HEADER PEPTIDE BINDING PROTEIN 23-MAR-12 3VQG 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; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: C-TERMINAL PEPTIDE FROM IMMUNOGLOBULIN SUPERFAMILY MEMBER COMPND 8 5; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: JAM-4; COMPND 11 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 14 ORGANISM_COMMON: MOUSE; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN MUS MUSCULUS KEYWDS PDZ DOMAIN, PEPTIDE BINDING, JAM4 (JUNCTIONAL ADHESION MOLECULE-4) C- KEYWDS 2 TERMINAL PEPTIDE, CYTOPLASM(LNX1), MEMBRANE(JAM4), PEPTIDE BINDING KEYWDS 3 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 3VQG 1 REMARK SEQADV REVDAT 1 27-MAR-13 3VQG 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 18904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 974 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 26.3329 - 2.5820 0.92 2447 136 0.1852 0.2166 REMARK 3 2 2.5820 - 2.0497 1.00 2573 166 0.1503 0.1943 REMARK 3 3 2.0497 - 1.7906 1.00 2592 133 0.1459 0.1759 REMARK 3 4 1.7906 - 1.6270 1.00 2608 135 0.1507 0.1972 REMARK 3 5 1.6270 - 1.5104 1.00 2606 129 0.1633 0.2054 REMARK 3 6 1.5104 - 1.4213 1.00 2598 137 0.2026 0.2558 REMARK 3 7 1.4213 - 1.3501 0.97 2506 138 0.2363 0.2600 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 35.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.35620 REMARK 3 B22 (A**2) : 6.16930 REMARK 3 B33 (A**2) : 10.35330 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.25770 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 : 0.005 748 REMARK 3 ANGLE : 1.032 1023 REMARK 3 CHIRALITY : 0.066 119 REMARK 3 PLANARITY : 0.005 137 REMARK 3 DIHEDRAL : 11.993 288 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 3VQG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000095372. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-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 : BL-1A 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 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09100 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) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.99100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 43.80 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 (%): 36.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% POLYETHLENE GLYCOL MONOMETHYL REMARK 280 ETHER 5000, 0.2M AMMONIUM SULFATE, 0.1M MES, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 30.42600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.38400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.42600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.38400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 227 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 238 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 465 TYR B 97 REMARK 465 LYS B 98 REMARK 465 VAL B 99 REMARK 465 ARG B 100 REMARK 465 ASN B 101 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NH2 ARG A 24 OD1 ASN A 50 2.16 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 ASN A 50 -5.71 80.40 REMARK 500 ARG A 78 -57.15 -145.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VQF RELATED DB: PDB REMARK 900 APO FORM OF THE SAME PROTEIN. DBREF 3VQG A 1 87 UNP O70263 LNX1_MOUSE 381 467 DBREF 3VQG B 98 105 UNP Q7TSN7 IGSF5_MOUSE 363 370 SEQADV 3VQG GLY A -6 UNP O70263 EXPRESSION TAG SEQADV 3VQG PRO A -5 UNP O70263 EXPRESSION TAG SEQADV 3VQG LEU A -4 UNP O70263 EXPRESSION TAG SEQADV 3VQG GLY A -3 UNP O70263 EXPRESSION TAG SEQADV 3VQG SER A -2 UNP O70263 EXPRESSION TAG SEQADV 3VQG ASP A -1 UNP O70263 EXPRESSION TAG SEQADV 3VQG HIS A 0 UNP O70263 EXPRESSION TAG SEQADV 3VQG TYR B 97 UNP Q7TSN7 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 SEQRES 1 B 9 TYR LYS VAL ARG ASN VAL THR LEU VAL HET SO4 A 101 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *117(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 4 PHE A 4 ASN A 9 0 SHEET 2 A 4 ARG A 79 SER A 85 -1 O LEU A 82 N VAL A 6 SHEET 3 A 4 ARG A 52 ILE A 56 -1 N ARG A 52 O SER A 85 SHEET 4 A 4 HIS A 59 ASP A 60 -1 O HIS A 59 N ILE A 56 SHEET 1 B 6 PHE A 4 ASN A 9 0 SHEET 2 B 6 ARG A 79 SER A 85 -1 O LEU A 82 N VAL A 6 SHEET 3 B 6 ARG A 52 ILE A 56 -1 N ARG A 52 O SER A 85 SHEET 4 B 6 VAL A 30 VAL A 35 -1 N VAL A 30 O VAL A 53 SHEET 5 B 6 ILE A 19 VAL A 22 -1 N LYS A 20 O PHE A 33 SHEET 6 B 6 THR B 103 VAL B 105 -1 O THR B 103 N LEU A 21 SITE 1 AC1 6 ILE A 7 ARG A 24 ARG A 79 HOH A 250 SITE 2 AC1 6 HOH A 295 HOH A 296 CRYST1 60.852 50.768 33.136 90.00 120.08 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 0.016433 0.000000 0.009519 0.00000 SCALE2 0.000000 0.019697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034876 0.00000