HEADER SIGNALING PROTEIN 05-JAN-15 4XH7 TITLE CRYSTAL STRUCTURE OF MUPP1 PDZ4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIPLE PDZ DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ 4 DOMAIN, UNP RESIDUES 521-665; 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: MPDZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MUPP1, PDZ DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.LIU,H.ZHU,W.LIU REVDAT 3 08-NOV-23 4XH7 1 SOURCE REMARK REVDAT 2 18-MAR-15 4XH7 1 JRNL REVDAT 1 04-MAR-15 4XH7 0 JRNL AUTH H.ZHU,Z.LIU,Y.HUANG,C.ZHANG,G.LI,W.LIU JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF MUPP1-PDZ4 JRNL TITL 2 DOMAIN FROM MUS MUSCULUS. JRNL REF ACTA BIOCHIM.BIOPHYS.SIN. V. 47 199 2015 JRNL REFN ESSN 1745-7270 JRNL PMID 25662616 JRNL DOI 10.1093/ABBS/GMV002 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 16031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 805 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 36.7040 - 2.9941 0.97 2615 131 0.1650 0.1789 REMARK 3 2 2.9941 - 2.3767 1.00 2569 136 0.1854 0.2179 REMARK 3 3 2.3767 - 2.0763 1.00 2544 133 0.1674 0.2158 REMARK 3 4 2.0763 - 1.8864 1.00 2513 135 0.1672 0.2184 REMARK 3 5 1.8864 - 1.7512 1.00 2543 132 0.1823 0.2213 REMARK 3 6 1.7512 - 1.6480 0.98 2442 138 0.2081 0.2967 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.012 830 REMARK 3 ANGLE : 1.372 1130 REMARK 3 CHIRALITY : 0.062 138 REMARK 3 PLANARITY : 0.008 145 REMARK 3 DIHEDRAL : 12.686 286 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 4XH7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0093 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16041 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.77300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3JXT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2%(V/V) POLYETHYLENE GLYCOL 400, 0.1 M REMARK 280 IMIDAZOLE, 24%(W/V) POLYETHYLENE GLYCOL MONOETHYL ETHER 5000, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 25.57100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.34050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.42200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.57100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.34050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.42200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.57100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.34050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.42200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.57100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.34050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.42200 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 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 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 517 REMARK 465 PRO A 518 REMARK 465 GLY A 519 REMARK 465 PRO A 630 REMARK 465 ILE A 631 REMARK 465 ALA A 632 REMARK 465 LEU A 633 REMARK 465 SER A 634 REMARK 465 GLU A 635 REMARK 465 MET A 636 REMARK 465 ASP A 637 REMARK 465 SER A 638 REMARK 465 LEU A 639 REMARK 465 ASP A 640 REMARK 465 ILE A 641 REMARK 465 ASN A 642 REMARK 465 ASP A 643 REMARK 465 LEU A 644 REMARK 465 GLU A 645 REMARK 465 LEU A 646 REMARK 465 THR A 647 REMARK 465 GLU A 648 REMARK 465 LYS A 649 REMARK 465 PRO A 650 REMARK 465 HIS A 651 REMARK 465 ILE A 652 REMARK 465 ASP A 653 REMARK 465 LEU A 654 REMARK 465 GLY A 655 REMARK 465 GLU A 656 REMARK 465 PHE A 657 REMARK 465 ILE A 658 REMARK 465 GLY A 659 REMARK 465 SER A 660 REMARK 465 SER A 661 REMARK 465 GLU A 662 REMARK 465 THR A 663 REMARK 465 GLU A 664 REMARK 465 ASP A 665 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 520 OG REMARK 470 GLU A 522 CG CD OE1 OE2 REMARK 470 ASP A 523 CG OD1 OD2 REMARK 470 GLN A 526 CG CD OE1 NE2 REMARK 470 ARG A 536 CD NE CZ NH1 NH2 REMARK 470 GLU A 554 CG CD OE1 OE2 REMARK 470 ASN A 555 CG OD1 ND2 REMARK 470 ARG A 572 NE CZ NH1 NH2 REMARK 470 LYS A 613 CD CE NZ REMARK 470 GLU A 614 CD OE1 OE2 REMARK 470 ARG A 626 CD NE CZ NH1 NH2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 701 DBREF 4XH7 A 521 665 UNP Q8VBX6 MPDZ_MOUSE 521 665 SEQADV 4XH7 GLY A 517 UNP Q8VBX6 EXPRESSION TAG SEQADV 4XH7 PRO A 518 UNP Q8VBX6 EXPRESSION TAG SEQADV 4XH7 GLY A 519 UNP Q8VBX6 EXPRESSION TAG SEQADV 4XH7 SER A 520 UNP Q8VBX6 EXPRESSION TAG SEQRES 1 A 149 GLY PRO GLY SER ALA GLU ASP VAL GLN GLN GLU ALA ALA SEQRES 2 A 149 LEU LEU THR LYS TRP GLN ARG ILE MET GLY ILE ASN TYR SEQRES 3 A 149 GLU ILE VAL VAL ALA HIS VAL SER LYS PHE SER GLU ASN SEQRES 4 A 149 SER GLY LEU GLY ILE SER LEU GLU ALA THR VAL GLY HIS SEQRES 5 A 149 HIS PHE ILE ARG SER VAL LEU PRO GLU GLY PRO VAL GLY SEQRES 6 A 149 HIS SER GLY LYS LEU PHE SER GLY ASP GLU LEU LEU GLU SEQRES 7 A 149 VAL ASN GLY ILE ASN LEU LEU GLY GLU ASN HIS GLN ASP SEQRES 8 A 149 VAL VAL ASN ILE LEU LYS GLU LEU PRO ILE ASP VAL THR SEQRES 9 A 149 MET VAL CYS CYS ARG ARG THR VAL PRO PRO ILE ALA LEU SEQRES 10 A 149 SER GLU MET ASP SER LEU ASP ILE ASN ASP LEU GLU LEU SEQRES 11 A 149 THR GLU LYS PRO HIS ILE ASP LEU GLY GLU PHE ILE GLY SEQRES 12 A 149 SER SER GLU THR GLU ASP HET IMD A 701 5 HETNAM IMD IMIDAZOLE FORMUL 2 IMD C3 H5 N2 1+ FORMUL 3 HOH *99(H2 O) HELIX 1 AA1 SER A 520 GLY A 539 1 20 HELIX 2 AA2 GLY A 578 GLY A 584 1 7 HELIX 3 AA3 ASN A 604 GLU A 614 1 11 SHEET 1 AA1 4 TYR A 542 SER A 550 0 SHEET 2 AA1 4 ASP A 618 ARG A 626 -1 O VAL A 619 N VAL A 549 SHEET 3 AA1 4 GLU A 591 VAL A 595 -1 N GLU A 591 O CYS A 624 SHEET 4 AA1 4 ILE A 598 ASN A 599 -1 O ILE A 598 N VAL A 595 SHEET 1 AA2 2 ILE A 560 THR A 565 0 SHEET 2 AA2 2 HIS A 568 VAL A 574 -1 O ARG A 572 N SER A 561 SITE 1 AC1 3 GLY A 584 LEU A 586 PHE A 587 CRYST1 51.142 52.681 96.844 90.00 90.00 90.00 I 2 2 2 8 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 0.019553 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018982 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010326 0.00000