN REVDAT 1 20-MAY-03 1K76 0 JRNL AUTH J.FERREON,D.VOLK,B.LUXON,D.GORENSTEIN,V.HILSER JRNL TITL SOLUTION STRUCTURE, DYNAMICS AND THERMODYNAMICS OF THE JRNL TITL 2 NATIVE STATE ENSEMBLE OF SEM-5 C-TERMINAL SH3 DOMAIN JRNL REF BIOCHEMISTRY V. 42 5582 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12741814 JRNL DOI 10.1021/BI030005J REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER (CNS), BRUNGER, ET AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014645. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.8 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 13C,15N 1MM SEM-5 SH3 DOMAIN 50 REMARK 210 MM SODIUM ACETATE BUFFER, 10 MM REMARK 210 CACL2, 100 MM NACL,PH 4.8, 90% REMARK 210 H20, 10%D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 15N-NOESY-HSQC; 3D 13C-NOESY REMARK 210 -HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, VNMR REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED REMARK 210 USING TRIPLE-RESONANCE NMR SPECTROSCOPY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 HIS A 1 REMARK 465 MET A 2 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 HE2 PHE A 51 HG13 VAL A 56 1.10 REMARK 500 OD2 ASP A 27 HD12 LEU A 44 1.42 REMARK 500 O SER A 61 HA ASN A 62 1.45 REMARK 500 OD1 ASP A 27 HD23 LEU A 44 1.52 REMARK 500 O ASN A 60 N ASN A 62 1.63 REMARK 500 C SER A 61 CA ASN A 62 1.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 3 N GLU A 3 CA -0.282 REMARK 500 GLU A 3 CA GLU A 3 CB -0.138 REMARK 500 GLU A 3 CA GLU A 3 C -0.273 REMARK 500 GLU A 3 C THR A 4 N -0.184 REMARK 500 THR A 4 N THR A 4 CA -0.218 REMARK 500 LYS A 5 CB LYS A 5 CG -0.192 REMARK 500 LYS A 24 CA LYS A 24 CB -0.141 REMARK 500 ARG A 25 CD ARG A 25 NE -0.136 REMARK 500 ARG A 25 NE ARG A 25 CZ -0.105 REMARK 500 ARG A 47 CZ ARG A 47 NH1 0.115 REMARK 500 ARG A 48 CD ARG A 48 NE -0.115 REMARK 500 ASN A 60 CA ASN A 60 C -0.226 REMARK 500 ASN A 60 C SER A 61 N -0.166 REMARK 500 SER A 61 N SER A 61 CA -0.254 REMARK 500 SER A 61 CA SER A 61 CB -0.100 REMARK 500 SER A 61 C ASN A 62 N -0.186 REMARK 500 ASN A 62 N ASN A 62 CA -0.290 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 3 CA - C - N ANGL. DEV. = -13.6 DEGREES REMARK 500 LYS A 5 CG - CD - CE ANGL. DEV. = -18.0 DEGREES REMARK 500 PHE A 11 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 LYS A 24 CB - CG - CD ANGL. DEV. = -30.0 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 25 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 48 NE - CZ - NH1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASN A 60 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 ASN A 60 N - CA - CB ANGL. DEV. = 15.6 DEGREES REMARK 500 ASN A 60 CA - C - N ANGL. DEV. = -15.4 DEGREES REMARK 500 ASN A 62 C - N - CA ANGL. DEV. = -23.5 DEGREES REMARK 500 ASN A 62 CA - CB - CG ANGL. DEV. = -23.9 DEGREES REMARK 500 ASN A 62 N - CA - C ANGL. DEV. = -22.9 DEGREES 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 LYS A 24 -166.19 -123.28 REMARK 500 ASN A 45 -37.75 79.65 REMARK 500 ASN A 46 -23.05 -171.78 REMARK 500 ALA A 57 114.65 -161.34 REMARK 500 ASN A 60 62.24 38.54 REMARK 500 SER A 61 94.93 -25.22 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 ARG A 47 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1K76 A 3 62 UNP P29355 SEM5_CAEEL 155 214 SEQADV 1K76 ALA A 57 UNP P29355 CYS 209 ENGINEERED MUTATION SEQRES 1 A 62 HIS MET GLU THR LYS PHE VAL GLN ALA LEU PHE ASP PHE SEQRES 2 A 62 ASN PRO GLN GLU SER GLY GLU LEU ALA PHE LYS ARG GLY SEQRES 3 A 62 ASP VAL ILE THR LEU ILE ASN LYS ASP ASP PRO ASN TRP SEQRES 4 A 62 TRP GLU GLY GLN LEU ASN ASN ARG ARG GLY ILE PHE PRO SEQRES 5 A 62 SER ASN TYR VAL ALA PRO TYR ASN SER ASN SHEET 1 A 5 ARG A 47 PRO A 52 0 SHEET 2 A 5 TRP A 39 LEU A 44 -1 N GLY A 42 O GLY A 49 SHEET 3 A 5 VAL A 28 ASN A 33 -1 N THR A 30 O GLN A 43 SHEET 4 A 5 PHE A 6 ALA A 9 -1 N VAL A 7 O ILE A 29 SHEET 5 A 5 VAL A 56 PRO A 58 -1 O ALA A 57 N GLN A 8 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