PDB Short entry for 4IGI HEADER CELL ADHESION 17-DEC-12 4IGI TITLE CRYSTAL STRUCTURE OF THE COLLAGEN VI ALPHA3 N5 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN ALPHA3(VI); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COLLAGEN VI ALPHA3 N5, UNP RESIDUES 1022-1224; 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 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 EXPDTA X-RAY DIFFRACTION AUTHOR H.MIKOLAJEK,A.K.A.BECKER,M.PAULSSON,R.WAGENER,J.M.WERNER REVDAT 2 05-DEC-18 4IGI 1 JRNL REVDAT 1 18-DEC-13 4IGI 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) 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) : 36.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 47631 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2413 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 36.0713 - 3.0798 0.97 2721 152 0.1473 0.1555 REMARK 3 2 3.0798 - 2.4447 0.97 2694 143 0.1323 0.1450 REMARK 3 3 2.4447 - 2.1357 0.98 2703 146 0.1085 0.1340 REMARK 3 4 2.1357 - 1.9404 0.98 2672 170 0.1027 0.1280 REMARK 3 5 1.9404 - 1.8014 0.98 2688 129 0.1077 0.1381 REMARK 3 6 1.8014 - 1.6952 0.98 2687 157 0.1069 0.1525 REMARK 3 7 1.6952 - 1.6103 0.97 2683 145 0.1065 0.1518 REMARK 3 8 1.6103 - 1.5402 0.97 2670 142 0.0976 0.1277 REMARK 3 9 1.5402 - 1.4809 0.97 2648 136 0.0988 0.1531 REMARK 3 10 1.4809 - 1.4298 0.98 2667 157 0.1081 0.1442 REMARK 3 11 1.4298 - 1.3851 0.97 2680 120 0.1132 0.1686 REMARK 3 12 1.3851 - 1.3455 0.97 2655 136 0.1076 0.1625 REMARK 3 13 1.3455 - 1.3101 0.97 2650 155 0.1106 0.1542 REMARK 3 14 1.3101 - 1.2781 0.97 2676 128 0.1176 0.1659 REMARK 3 15 1.2781 - 1.2490 0.97 2643 143 0.1172 0.1507 REMARK 3 16 1.2490 - 1.2225 0.95 2593 121 0.1223 0.1983 REMARK 3 17 1.2225 - 1.2000 0.90 2488 133 0.1570 0.1981 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.98 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 : 0.011 1642 REMARK 3 ANGLE : 1.486 2254 REMARK 3 CHIRALITY : 0.078 269 REMARK 3 PLANARITY : 0.010 304 REMARK 3 DIHEDRAL : 12.896 628 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 4IGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-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 : 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 : 47672 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 10.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.17400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.500 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 3GXB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CACODYLATE, 1M TRI-SODIUM REMARK 280 CITRATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.23000 REMARK 290 SMTRY3 2 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: 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 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 SER A 1022 REMARK 465 GLY A 1023 REMARK 465 THR A 1221 REMARK 465 GLY A 1222 REMARK 465 ALA A 1223 REMARK 465 GLY A 1224 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 ARG A1061 -112.94 -123.10 REMARK 500 ARG A1061 -113.82 -121.92 REMARK 500 SER A1070 -105.55 -139.88 REMARK 500 SER A1070 -106.07 -138.13 REMARK 500 THR A1218 63.22 -155.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 4IGI A 1022 1224 UNP Q9Z0I9 Q9Z0I9_MOUSE 1022 1224 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 ARG 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 *240(H2 O) HELIX 1 11 SER A 1034 ARG A 1038 1 5 HELIX 2 12 GLY A 1040 SER A 1054 1 15 HELIX 3 13 ASP A 1084 ARG A 1094 1 11 HELIX 4 14 ASN A 1104 ILE A 1116 1 13 HELIX 5 15 THR A 1118 GLY A 1122 1 5 HELIX 6 16 ARG A 1124 GLY A 1128 1 5 HELIX 7 17 VAL A 1145 GLY A 1155 1 11 HELIX 8 18 ASP A 1168 SER A 1176 1 9 HELIX 9 19 ILE A 1178 ALA A 1182 1 5 HELIX 10 20 THR A 1187 LEU A 1213 1 27 SHEET 1 7 7 LYS A1025 ASP A1032 0 SHEET 1 8 8 VAL A1062 TYR A1069 0 SHEET 1 9 9 THR A1073 PHE A1077 0 SHEET 1 1010 GLN A1131 THR A1137 0 SHEET 1 1111 ALA A1157 ILE A1164 0 SHEET 1 1212 VAL A1183 ILE A1185 0 CRYST1 37.730 58.460 39.160 90.00 112.97 90.00 P 1 21 1 2 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 0.026504 0.000000 0.011234 0.00000 SCALE2 0.000000 0.017106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027735 0.00000