HEADER PROTEIN BINDING 23-FEB-06 2G5M TITLE SPINOPHILIN PDZ DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURABIN-2; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 SYNONYM: NEURABIN-II, NEURAL TISSUE-SPECIFIC F-ACTIN BINDING PROTEIN COMPND 6 II, PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 9B, SPINOPHILIN, P130, COMPND 7 PP1BP134; COMPND 8 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: PPP1R9B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: DERIVITIVE OF PET28A KEYWDS SPINOPHILIN, PDZ DOMAIN, CNS, SYNAPTIC TRANSMISSION, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.S.KELKER,W.PETI REVDAT 5 29-MAY-24 2G5M 1 REMARK REVDAT 4 09-MAR-22 2G5M 1 REMARK SEQADV REVDAT 3 24-FEB-09 2G5M 1 VERSN REVDAT 2 27-MAR-07 2G5M 1 JRNL REVDAT 1 09-JAN-07 2G5M 0 JRNL AUTH M.S.KELKER,B.DANCHECK,T.JU,R.P.KESSLER,J.HUDAK,A.C.NAIRN, JRNL AUTH 2 W.PETI JRNL TITL STRUCTURAL BASIS FOR SPINOPHILIN-NEURABIN RECEPTOR JRNL TITL 2 INTERACTION. JRNL REF BIOCHEMISTRY V. 46 2333 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17279777 JRNL DOI 10.1021/BI602341C REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, CNS 1.1 REMARK 3 AUTHORS : BRUKER (TOPSPIN), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE AMINO ACID SEQUENCE, THE CHEMICAL REMARK 3 SHIFT ASSIGNMENT, AND THE NOESY SPECTRA WERE INPUT FOR THE REMARK 3 AUTOMATED NOESY PEAK PICKING AND NOE ASSIGNMENT METHOD OF ATNOS/ REMARK 3 CANDID/CYANA. THE RESULTS OF ATNOS/CANDID/CYANA WERE REFINED BY REMARK 3 MANUAL PEAK ADJUSTMENT AND ADDITIONAL CALCULATIONS IN CYANA. THE REMARK 3 20 CONFORMERS FROM THE ATNOS/CANDID CYCLE 7 WITH THE LOWEST REMARK 3 RESIDUAL CYANA TARGET FUNCTION VALUES WERE ENERGY-MINIMIZED IN A REMARK 3 WATER SHELL WITH THE PROGRAM CNS. REMARK 4 REMARK 4 2G5M COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036717. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 MM NA PHOSPHATE; 50 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.8 MM PDZ DOMAIN, 15N SAMPLES; REMARK 210 20 MM NA PHOSPHATE BUFFER 50 MM REMARK 210 NACL, PH 6.5; 90% H2O, 10% D2O; REMARK 210 1.8 MM PDZ DOMAIN, 13C/15N REMARK 210 SAMPLES; 20 MM NA PHOSPHATE REMARK 210 BUFFER 50 MM NACL, PH 6.5; 90% REMARK 210 H2O, 10% D2O; 1.8 MM PDZ DOMAIN, REMARK 210 13C/15N SAMPLES; 20 MM NA REMARK 210 PHOSPHATE BUFFER 50 MM NACL, PH REMARK 210 6.5; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 15N RESOLVED [1H,1H] NOESY; REMARK 210 3D 13C RESOLVED [1H,1H] NOESY; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0, ATNOS/CANDID 2.0, REMARK 210 CARA 1.5 REMARK 210 METHOD USED : SIMULATED ANNEALING TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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: REMARK 210 THE FOLLOWING SPECTRA WERE USED TO ACHIEVE THE SEQUENCE-SPECIFIC REMARK 210 BACKBONE AND SIDE CHAIN ASSIGNMENTS OF ALL ALIPHATIC RESIDUES: 2D REMARK 210 [1H,15N]-HSQC, 2D [1H,13C]-HSQC, 3D HNCACB, 3D CBCA(CO)NH, 3D REMARK 210 CC(CO)NH, 3D HNCO, 3D HNCA, 3D HBHA(CO)NH, 3D 15N-RESOLVED [1H,1H]- REMARK 210 TOCSY, 3D HC(C)H-TOCSY6. THE 2D [1H,1H]-NOESY, 2D [1H,1H]-TOCSY REMARK 210 AND 2D [1H,1H]-COSY SPECTRA OF THE SPINOPHILIN493-602 SAMPLE IN REMARK 210 D2O SOLUTION AFTER COMPLETE H/D EXCHANGE OF THE LABILE PROTONS REMARK 210 WERE USED FOR THE ASSIGNMENT OF THE AROMATIC SIDE CHAINS. THE NMR REMARK 210 SPECTRA WERE PROCESSED WITH TOPSPIN1.3, AND ANALYZED WITH THE CARA REMARK 210 SOFTWARE PACKAGE. REMARK 210 SPECTRA USED FOR THE STRUCTURE CALCULATION WERE: 3D 15N- REMARK 210 RESOLVED [1H,1H]-NOESY, 3D 13C-RESOLVED [1H,1H]-NOESY (MIXING TIME REMARK 210 OF 85 MS) AND 2D [1H,1H]-NOESY (MIXING TIME 85 MS, D2O SOLUTION). 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: B 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 MET B 30 77.85 61.89 REMARK 500 1 LEU B 32 -64.24 178.44 REMARK 500 1 GLU B 33 86.86 45.86 REMARK 500 1 ARG B 53 -69.41 -103.07 REMARK 500 1 THR B 66 115.66 -160.64 REMARK 500 1 VAL B 69 -40.46 70.05 REMARK 500 1 LYS B 84 -173.76 -67.89 REMARK 500 1 GLU B 98 23.27 -79.29 REMARK 500 1 ALA B 103 -65.68 67.50 REMARK 500 1 LEU B 105 -172.26 60.47 REMARK 500 1 GLN B 107 94.61 55.94 REMARK 500 2 ALA B 28 79.26 -68.91 REMARK 500 2 LEU B 32 -53.62 -121.55 REMARK 500 2 ARG B 53 -63.46 -91.96 REMARK 500 2 VAL B 61 -74.36 -79.20 REMARK 500 2 LYS B 84 -162.40 -73.56 REMARK 500 2 ARG B 93 94.57 -69.72 REMARK 500 2 ALA B 103 -91.73 -118.93 REMARK 500 3 ASP B 29 49.89 -75.24 REMARK 500 3 LEU B 32 26.91 -150.50 REMARK 500 3 LYS B 34 86.58 -64.91 REMARK 500 3 VAL B 63 -168.45 -102.39 REMARK 500 3 LYS B 84 -166.07 -66.56 REMARK 500 3 GLU B 98 77.45 -103.53 REMARK 500 3 GLN B 99 -66.69 -129.72 REMARK 500 3 GLN B 108 34.80 -84.04 REMARK 500 4 ALA B 26 -45.95 -163.72 REMARK 500 4 MET B 30 45.75 -91.74 REMARK 500 4 GLU B 33 22.04 49.01 REMARK 500 4 ARG B 53 -79.44 -109.75 REMARK 500 4 LYS B 84 -178.70 -60.37 REMARK 500 4 GLN B 99 -51.13 -157.16 REMARK 500 4 GLU B 101 73.45 54.40 REMARK 500 4 ALA B 103 86.84 71.86 REMARK 500 4 GLN B 104 88.51 55.71 REMARK 500 4 ILE B 106 -57.71 -150.81 REMARK 500 4 LEU B 110 -79.70 68.12 REMARK 500 4 GLU B 111 -49.34 65.34 REMARK 500 5 ASP B 13 -164.37 -103.17 REMARK 500 5 LEU B 32 18.11 167.40 REMARK 500 5 LEU B 35 119.37 -35.70 REMARK 500 5 ARG B 53 -60.17 -101.39 REMARK 500 5 VAL B 69 -27.20 73.28 REMARK 500 5 LYS B 84 -169.18 -75.64 REMARK 500 5 ALA B 103 -65.83 -141.92 REMARK 500 5 GLN B 108 -23.27 167.50 REMARK 500 5 LEU B 110 33.07 73.70 REMARK 500 5 GLN B 112 -35.86 -176.85 REMARK 500 6 ALA B 28 86.71 -160.57 REMARK 500 6 ARG B 53 -74.77 -107.82 REMARK 500 REMARK 500 THIS ENTRY HAS 172 RAMACHANDRAN OUTLIERS. 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 4 ARG B 50 0.07 SIDE CHAIN REMARK 500 4 ARG B 86 0.07 SIDE CHAIN REMARK 500 4 ARG B 93 0.07 SIDE CHAIN REMARK 500 7 ARG B 86 0.08 SIDE CHAIN REMARK 500 15 ARG B 86 0.07 SIDE CHAIN REMARK 500 16 ARG B 95 0.07 SIDE CHAIN REMARK 500 17 ARG B 93 0.09 SIDE CHAIN REMARK 500 18 ARG B 95 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FN5 RELATED DB: PDB REMARK 900 NEURABIN PDZ DOMAIN COORDINATES REMARK 900 RELATED ID: 6927 RELATED DB: BMRB REMARK 900 SPINOPHILIN PDZ DOMAIN PEAK LISTS REMARK 900 RELATED ID: 6933 RELATED DB: BMRB REMARK 900 NEURABIN PDZ DOMAIN PEAK LISTS DBREF 2G5M B 4 113 UNP O35274 NEB2_RAT 493 602 SEQADV 2G5M GLY B 1 UNP O35274 CLONING ARTIFACT SEQADV 2G5M HIS B 2 UNP O35274 CLONING ARTIFACT SEQADV 2G5M MET B 3 UNP O35274 CLONING ARTIFACT SEQRES 1 B 113 GLY HIS MET GLU LEU PHE PRO VAL GLU LEU GLU LYS ASP SEQRES 2 B 113 SER GLU GLY LEU GLY ILE SER ILE ILE GLY MET GLY ALA SEQRES 3 B 113 GLY ALA ASP MET GLY LEU GLU LYS LEU GLY ILE PHE VAL SEQRES 4 B 113 LYS THR VAL THR GLU GLY GLY ALA ALA HIS ARG ASP GLY SEQRES 5 B 113 ARG ILE GLN VAL ASN ASP LEU LEU VAL GLU VAL ASP GLY SEQRES 6 B 113 THR SER LEU VAL GLY VAL THR GLN SER PHE ALA ALA SER SEQRES 7 B 113 VAL LEU ARG ASN THR LYS GLY ARG VAL ARG PHE MET ILE SEQRES 8 B 113 GLY ARG GLU ARG PRO GLY GLU GLN SER GLU VAL ALA GLN SEQRES 9 B 113 LEU ILE GLN GLN THR LEU GLU GLN GLU HELIX 1 1 GLY B 46 GLY B 52 1 7 HELIX 2 2 THR B 72 THR B 83 1 12 SHEET 1 A 4 GLU B 4 GLU B 9 0 SHEET 2 A 4 ARG B 88 ARG B 93 -1 O PHE B 89 N VAL B 8 SHEET 3 A 4 LEU B 60 VAL B 63 -1 N GLU B 62 O MET B 90 SHEET 4 A 4 THR B 66 SER B 67 -1 O THR B 66 N VAL B 63 SHEET 1 B 2 SER B 20 GLY B 25 0 SHEET 2 B 2 LEU B 35 THR B 41 -1 O GLY B 36 N MET B 24 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