PDB Short entry for 2KJD HEADER SIGNALING PROTEIN 27-MAY-09 2KJD TITLE SOLUTION STRUCTURE OF EXTENDED PDZ2 DOMAIN FROM NHERF1 (150-270) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM/HYDROGEN EXCHANGE REGULATORY COFACTOR NHE-RF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTENDED PDZ2 DOMAIN: UNP RESIDUES 150-270; COMPND 5 SYNONYM: NHERF-1, EZRIN-RADIXIN-MOESIN-BINDING PHOSPHOPROTEIN 50, COMPND 6 EBP50, REGULATORY COFACTOR OF NA(+)/H(+) EXCHANGER, SODIUM-HYDROGEN COMPND 7 EXCHANGER REGULATORY FACTOR 1, SOLUTE CARRIER FAMILY 9 ISOFORM A3 COMPND 8 REGULATORY FACTOR 1; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SLC9A3R1, NHERF, NHERF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET151/D-TOPO KEYWDS PDZ DOMAIN, PROTEIN, ACETYLATION, CELL PROJECTION, DISEASE MUTATION, KEYWDS 2 MEMBRANE, PHOSPHOPROTEIN, POLYMORPHISM, WNT SIGNALING PATHWAY, KEYWDS 3 SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.BHATTACHARYA,D.COWBURN,Z.BU REVDAT 2 16-MAR-22 2KJD 1 REMARK SEQADV REVDAT 1 29-DEC-09 2KJD 0 JRNL AUTH S.BHATTACHARYA,Z.DAI,J.LI,S.BAXTER,D.J.E.CALLAWAY,D.COWBURN, JRNL AUTH 2 Z.BU JRNL TITL A DYNAMIC INTRAMOLECULAR CONFORMATIONAL SWITCH AUTOREGULATES JRNL TITL 2 THE SCAFFOLDING PROTEIN NHERF1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 1.3, ARIA 2.2 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000101192. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0.150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 550 UM [U-100% 13C; U-100% 15N] REMARK 210 PDZ2-270-1, 20 MM HEPES-2, 0.5 REMARK 210 MM DTT-3, 0.1 MM PMSF-4, 150 MM REMARK 210 SODIUM CHLORIDE-5, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D HCCH-TOCSY; 3D REMARK 210 H(CCO)NH; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.5, TOPSPIN 2.1, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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 HH12 ARG A 56 OD1 ASP A 94 1.57 REMARK 500 OE2 GLU A 59 HG SER A 105 1.58 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 ILE A 2 52.65 -93.97 REMARK 500 1 PRO A 19 -72.92 -60.62 REMARK 500 1 SER A 20 20.26 -146.19 REMARK 500 1 ASP A 43 50.34 -105.39 REMARK 500 1 GLN A 54 -0.02 78.96 REMARK 500 1 PRO A 112 30.49 -76.76 REMARK 500 1 LEU A 113 164.18 59.24 REMARK 500 1 THR A 118 -58.65 73.58 REMARK 500 1 ASN A 119 -81.64 -125.02 REMARK 500 1 GLU A 121 87.56 59.12 REMARK 500 2 PRO A 19 47.50 -76.98 REMARK 500 2 TYR A 22 -162.06 -106.55 REMARK 500 2 MET A 65 68.78 -105.14 REMARK 500 2 GLU A 66 -73.17 -66.70 REMARK 500 2 PRO A 116 109.27 -58.15 REMARK 500 2 LYS A 124 48.96 -86.69 REMARK 500 2 ASN A 126 -71.40 -67.06 REMARK 500 2 SER A 127 90.00 -169.88 REMARK 500 3 MET A 7 53.43 -91.21 REMARK 500 3 PRO A 116 39.35 -79.63 REMARK 500 3 GLN A 123 -41.69 -139.92 REMARK 500 3 LYS A 124 -28.24 -176.08 REMARK 500 3 GLU A 125 73.04 52.30 REMARK 500 4 THR A 6 -150.62 -79.91 REMARK 500 4 LYS A 17 98.89 -69.17 REMARK 500 4 SER A 20 67.38 63.30 REMARK 500 4 TYR A 22 -75.02 68.08 REMARK 500 4 THR A 118 21.00 -149.07 REMARK 500 4 LYS A 124 78.27 50.08 REMARK 500 4 GLU A 125 -70.92 -66.44 REMARK 500 4 ASN A 126 97.59 -169.25 REMARK 500 5 ILE A 2 47.76 -88.16 REMARK 500 5 MET A 7 -70.54 -77.57 REMARK 500 5 LEU A 109 93.73 -55.00 REMARK 500 5 ASN A 110 -14.70 72.54 REMARK 500 5 VAL A 115 121.13 68.75 REMARK 500 5 PHE A 117 96.59 62.85 REMARK 500 5 GLN A 123 74.36 50.82 REMARK 500 5 GLU A 125 -66.40 -175.00 REMARK 500 6 PRO A 4 -71.13 -57.86 REMARK 500 6 PHE A 5 58.96 -143.72 REMARK 500 6 PRO A 19 97.97 -65.43 REMARK 500 6 SER A 20 -47.19 71.39 REMARK 500 6 TYR A 22 -79.79 68.13 REMARK 500 6 ARG A 52 -164.30 -124.56 REMARK 500 6 THR A 118 -85.44 59.09 REMARK 500 6 ASN A 119 31.55 -151.33 REMARK 500 7 ILE A 2 86.77 53.00 REMARK 500 7 PRO A 4 46.66 -76.35 REMARK 500 7 PHE A 5 74.33 62.30 REMARK 500 REMARK 500 THIS ENTRY HAS 160 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JXO RELATED DB: PDB REMARK 900 NMR STRUCTURE OF CANONICAL PDZ DOMAIN (150-240) REMARK 900 RELATED ID: 2OZF RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF CANONICAL PDZ DOMAIN (150-239) DBREF 2KJD A 8 128 UNP O14745 NHRF1_HUMAN 150 270 SEQADV 2KJD GLY A 1 UNP O14745 EXPRESSION TAG SEQADV 2KJD ILE A 2 UNP O14745 EXPRESSION TAG SEQADV 2KJD ASP A 3 UNP O14745 EXPRESSION TAG SEQADV 2KJD PRO A 4 UNP O14745 EXPRESSION TAG SEQADV 2KJD PHE A 5 UNP O14745 EXPRESSION TAG SEQADV 2KJD THR A 6 UNP O14745 EXPRESSION TAG SEQADV 2KJD MET A 7 UNP O14745 EXPRESSION TAG SEQRES 1 A 128 GLY ILE ASP PRO PHE THR MET LEU ARG PRO ARG LEU CYS SEQRES 2 A 128 THR MET LYS LYS GLY PRO SER GLY TYR GLY PHE ASN LEU SEQRES 3 A 128 HIS SER ASP LYS SER LYS PRO GLY GLN PHE ILE ARG SER SEQRES 4 A 128 VAL ASP PRO ASP SER PRO ALA GLU ALA SER GLY LEU ARG SEQRES 5 A 128 ALA GLN ASP ARG ILE VAL GLU VAL ASN GLY VAL CYS MET SEQRES 6 A 128 GLU GLY LYS GLN HIS GLY ASP VAL VAL SER ALA ILE ARG SEQRES 7 A 128 ALA GLY GLY ASP GLU THR LYS LEU LEU VAL VAL ASP ARG SEQRES 8 A 128 GLU THR ASP GLU PHE PHE LYS LYS CYS ARG VAL ILE PRO SEQRES 9 A 128 SER GLN GLU HIS LEU ASN GLY PRO LEU PRO VAL PRO PHE SEQRES 10 A 128 THR ASN GLY GLU ILE GLN LYS GLU ASN SER ARG HELIX 1 1 SER A 44 GLY A 50 1 7 HELIX 2 2 GLN A 69 ALA A 79 1 11 HELIX 3 3 ASP A 90 ARG A 101 1 12 HELIX 4 4 SER A 105 ASN A 110 1 6 SHEET 1 A 4 ARG A 11 LYS A 16 0 SHEET 2 A 4 GLU A 83 VAL A 89 -1 O LEU A 86 N CYS A 13 SHEET 3 A 4 ARG A 56 VAL A 60 -1 N VAL A 58 O LEU A 87 SHEET 4 A 4 VAL A 63 CYS A 64 -1 O VAL A 63 N VAL A 60 SHEET 1 B 2 PHE A 24 SER A 28 0 SHEET 2 B 2 GLN A 35 VAL A 40 -1 O SER A 39 N ASN A 25 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