PDB Short entry for 2M4N HEADER UNKNOWN FUNCTION 07-FEB-13 2M4N TITLE SOLUTION STRUCTURE OF THE PUTATIVE RAS INTERACTION DOMAIN OF AFD-1, TITLE 2 ISOFORM A FROM CAENORHABDITIS ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN AFD-1, ISOFORM A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 214-320; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: AFD-1, W03F11.6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: MODIFIED PET28A KEYWDS STRUCTURAL GENOMICS, UNKNOWN FUNCTION, THIOREDOXIN-LIKE, NEW YORK KEYWDS 2 STRUCTURAL GENOMICS RESEARCH CONSORTIUM, NYSGRC, ASSEMBLY, DYNAMICS KEYWDS 3 AND EVOLUTION OF CELL-CELL AND CELL-MATRIX ADHESIONS, CELLMAT, PSI- KEYWDS 4 BIOLOGY EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.HARRIS,B.HILLERICH,M.AHMED,J.B.BONANNO,S.CHAMALA,B.EVANS,J.LAFLEUR, AUTHOR 2 J.HAMMONDS,E.WASHINGTON,M.STEAD,J.LOVE,J.ATTONITO,R.D.SEIDEL, AUTHOR 3 R.C.LIDDINGTON,W.I.WEIS,W.J.NELSON,M.E.GIRVIN,S.C.ALMO,NEW YORK AUTHOR 4 STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NYSGRC),ASSEMBLY,DYNAMICS AUTHOR 5 AND EVOLUTION OF CELL-CELL AND CELL-MATRIX ADHESIONS (CELLMAT) REVDAT 2 14-JUN-23 2M4N 1 REMARK SEQADV REVDAT 1 20-MAR-13 2M4N 0 JRNL AUTH R.HARRIS,B.HILLERICH,M.AHMED,J.B.BONANNO,S.CHAMALA,B.EVANS, JRNL AUTH 2 J.LAFLEUR,J.HAMMONDS,E.WASHINGTON,M.STEAD,J.LOVE,J.ATTONITO, JRNL AUTH 3 R.D.SEIDEL,Y.M.CHOOK,M.P.ROUT,R.C.LIDDINGTON,W.I.WEIS, JRNL AUTH 4 W.J.NELSON,M.E.GIRVIN,S.C.ALMO JRNL TITL SOLUTION STRUCTURE OF THE PUTATIVE RAS INTERACTION DOMAIN OF JRNL TITL 2 AFD-1, ISOFORM A FROM CAENORHABDITIS ELEGANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.21, X-PLOR NIH 2.32 REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. (CNS), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN A BOX OF WATER REMARK 4 REMARK 4 2M4N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000103203. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 13C; U-100% 15N] REMARK 210 PUTATIVE RAS INTERACTION DOMAIN REMARK 210 OF AFD, ISOFORM A, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 1 MM DTT, 0.1 MM EDTA, 90% H2O, REMARK 210 10% D2O; 1.0 MM [U-100% 13C; U- REMARK 210 100% 15N] PUTATIVE RAS REMARK 210 INTERACTION DOMAIN OF AFD, REMARK 210 ISOFORM A, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 1 MM DTT, 0.1 MM EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N HSQC; 15N NOESY-HSQC; 13C REMARK 210 HSQC; AROMATIC 13C HSQC; 13C REMARK 210 NOESY-HSQC; 13C AROMATIC NOESY- REMARK 210 HSQC; HNCO; HNCACO; HNCOCA; REMARK 210 HNCACB; CBCACONH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ 2.2D, TOPSPIN 1.3 & 2.1, REMARK 210 NMRPIPE 7.5, MDDNMR 2.2, MDDGUI REMARK 210 1.0, CCPN_ANALYSIS, ARIA 2.3, REMARK 210 SIDER, X-PLOR NIH 2.32 REMARK 210 METHOD USED : SIMULATING ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 STRUCTURES FOR LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: ALL 3D EXPERIMENTS WERE ACQUIRED USING 30% NON-UNIFORM REMARK 210 SAMPLING USING THE MDDNMR APPROACH 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 ASP A 67 -163.57 63.25 REMARK 500 1 ILE A 71 125.91 70.77 REMARK 500 1 ASN A 92 108.88 67.91 REMARK 500 1 GLU A 94 -71.23 -176.27 REMARK 500 2 GLU A 13 -47.16 71.99 REMARK 500 2 SER A 47 -81.85 -83.41 REMARK 500 2 LYS A 48 -40.80 65.44 REMARK 500 2 MET A 65 -9.23 67.42 REMARK 500 2 ASP A 67 -162.29 66.88 REMARK 500 2 ILE A 71 95.33 43.61 REMARK 500 2 SER A 90 -158.03 49.89 REMARK 500 2 GLU A 94 -95.78 -87.50 REMARK 500 3 ASP A 60 -127.17 59.37 REMARK 500 3 ARG A 62 -11.63 153.04 REMARK 500 3 SER A 64 -56.37 -169.72 REMARK 500 3 SER A 66 -31.56 166.67 REMARK 500 3 ASP A 67 109.41 64.31 REMARK 500 3 ASP A 72 -82.80 -96.26 REMARK 500 3 GLU A 94 -77.77 -61.21 REMARK 500 4 PHE A 3 -71.50 74.53 REMARK 500 4 SER A 47 30.43 -93.93 REMARK 500 4 ASP A 67 -148.53 65.76 REMARK 500 4 ILE A 71 88.48 35.24 REMARK 500 4 SER A 90 -171.14 46.68 REMARK 500 4 GLU A 94 -28.49 64.08 REMARK 500 4 PHE A 97 -100.94 43.99 REMARK 500 5 MET A 2 -87.99 -101.16 REMARK 500 5 PHE A 3 -71.65 64.58 REMARK 500 5 SER A 47 -81.97 -98.14 REMARK 500 5 LYS A 48 -49.03 70.09 REMARK 500 5 ASP A 60 -43.20 -161.51 REMARK 500 5 ASP A 61 -45.80 166.35 REMARK 500 5 ARG A 62 22.52 136.22 REMARK 500 5 LYS A 63 -64.13 -135.62 REMARK 500 5 ASP A 67 75.23 58.78 REMARK 500 5 LEU A 68 87.77 58.50 REMARK 500 5 ARG A 69 -76.72 -96.72 REMARK 500 5 ILE A 71 97.75 63.74 REMARK 500 5 CYS A 81 78.58 -111.68 REMARK 500 5 ASN A 95 -30.50 -176.29 REMARK 500 6 MET A 2 73.90 59.68 REMARK 500 6 PHE A 3 -69.61 68.89 REMARK 500 6 GLU A 13 -66.69 72.89 REMARK 500 6 ASP A 59 -20.79 -144.92 REMARK 500 6 LEU A 68 67.88 61.92 REMARK 500 6 ASP A 72 116.79 -167.50 REMARK 500 6 SER A 90 87.27 15.86 REMARK 500 6 ASN A 92 -71.10 -71.95 REMARK 500 6 ASP A 98 -51.06 70.51 REMARK 500 6 PRO A 107 -155.65 -76.49 REMARK 500 REMARK 500 THIS ENTRY HAS 176 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGRC-010744 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 19014 RELATED DB: BMRB DBREF 2M4N A 2 108 UNP Q9BIC1 Q9BIC1_CAEEL 214 320 SEQADV 2M4N SER A 1 UNP Q9BIC1 EXPRESSION TAG SEQRES 1 A 108 SER MET PHE GLY GLY SER LEU LYS VAL TYR GLY GLY GLU SEQRES 2 A 108 ILE VAL PRO THR ARG PRO TYR VAL SER ILE LEU ALA GLU SEQRES 3 A 108 ILE ASN GLU ASN ALA ASP ARG ILE LEU GLY ALA ALA LEU SEQRES 4 A 108 GLU LYS TYR GLY LEU GLU HIS SER LYS ASP ASP PHE ILE SEQRES 5 A 108 LEU VAL GLU VAL SER ASN ASP ASP ASP ARG LYS SER MET SEQRES 6 A 108 SER ASP LEU ARG GLU ILE ASP GLY ARG PRO ILE PRO PRO SEQRES 7 A 108 THR GLU CYS PRO LEU PHE GLU MET THR ALA ARG SER GLY SEQRES 8 A 108 ASN GLY GLU ASN GLY PHE ASP SER PHE LEU ALA ILE LYS SEQRES 9 A 108 ARG LYS PRO HIS HELIX 1 1 ASN A 30 TYR A 42 1 13 HELIX 2 2 LEU A 44 ASP A 49 5 6 HELIX 3 3 PRO A 82 SER A 90 1 9 SHEET 1 A 2 SER A 6 TYR A 10 0 SHEET 2 A 2 TYR A 20 LEU A 24 -1 O VAL A 21 N VAL A 9 SHEET 1 B 3 ARG A 74 ILE A 76 0 SHEET 2 B 3 PHE A 51 SER A 57 -1 N LEU A 53 O ILE A 76 SHEET 3 B 3 SER A 99 ARG A 105 -1 O ALA A 102 N VAL A 54 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