HEADER SIGNALING PROTEIN 19-JUN-17 5W72 TITLE IMPACT OF IR ACTIVE PROBES ON PDZ3 AND ITS LIGAND BINDING STUDIED BY TITLE 2 NMR AND X-RAY CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISKS LARGE HOMOLOG 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POSTSYNAPTIC DENSITY PROTEIN 95,PSD-95,SYNAPSE-ASSOCIATED COMPND 5 PROTEIN 90,SAP90,PDZ3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: DLG4, DLGH4, PSD95; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: B834 KEYWDS SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.LEHNER,D.KUDLINZKI,H.SCHWALBE,R.SILVERS REVDAT 5 15-NOV-23 5W72 1 LINK ATOM REVDAT 4 30-OCT-19 5W72 1 REMARK REVDAT 3 08-MAY-19 5W72 1 REMARK REVDAT 2 24-APR-19 5W72 1 SEQRES REVDAT 1 13-DEC-17 5W72 0 JRNL AUTH F.LEHNER,D.KUDLINZKI,C.RICHTER,H.M.MULLER-WERKMEISTER, JRNL AUTH 2 K.B.EBERL,J.BREDENBECK,H.SCHWALBE,R.SILVERS JRNL TITL IMPACT OF AZIDOHOMOALANINE INCORPORATION ON PROTEIN JRNL TITL 2 STRUCTURE AND LIGAND BINDING. JRNL REF CHEMBIOCHEM V. 18 2340 2017 JRNL REFN ESSN 1439-7633 JRNL PMID 28950050 JRNL DOI 10.1002/CBIC.201700437 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY REMARK 3 AUTHORS : GODDARD REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CYANA REMARK 4 REMARK 4 5W72 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000228535. 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 : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-98% 13C; U-98% 15N] REMARK 210 PDZ3, 50 MM SODIUM PHOSPHATE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H NOESY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 2D 13C-15N DF-NOESY; 3D 13C REMARK 210 EDITED 13C-15N DF-NOESY; 3D 15N REMARK 210 EDITED 13C-15N DF-NOESY; 3D REMARK 210 HNCACB; 3D HNCO; 3D HNHA; 3D REMARK 210 HCCCONH REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.97, TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 LEU A 302 -64.88 -126.46 REMARK 500 1 ASP A 306 -171.55 -60.93 REMARK 500 1 ILE A 307 77.12 64.27 REMARK 500 1 ARG A 309 101.87 -54.40 REMARK 500 1 SER A 371 177.40 -57.64 REMARK 500 1 LYS A 393 70.46 -150.04 REMARK 500 2 PRO A 308 -171.01 -69.79 REMARK 500 2 ARG A 309 36.73 -95.07 REMARK 500 2 GLU A 352 -52.51 -124.63 REMARK 500 2 LYS A 393 67.32 -150.08 REMARK 500 3 GLU A 305 147.99 -175.71 REMARK 500 3 ASP A 306 -178.63 -58.87 REMARK 500 3 ILE A 307 82.08 -177.72 REMARK 500 3 SER A 339 -72.73 -94.60 REMARK 500 3 GLU A 352 -53.43 -121.37 REMARK 500 3 SER A 371 175.51 -58.63 REMARK 500 3 LYS A 393 75.05 -150.06 REMARK 500 4 GLU A 304 -69.93 -108.64 REMARK 500 4 GLU A 305 108.54 -175.18 REMARK 500 4 ASP A 306 131.93 -179.42 REMARK 500 4 PRO A 308 -170.95 -69.72 REMARK 500 4 SER A 339 -66.74 -95.66 REMARK 500 4 SER A 371 177.26 -58.16 REMARK 500 5 LEU A 302 -59.93 -127.01 REMARK 500 5 GLU A 352 -50.65 -128.56 REMARK 500 5 THR A 385 119.00 -161.96 REMARK 500 6 ASP A 306 -75.43 -113.31 REMARK 500 6 PRO A 308 92.42 -69.76 REMARK 500 6 SER A 339 -70.46 -98.77 REMARK 500 6 GLN A 384 -71.30 -108.75 REMARK 500 6 LYS A 393 67.52 -150.02 REMARK 500 7 ASP A 306 -74.57 -71.38 REMARK 500 7 SER A 339 -64.57 -100.41 REMARK 500 7 SER A 371 172.75 -59.40 REMARK 500 7 LYS A 393 68.23 -150.03 REMARK 500 8 LEU A 302 -74.63 -123.60 REMARK 500 8 ASP A 306 -177.11 -179.35 REMARK 500 8 ILE A 307 63.73 -152.93 REMARK 500 8 SER A 339 -67.89 -105.96 REMARK 500 8 TYR A 392 109.69 -53.40 REMARK 500 8 LYS A 393 75.05 -150.04 REMARK 500 9 GLU A 305 -57.20 -132.05 REMARK 500 9 ILE A 307 74.12 35.58 REMARK 500 9 PRO A 308 78.61 -69.76 REMARK 500 9 SER A 339 -73.23 -101.78 REMARK 500 9 SER A 371 177.01 -59.78 REMARK 500 9 THR A 385 116.89 -162.65 REMARK 500 10 GLU A 305 -74.68 -101.82 REMARK 500 10 PRO A 308 -170.85 -69.81 REMARK 500 10 ARG A 309 95.01 -61.90 REMARK 500 REMARK 500 THIS ENTRY HAS 108 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30307 RELATED DB: BMRB REMARK 900 IMPACT OF IR ACTIVE PROBES ON PDZ3 AND ITS LIGAND BINDING STUDIED REMARK 900 BY NMR AND X-RAY CRYSTALLOGRAPHY DBREF 5W72 A 301 402 UNP P31016 DLG4_RAT 301 402 SEQADV 5W72 PHE A 301 UNP P31016 LEU 301 CONFLICT SEQADV 5W72 ILE A 328 UNP P31016 VAL 328 CONFLICT SEQADV 5W72 AZH A 341 UNP P31016 ILE 341 CONFLICT SEQRES 1 A 102 PHE LEU GLY GLU GLU ASP ILE PRO ARG GLU PRO ARG ARG SEQRES 2 A 102 ILE VAL ILE HIS ARG GLY SER THR GLY LEU GLY PHE ASN SEQRES 3 A 102 ILE ILE GLY GLY GLU ASP GLY GLU GLY ILE PHE ILE SER SEQRES 4 A 102 PHE AZH LEU ALA GLY GLY PRO ALA ASP LEU SER GLY GLU SEQRES 5 A 102 LEU ARG LYS GLY ASP GLN ILE LEU SER VAL ASN GLY VAL SEQRES 6 A 102 ASP LEU ARG ASN ALA SER HIS GLU GLN ALA ALA ILE ALA SEQRES 7 A 102 LEU LYS ASN ALA GLY GLN THR VAL THR ILE ILE ALA GLN SEQRES 8 A 102 TYR LYS PRO GLU GLU TYR SER ARG PHE GLU ALA HET AZH A 341 15 HETNAM AZH AZIDOHOMOALANINE FORMUL 1 AZH C4 H9 N4 O2 1+ HELIX 1 AA1 ARG A 318 GLY A 322 5 5 HELIX 2 AA2 GLY A 345 GLY A 351 1 7 HELIX 3 AA3 SER A 371 ASN A 381 1 11 HELIX 4 AA4 LYS A 393 ARG A 399 1 7 SHEET 1 AA1 4 ARG A 312 ILE A 314 0 SHEET 2 AA1 4 ILE A 388 GLN A 391 -1 O ILE A 388 N ILE A 314 SHEET 3 AA1 4 GLN A 358 VAL A 362 -1 N SER A 361 O ILE A 389 SHEET 4 AA1 4 VAL A 365 ASP A 366 -1 O VAL A 365 N VAL A 362 SHEET 1 AA2 2 PHE A 325 ILE A 328 0 SHEET 2 AA2 2 PHE A 337 AZH A 341 -1 O PHE A 337 N ILE A 328 LINK C PHE A 340 N AZH A 341 1555 1555 1.34 LINK C AZH A 341 N LEU A 342 1555 1555 1.33 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