HEADER PEPTIDE BINDING PROTEIN 22-MAR-12 3VQF TITLE CRYSTAL STRUCTURE ANALYSIS OF THE PDZ DOMAIN DERIVED FROM THE TIGHT TITLE 2 JUNCTION REGULATING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE LNX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SECOND PDZ DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: LNX1; 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: PGEX-6P3-PRESAT KEYWDS PDZ DOMAIN, CLAUDIN C-TERMINUS, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.AKIYOSHI,D.HAMADA,N.GODA,T.TENNO,H.NARITA,A.NAKAGAWA,M.FURUSE, AUTHOR 2 M.SUZUKI,H.HIROAKI REVDAT 2 08-NOV-23 3VQF 1 SEQADV REVDAT 1 27-MAR-13 3VQF 0 JRNL AUTH Y.AKIYOSHI,Y.NAKAKURA,D.HAMADA,N.GODA,T.TENNO,H.NARITA, JRNL AUTH 2 A.NAKAGAWA,M.FURUSE,M.SUZUKI,H.HIROAKI JRNL TITL STRUCTURAL BASIS FOR DOWN REGULATION OF TIGHT JUNCTION BY JRNL TITL 2 PDZ-DOMAIN CONTAINING E3-UBIQUITIN LIGASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 27350 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.2010 - 2.5815 0.99 2637 155 0.1548 0.1525 REMARK 3 2 2.5815 - 2.0492 1.00 2621 147 0.1494 0.1685 REMARK 3 3 2.0492 - 1.7903 1.00 2634 137 0.1471 0.1768 REMARK 3 4 1.7903 - 1.6266 1.00 2610 138 0.1346 0.1838 REMARK 3 5 1.6266 - 1.5100 1.00 2601 149 0.1177 0.1530 REMARK 3 6 1.5100 - 1.4210 0.99 2583 144 0.1186 0.1520 REMARK 3 7 1.4210 - 1.3499 0.99 2613 129 0.1251 0.1499 REMARK 3 8 1.3499 - 1.2911 0.99 2589 123 0.1380 0.1768 REMARK 3 9 1.2911 - 1.2414 0.98 2541 143 0.1498 0.2034 REMARK 3 10 1.2414 - 1.1986 0.97 2525 131 0.1599 0.1631 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 39.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07730 REMARK 3 B22 (A**2) : -0.59690 REMARK 3 B33 (A**2) : 0.67420 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.40670 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 734 REMARK 3 ANGLE : 1.087 1005 REMARK 3 CHIRALITY : 0.075 112 REMARK 3 PLANARITY : 0.005 138 REMARK 3 DIHEDRAL : 12.444 293 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VQF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000095371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27350 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.199 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.18400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2VWR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 8000, 0.2M SODIUM ACETATE, REMARK 280 0.1M BIS-TRIS, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 30.24650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.60500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.24650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.60500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 275 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 277 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -6 REMARK 465 PRO A -5 REMARK 465 LEU A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 ASP A -1 REMARK 465 HIS A 0 REMARK 465 ASP A 1 REMARK 465 ASP A 2 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 ASN A 50 -4.49 81.33 REMARK 500 ARG A 78 -59.10 -146.12 REMARK 500 ARG A 78 -56.96 -147.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 3VQF A 1 87 UNP O70263 LNX1_MOUSE 381 467 SEQADV 3VQF GLY A -6 UNP O70263 EXPRESSION TAG SEQADV 3VQF PRO A -5 UNP O70263 EXPRESSION TAG SEQADV 3VQF LEU A -4 UNP O70263 EXPRESSION TAG SEQADV 3VQF GLY A -3 UNP O70263 EXPRESSION TAG SEQADV 3VQF SER A -2 UNP O70263 EXPRESSION TAG SEQADV 3VQF ASP A -1 UNP O70263 EXPRESSION TAG SEQADV 3VQF HIS A 0 UNP O70263 EXPRESSION TAG SEQRES 1 A 94 GLY PRO LEU GLY SER ASP HIS ASP ASP SER PHE HIS VAL SEQRES 2 A 94 ILE LEU ASN LYS SER SER PRO GLU GLU GLN LEU GLY ILE SEQRES 3 A 94 LYS LEU VAL ARG ARG VAL ASP GLU PRO GLY VAL PHE ILE SEQRES 4 A 94 PHE ASN VAL LEU ASN GLY GLY VAL ALA ASP ARG HIS GLY SEQRES 5 A 94 GLN LEU GLU GLU ASN ASP ARG VAL LEU ALA ILE ASN GLY SEQRES 6 A 94 HIS ASP LEU ARG PHE GLY SER PRO GLU SER ALA ALA HIS SEQRES 7 A 94 LEU ILE GLN ALA SER GLU ARG ARG VAL HIS LEU VAL VAL SEQRES 8 A 94 SER ARG GLN FORMUL 2 HOH *181(H2 O) HELIX 1 1 GLY A 39 GLY A 45 1 7 HELIX 2 2 SER A 65 SER A 76 1 12 SHEET 1 A 5 PHE A 4 ASN A 9 0 SHEET 2 A 5 ARG A 79 SER A 85 -1 O LEU A 82 N VAL A 6 SHEET 3 A 5 ARG A 52 ILE A 56 -1 N ARG A 52 O SER A 85 SHEET 4 A 5 VAL A 30 VAL A 35 -1 N VAL A 30 O VAL A 53 SHEET 5 A 5 ILE A 19 VAL A 22 -1 N LYS A 20 O PHE A 33 SHEET 1 B 4 PHE A 4 ASN A 9 0 SHEET 2 B 4 ARG A 79 SER A 85 -1 O LEU A 82 N VAL A 6 SHEET 3 B 4 ARG A 52 ILE A 56 -1 N ARG A 52 O SER A 85 SHEET 4 B 4 HIS A 59 ASP A 60 -1 O HIS A 59 N ILE A 56 CRYST1 60.493 51.210 33.291 90.00 120.00 90.00 C 1 2 1 4 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 0.016531 0.000000 0.009543 0.00000 SCALE2 0.000000 0.019527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034684 0.00000