HEADER CHAPERONE 14-AUG-10 3OFH TITLE STRUCTURED DOMAIN OF MUS MUSCULUS MESD COMPND MOL_ID: 1; COMPND 2 MOLECULE: LDLR CHAPERONE MESD; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: STRUCTURED CORE RESIDUES 98-183; COMPND 5 SYNONYM: MESODERM DEVELOPMENT PROTEIN, MESODERM DEVELOPMENT CANDIDATE COMPND 6 2; COMPND 7 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: MESD, MESDC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS MESD, MOLECULAR CHAPERONE, PROTEIN FOLDING, YWTD PROPELLER, LRP, KEYWDS 2 CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR M.N.COLLINS,W.A.HENDRICKSON REVDAT 3 21-FEB-24 3OFH 1 SEQADV REVDAT 2 08-NOV-17 3OFH 1 REMARK REVDAT 1 02-MAR-11 3OFH 0 JRNL AUTH M.N.COLLINS,W.A.HENDRICKSON JRNL TITL STRUCTURAL CHARACTERIZATION OF THE BOCA/MESD MATURATION JRNL TITL 2 FACTORS FOR LDL-RECEPTOR-TYPE BETA-PROPELLER DOMAINS JRNL REF STRUCTURE 2011 JRNL REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1273 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 29.9373 - 3.6555 0.98 1911 212 0.1216 0.1425 REMARK 3 2 3.6555 - 2.9023 0.98 1906 214 0.1324 0.1538 REMARK 3 3 2.9023 - 2.5356 0.98 1897 212 0.1624 0.2217 REMARK 3 4 2.5356 - 2.3039 0.98 1883 206 0.1831 0.2288 REMARK 3 5 2.3039 - 2.1388 0.98 1894 215 0.1783 0.1873 REMARK 3 6 2.1388 - 2.0127 0.98 1849 207 0.1887 0.2117 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 : 0.39 REMARK 3 B_SOL : 49.82 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.11820 REMARK 3 B22 (A**2) : -2.11820 REMARK 3 B33 (A**2) : 1.33490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.2460 REMARK 3 OPERATOR: H,-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 1320 REMARK 3 ANGLE : 0.563 1788 REMARK 3 CHIRALITY : 0.035 198 REMARK 3 PLANARITY : 0.002 229 REMARK 3 DIHEDRAL : 13.767 465 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 22.4277 6.0224 -2.7908 REMARK 3 T TENSOR REMARK 3 T11: 0.0297 T22: 0.0731 REMARK 3 T33: 0.0665 T12: 0.0055 REMARK 3 T13: 0.0124 T23: -0.0419 REMARK 3 L TENSOR REMARK 3 L11: 0.0208 L22: 0.5670 REMARK 3 L33: 1.6846 L12: 0.3211 REMARK 3 L13: -0.1390 L23: -0.7939 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: -0.1290 S13: 0.0154 REMARK 3 S21: -0.0889 S22: -0.0378 S23: -0.0773 REMARK 3 S31: 0.1304 S32: 0.0525 S33: 0.0156 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 24.8114 -8.7399 11.6679 REMARK 3 T TENSOR REMARK 3 T11: 0.0475 T22: 0.1056 REMARK 3 T33: 0.0503 T12: -0.0534 REMARK 3 T13: -0.0019 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.7655 L22: 0.9172 REMARK 3 L33: 0.4013 L12: 0.6075 REMARK 3 L13: 0.4333 L23: -0.1199 REMARK 3 S TENSOR REMARK 3 S11: 0.1232 S12: 0.2037 S13: 0.0091 REMARK 3 S21: 0.0879 S22: -0.1380 S23: -0.0212 REMARK 3 S31: -0.0233 S32: 0.1368 S33: 0.0235 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 3OFH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000061049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : MONOCHROMATOR + MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12634 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.14800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7-0.9M AMPO4 AND 100MM HEPES PH7.5, REMARK 280 STREAK SEEDED WITH MICRO-CRYSTALS, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 18.55100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.82650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.27550 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 95 REMARK 465 SER A 96 REMARK 465 HIS A 97 REMARK 465 GLY B 95 REMARK 465 SER B 96 REMARK 465 HIS B 97 REMARK 465 MET B 98 REMARK 465 THR B 99 REMARK 465 LYS B 100 REMARK 465 LYS B 101 REMARK 465 GLY B 102 REMARK 465 PRO B 182 REMARK 465 GLY B 183 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 LYS A 103 CD CE NZ REMARK 470 ASN A 114 OD1 ND2 REMARK 470 LYS A 118 CE NZ REMARK 470 ARG A 147 NE CZ NH1 NH2 REMARK 470 ARG A 153 CD NE CZ NH1 NH2 REMARK 470 GLN A 179 CG CD OE1 NE2 REMARK 470 LYS B 103 CB CG CD CE NZ REMARK 470 LEU B 105 CD1 CD2 REMARK 470 LYS B 118 CD CE NZ REMARK 470 ASN B 135 CG OD1 ND2 REMARK 470 ARG B 153 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 179 CG CD OE1 NE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OFE RELATED DB: PDB REMARK 900 ORTHOLOG REMARK 900 RELATED ID: 3OFF RELATED DB: PDB REMARK 900 ORTHOLOG REMARK 900 RELATED ID: 3OFG RELATED DB: PDB REMARK 900 ORTHOLOG REMARK 900 RELATED ID: 2I9S RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF MESD STRUCTURE DOMAIN REMARK 900 RELATED ID: 2RQK RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF MESD REMARK 900 RELATED ID: 2RQM RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF MESD DBREF 3OFH A 98 183 UNP Q9ERE7 MESD_MOUSE 98 183 DBREF 3OFH B 98 183 UNP Q9ERE7 MESD_MOUSE 98 183 SEQADV 3OFH GLY A 95 UNP Q9ERE7 EXPRESSION TAG SEQADV 3OFH SER A 96 UNP Q9ERE7 EXPRESSION TAG SEQADV 3OFH HIS A 97 UNP Q9ERE7 EXPRESSION TAG SEQADV 3OFH GLY B 95 UNP Q9ERE7 EXPRESSION TAG SEQADV 3OFH SER B 96 UNP Q9ERE7 EXPRESSION TAG SEQADV 3OFH HIS B 97 UNP Q9ERE7 EXPRESSION TAG SEQRES 1 A 89 GLY SER HIS MET THR LYS LYS GLY LYS THR LEU MET MET SEQRES 2 A 89 PHE VAL THR VAL SER GLY ASN PRO THR GLU LYS GLU THR SEQRES 3 A 89 GLU GLU ILE THR SER LEU TRP GLN GLY SER LEU PHE ASN SEQRES 4 A 89 ALA ASN TYR ASP VAL GLN ARG PHE ILE VAL GLY SER ASP SEQRES 5 A 89 ARG ALA ILE PHE MET LEU ARG ASP GLY SER TYR ALA TRP SEQRES 6 A 89 GLU ILE LYS ASP PHE LEU VAL SER GLN ASP ARG CYS ALA SEQRES 7 A 89 GLU VAL THR LEU GLU GLY GLN MET TYR PRO GLY SEQRES 1 B 89 GLY SER HIS MET THR LYS LYS GLY LYS THR LEU MET MET SEQRES 2 B 89 PHE VAL THR VAL SER GLY ASN PRO THR GLU LYS GLU THR SEQRES 3 B 89 GLU GLU ILE THR SER LEU TRP GLN GLY SER LEU PHE ASN SEQRES 4 B 89 ALA ASN TYR ASP VAL GLN ARG PHE ILE VAL GLY SER ASP SEQRES 5 B 89 ARG ALA ILE PHE MET LEU ARG ASP GLY SER TYR ALA TRP SEQRES 6 B 89 GLU ILE LYS ASP PHE LEU VAL SER GLN ASP ARG CYS ALA SEQRES 7 B 89 GLU VAL THR LEU GLU GLY GLN MET TYR PRO GLY FORMUL 3 HOH *108(H2 O) HELIX 1 1 THR A 116 ALA A 134 1 19 HELIX 2 2 ASP A 154 SER A 156 5 3 HELIX 3 3 TYR A 157 SER A 167 1 11 HELIX 4 4 THR B 116 ALA B 134 1 19 HELIX 5 5 TYR B 157 SER B 167 1 11 SHEET 1 A 5 VAL A 138 ILE A 142 0 SHEET 2 A 5 ARG A 147 LEU A 152 -1 O ILE A 149 N PHE A 141 SHEET 3 A 5 LEU A 105 VAL A 111 -1 N MET A 107 O PHE A 150 SHEET 4 A 5 CYS A 171 LEU A 176 -1 O THR A 175 N PHE A 108 SHEET 5 A 5 GLN A 179 TYR A 181 -1 O GLN A 179 N LEU A 176 SHEET 1 B 5 VAL B 138 ILE B 142 0 SHEET 2 B 5 ARG B 147 LEU B 152 -1 O MET B 151 N GLN B 139 SHEET 3 B 5 LEU B 105 VAL B 111 -1 N LEU B 105 O LEU B 152 SHEET 4 B 5 CYS B 171 LEU B 176 -1 O ALA B 172 N THR B 110 SHEET 5 B 5 GLN B 179 TYR B 181 -1 O TYR B 181 N VAL B 174 CISPEP 1 TYR A 181 PRO A 182 0 5.46 CISPEP 2 PRO A 182 GLY A 183 0 6.42 CRYST1 71.651 71.651 37.102 90.00 90.00 90.00 P 43 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 0.013957 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026953 0.00000