HEADER PROTEIN BINDING 04-MAR-14 4PQQ TITLE THE CRYSTAL STRUCTURE OF DISCOIDIN DOMAIN FROM MUSKELIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUSKELIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, UNP RESIDUES 12-167; 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: MKLN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS JELLY-ROLL, CELL SPREADING MEDIATOR, PROSTAGLANDIN EP3 RECEPTOR, KEYWDS 2 ALPHA ISOFORM, RANBP9, PHOSPHORYLATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.-H.KIM,S.K.HONG,E.E.KIM REVDAT 3 28-FEB-24 4PQQ 1 REMARK REVDAT 2 19-NOV-14 4PQQ 1 JRNL REVDAT 1 12-NOV-14 4PQQ 0 JRNL AUTH K.H.KIM,S.K.HONG,K.Y.HWANG,E.E.KIM JRNL TITL STRUCTURE OF MOUSE MUSKELIN DISCOIDIN DOMAIN AND BIOCHEMICAL JRNL TITL 2 CHARACTERIZATION OF ITS SELF-ASSOCIATION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 2863 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25372678 JRNL DOI 10.1107/S139900471401894X REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 29469 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2024 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 27.1650 - 3.7323 0.99 1977 138 0.1355 0.1364 REMARK 3 2 3.7323 - 2.9636 1.00 1980 154 0.1477 0.1759 REMARK 3 3 2.9636 - 2.5893 1.00 2000 137 0.1655 0.2120 REMARK 3 4 2.5893 - 2.3527 1.00 2000 151 0.1618 0.1514 REMARK 3 5 2.3527 - 2.1842 1.00 1962 162 0.1541 0.1988 REMARK 3 6 2.1842 - 2.0554 1.00 1998 146 0.1432 0.1700 REMARK 3 7 2.0554 - 1.9525 0.99 1998 129 0.1508 0.1926 REMARK 3 8 1.9525 - 1.8676 1.00 1954 148 0.1514 0.1931 REMARK 3 9 1.8676 - 1.7957 0.99 1983 139 0.1500 0.1632 REMARK 3 10 1.7957 - 1.7337 0.98 1977 157 0.1574 0.2048 REMARK 3 11 1.7337 - 1.6795 0.98 1953 140 0.1733 0.2076 REMARK 3 12 1.6795 - 1.6315 0.98 1938 150 0.1764 0.2120 REMARK 3 13 1.6315 - 1.5886 0.97 1918 142 0.1916 0.1912 REMARK 3 14 1.5886 - 1.5498 0.89 1807 131 0.1938 0.2268 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) : 17.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.31 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 : 0.007 1353 REMARK 3 ANGLE : 1.142 1827 REMARK 3 CHIRALITY : 0.091 190 REMARK 3 PLANARITY : 0.006 228 REMARK 3 DIHEDRAL : 14.894 512 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 4PQQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085104. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-13; 20-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PAL/PLS; PAL/PLS REMARK 200 BEAMLINE : 5C (4A); 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97951; 0.97918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL; DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS; MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R; ADSC QUANTUM REMARK 200 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 24.3950 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.18400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500, 0.1M SPG(SUCCINATE REMARK 280 -PHOSPHATE-GLYCINE), PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 49.15150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.37763 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.10567 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 49.15150 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 28.37763 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.10567 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 49.15150 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 28.37763 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.10567 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.75526 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 38.21133 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 56.75526 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 38.21133 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 56.75526 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 38.21133 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 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 202 REMARK 610 PG4 A 203 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 203 DBREF 4PQQ A 12 167 UNP O89050 MKLN1_MOUSE 12 167 SEQRES 1 A 156 GLU CYS ARG LEU LEU PRO TYR ALA LEU HIS LYS TRP SER SEQRES 2 A 156 SER PHE SER SER THR TYR LEU PRO GLU ASN ILE LEU VAL SEQRES 3 A 156 ASP LYS PRO ASN ASP GLN SER SER ARG TRP SER SER GLU SEQRES 4 A 156 SER ASN TYR PRO PRO GLN TYR LEU ILE LEU LYS LEU GLU SEQRES 5 A 156 ARG PRO ALA ILE VAL GLN ASN ILE THR PHE GLY LYS TYR SEQRES 6 A 156 GLU LYS THR HIS VAL CYS ASN LEU LYS LYS PHE LYS VAL SEQRES 7 A 156 PHE GLY GLY MET ASN GLU GLU ASN MET THR GLU LEU LEU SEQRES 8 A 156 SER SER GLY LEU LYS ASN ASP TYR ASN LYS GLU THR PHE SEQRES 9 A 156 THR LEU LYS HIS LYS ILE ASP GLU GLN MET PHE PRO CYS SEQRES 10 A 156 ARG PHE ILE LYS ILE VAL PRO LEU LEU SER TRP GLY PRO SEQRES 11 A 156 SER PHE ASN PHE SER ILE TRP TYR VAL GLU LEU SER GLY SEQRES 12 A 156 ILE ASP ASP PRO ASP ILE VAL GLN PRO CYS LEU ASN TRP HET PO4 A 201 5 HET PG4 A 202 12 HET PG4 A 203 12 HETNAM PO4 PHOSPHATE ION HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 2 PO4 O4 P 3- FORMUL 3 PG4 2(C8 H18 O5) FORMUL 5 HOH *203(H2 O) HELIX 1 1 LEU A 31 VAL A 37 5 7 HELIX 2 2 ASP A 157 GLN A 162 1 6 HELIX 3 3 PRO A 163 LEU A 165 5 3 SHEET 1 A 6 ARG A 14 LEU A 15 0 SHEET 2 A 6 VAL A 150 ILE A 155 -1 O GLY A 154 N ARG A 14 SHEET 3 A 6 LEU A 58 PHE A 73 -1 N ILE A 67 O ILE A 155 SHEET 4 A 6 CYS A 128 SER A 138 -1 O ILE A 131 N LEU A 60 SHEET 5 A 6 LEU A 84 ASN A 94 -1 N LYS A 88 O VAL A 134 SHEET 6 A 6 ASN A 97 SER A 104 -1 O LEU A 101 N VAL A 89 SHEET 1 B 3 TYR A 18 TRP A 23 0 SHEET 2 B 3 LEU A 58 PHE A 73 -1 O ILE A 59 N LYS A 22 SHEET 3 B 3 GLU A 113 THR A 116 -1 O PHE A 115 N ILE A 71 SHEET 1 C 2 TRP A 47 SER A 48 0 SHEET 2 C 2 SER A 146 ILE A 147 -1 O ILE A 147 N TRP A 47 SHEET 1 D 2 LYS A 120 ILE A 121 0 SHEET 2 D 2 GLN A 124 MET A 125 -1 O GLN A 124 N ILE A 121 CISPEP 1 PRO A 54 PRO A 55 0 0.23 SITE 1 AC1 11 PHE A 26 SER A 27 SER A 28 GLU A 50 SITE 2 AC1 11 ARG A 129 HOH A 335 HOH A 352 HOH A 356 SITE 3 AC1 11 HOH A 369 HOH A 438 HOH A 453 SITE 1 AC2 4 PHE A 90 GLU A 95 LYS A 132 HOH A 370 SITE 1 AC3 8 TYR A 53 ASN A 97 THR A 99 ILE A 121 SITE 2 AC3 8 ASN A 166 HOH A 325 HOH A 349 HOH A 456 CRYST1 98.303 98.303 57.317 90.00 90.00 120.00 H 3 9 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 0.010173 0.005873 0.000000 0.00000 SCALE2 0.000000 0.011746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017447 0.00000