HEADER CELL ADHESION 19-DEC-12 4IHK TITLE CRYSTAL STRUCTURE OF THE COLLAGEN VI ALPHA3 N5 DOMAIN R1061Q COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN ALPHA3(VI); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COLLAGEN VI ALPHA3 N5M, UNP RESIDUES 1022-1224; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: C57BL6; SOURCE 6 GENE: COL6A3; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET 15B KEYWDS CELL ADHESION, COLLAGEN VI 3N5, VWA EXPDTA X-RAY DIFFRACTION AUTHOR H.MIKOLAJEK,A.K.A.BECKER,M.PAULSSON,R.WAGENER,J.M.WERNER REVDAT 3 08-NOV-23 4IHK 1 SEQADV REVDAT 2 05-DEC-18 4IHK 1 JRNL REVDAT 1 18-DEC-13 4IHK 0 JRNL AUTH A.K.BECKER,H.MIKOLAJEK,M.PAULSSON,R.WAGENER,J.M.WERNER JRNL TITL A STRUCTURE OF A COLLAGEN VI VWA DOMAIN DISPLAYS N AND C JRNL TITL 2 TERMINI AT OPPOSITE SIDES OF THE PROTEIN JRNL REF STRUCTURE V. 22 199 2014 JRNL REFN ISSN 1878-4186 JRNL PMID 24332716 JRNL DOI 10.1016/J.STR.2013.06.028 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 38.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 53314 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2707 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 38.3692 - 3.1749 0.99 2915 152 0.1650 0.1716 REMARK 3 2 3.1749 - 2.5201 1.00 2761 139 0.1575 0.1993 REMARK 3 3 2.5201 - 2.2016 1.00 2724 137 0.1291 0.1457 REMARK 3 4 2.2016 - 2.0003 1.00 2709 153 0.1179 0.1459 REMARK 3 5 2.0003 - 1.8570 1.00 2675 145 0.1187 0.1436 REMARK 3 6 1.8570 - 1.7475 1.00 2682 140 0.1141 0.1482 REMARK 3 7 1.7475 - 1.6600 1.00 2647 147 0.1076 0.1418 REMARK 3 8 1.6600 - 1.5877 1.00 2653 160 0.1013 0.1245 REMARK 3 9 1.5877 - 1.5266 1.00 2641 147 0.1030 0.1308 REMARK 3 10 1.5266 - 1.4739 1.00 2680 125 0.1132 0.1687 REMARK 3 11 1.4739 - 1.4278 1.00 2628 140 0.1209 0.1696 REMARK 3 12 1.4278 - 1.3870 1.00 2650 146 0.1238 0.1858 REMARK 3 13 1.3870 - 1.3505 1.00 2614 144 0.1288 0.1900 REMARK 3 14 1.3505 - 1.3175 1.00 2656 142 0.1434 0.1967 REMARK 3 15 1.3175 - 1.2876 1.00 2645 129 0.1446 0.2169 REMARK 3 16 1.2876 - 1.2602 1.00 2588 161 0.1486 0.1799 REMARK 3 17 1.2602 - 1.2350 1.00 2617 127 0.1629 0.1756 REMARK 3 18 1.2350 - 1.2117 1.00 2658 128 0.1791 0.2605 REMARK 3 19 1.2117 - 1.2000 0.95 2464 145 0.1888 0.2230 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.92 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 : 0.008 1652 REMARK 3 ANGLE : 1.319 2276 REMARK 3 CHIRALITY : 0.076 268 REMARK 3 PLANARITY : 0.008 313 REMARK 3 DIHEDRAL : 12.118 632 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 4IHK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97780 REMARK 200 MONOCHROMATOR : ACCEL FIXED EXIT DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53401 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 19.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04000 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 (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: PDB ENTRY 4IGI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CHLORIDE, 0.1M REMARK 280 PHOSPHATE/CITRATE, 20% PEG 8000, PH 4.2, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 53.43500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.53500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.53500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 80.15250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.53500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.53500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.71750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.53500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.53500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 80.15250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.53500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.53500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.71750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.43500 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 A1434 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1491 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 PRO A 1215 REMARK 465 ILE A 1216 REMARK 465 LEU A 1217 REMARK 465 THR A 1218 REMARK 465 PRO A 1219 REMARK 465 SER A 1220 REMARK 465 THR A 1221 REMARK 465 GLY A 1222 REMARK 465 ALA A 1223 REMARK 465 GLY A 1224 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 A1214 CG CD CE NZ 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 GLN A1061 -122.03 -131.33 REMARK 500 SER A1070 -107.23 -146.90 REMARK 500 SER A1070 -106.47 -144.39 REMARK 500 LEU A1117 57.48 -90.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IGI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COLLAGEN VI ALPHA3 N5 DOMAIN DBREF 4IHK A 1022 1224 UNP Q9Z0I9 Q9Z0I9_MOUSE 1022 1224 SEQADV 4IHK GLN A 1061 UNP Q9Z0I9 ARG 1061 ENGINEERED MUTATION SEQRES 1 A 203 SER GLY GLU LYS ASP VAL VAL PHE LEU ILE ASP GLY SER SEQRES 2 A 203 GLU GLY VAL ARG SER GLY PHE PRO LEU LEU LYS ASP PHE SEQRES 3 A 203 VAL GLN ARG VAL VAL GLU SER LEU ASP VAL GLY PRO ASP SEQRES 4 A 203 GLN VAL ARG VAL ALA LEU VAL GLN TYR SER ASP ARG THR SEQRES 5 A 203 ARG PRO GLU PHE TYR LEU ASN SER HIS MET ASP GLN GLN SEQRES 6 A 203 GLY VAL ILE SER ALA ILE ARG ARG LEU THR LEU LEU GLY SEQRES 7 A 203 GLY PRO THR PRO ASN THR GLY ALA ALA LEU GLU PHE VAL SEQRES 8 A 203 LEU ARG ASN ILE LEU THR SER SER THR GLY SER ARG ILE SEQRES 9 A 203 ALA GLU GLY VAL PRO GLN LEU LEU ILE VAL LEU THR ALA SEQRES 10 A 203 GLU PRO SER GLY ASP ASP VAL ARG GLY PRO SER VAL VAL SEQRES 11 A 203 LEU LYS GLN GLY GLY ALA VAL PRO ILE GLY ILE GLY ILE SEQRES 12 A 203 GLY ASN ALA ASP ILE SER GLU MET GLN THR ILE SER PHE SEQRES 13 A 203 ILE PRO ASP PHE ALA VAL ALA ILE PRO THR PHE ARG GLU SEQRES 14 A 203 LEU GLY THR ILE GLN GLN VAL ILE SER GLU ARG VAL ILE SEQRES 15 A 203 GLN LEU ASN ARG GLU GLU LEU SER SER LEU LYS PRO ILE SEQRES 16 A 203 LEU THR PRO SER THR GLY ALA GLY FORMUL 2 HOH *215(H2 O) HELIX 1 1 SER A 1034 SER A 1039 5 6 HELIX 2 2 GLY A 1040 SER A 1054 1 15 HELIX 3 3 ASP A 1084 ARG A 1094 1 11 HELIX 4 4 ASN A 1104 ILE A 1116 1 13 HELIX 5 5 THR A 1118 GLY A 1122 5 5 HELIX 6 6 ARG A 1124 GLY A 1128 5 5 HELIX 7 7 VAL A 1145 GLY A 1155 1 11 HELIX 8 8 ASP A 1168 SER A 1176 1 9 HELIX 9 9 ILE A 1178 ALA A 1182 5 5 HELIX 10 10 THR A 1187 THR A 1193 5 7 HELIX 11 11 ILE A 1194 LEU A 1205 1 12 HELIX 12 12 ASN A 1206 SER A 1212 1 7 SHEET 1 A 6 THR A1073 PHE A1077 0 SHEET 2 A 6 VAL A1062 TYR A1069 -1 N GLN A1068 O ARG A1074 SHEET 3 A 6 LYS A1025 ASP A1032 1 N ILE A1031 O VAL A1067 SHEET 4 A 6 GLN A1131 THR A1137 1 O LEU A1132 N VAL A1028 SHEET 5 A 6 ALA A1157 ILE A1164 1 O ILE A1162 N VAL A1135 SHEET 6 A 6 VAL A1183 ILE A1185 1 O VAL A1183 N GLY A1163 CRYST1 55.070 55.070 106.870 90.00 90.00 90.00 P 43 21 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 0.018159 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009357 0.00000