HEADER CELL ADHESION 20-FEB-17 5N7H TITLE CRYSTAL STRUCTURE OF THE COILED-COIL DOMAIN OF HUMAN TRICELLULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MARVEL DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRICELLULIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MARVELD2, TRIC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TIGHT JUNCTION, CC DOMAIN, DIMERIZATION, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR A.SCHUETZ,U.HEINEMANN REVDAT 2 18-OCT-17 5N7H 1 JRNL REVDAT 1 12-JUL-17 5N7H 0 JRNL AUTH A.SCHUETZ,V.RADUSHEVA,S.M.KRUG,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF THE TRICELLULIN C-TERMINAL COILED-COIL JRNL TITL 2 DOMAIN REVEALS A UNIQUE MODE OF DIMERIZATION. JRNL REF ANN. N. Y. ACAD. SCI. V.1405 147 2017 JRNL REFN ISSN 1749-6632 JRNL PMID 28661558 JRNL DOI 10.1111/NYAS.13408 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6565 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.510 REMARK 3 FREE R VALUE TEST SET COUNT : 493 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.46 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1781 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2556 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1648 REMARK 3 BIN R VALUE (WORKING SET) : 0.2525 REMARK 3 BIN FREE R VALUE : 0.2905 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.47 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 133 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 902 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.29220 REMARK 3 B22 (A**2) : -4.29220 REMARK 3 B33 (A**2) : 8.58430 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.380 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.349 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.221 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.307 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.212 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 917 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1222 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 356 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 31 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 125 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 917 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 112 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1081 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.95 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.34 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.25 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|438 - 480} REMARK 3 ORIGIN FOR THE GROUP (A): 7.4370 13.9388 90.8188 REMARK 3 T TENSOR REMARK 3 T11: -0.3863 T22: 0.0053 REMARK 3 T33: -0.1150 T12: 0.0265 REMARK 3 T13: -0.0061 T23: -0.0908 REMARK 3 L TENSOR REMARK 3 L11: 2.0701 L22: 4.7407 REMARK 3 L33: 5.3957 L12: -0.9669 REMARK 3 L13: 1.0514 L23: -0.8650 REMARK 3 S TENSOR REMARK 3 S11: 0.0485 S12: 0.6193 S13: -0.1204 REMARK 3 S21: -0.2221 S22: -0.0490 S23: -0.4537 REMARK 3 S31: 0.0664 S32: 0.5282 S33: 0.0005 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|481 - 515} REMARK 3 ORIGIN FOR THE GROUP (A): 13.8718 -0.3723 125.1700 REMARK 3 T TENSOR REMARK 3 T11: 0.1746 T22: 0.1173 REMARK 3 T33: 0.1558 T12: -0.1394 REMARK 3 T13: -0.1644 T23: 0.0985 REMARK 3 L TENSOR REMARK 3 L11: -1.3306 L22: 3.7932 REMARK 3 L33: 3.9002 L12: 0.0573 REMARK 3 L13: -3.3152 L23: -2.6596 REMARK 3 S TENSOR REMARK 3 S11: 0.1569 S12: -0.1910 S13: -0.1459 REMARK 3 S21: 0.1095 S22: -0.4824 S23: 0.1486 REMARK 3 S31: 0.0122 S32: -0.1709 S33: 0.3255 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|516 - 550} REMARK 3 ORIGIN FOR THE GROUP (A): 4.6658 11.1712 96.3620 REMARK 3 T TENSOR REMARK 3 T11: -0.2958 T22: -0.0216 REMARK 3 T33: -0.0482 T12: 0.0174 REMARK 3 T13: 0.0276 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 1.8769 L22: 2.5507 REMARK 3 L33: 12.8802 L12: -0.1583 REMARK 3 L13: 2.2871 L23: 1.1384 REMARK 3 S TENSOR REMARK 3 S11: 0.1273 S12: 0.1822 S13: -0.5109 REMARK 3 S21: -0.0989 S22: 0.0488 S23: -0.2076 REMARK 3 S31: 0.2418 S32: -0.0883 S33: -0.1760 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5N7H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918409 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6591 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.198 REMARK 200 RESOLUTION RANGE LOW (A) : 44.039 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 0.88700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (V/V) ISOPROPANOL, 0.1 M CITRATE REMARK 280 PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 135.22867 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 67.61433 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 135.22867 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.61433 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 135.22867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 67.61433 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 135.22867 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 67.61433 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 437 REMARK 465 SER A 491 REMARK 465 ARG A 492 REMARK 465 LEU A 493 REMARK 465 PRO A 494 REMARK 465 HIS A 495 REMARK 465 HIS A 496 REMARK 465 SER A 497 REMARK 465 GLU A 498 REMARK 465 ASN A 551 DBREF 5N7H A 439 551 UNP Q8N4S9 MALD2_HUMAN 439 551 SEQADV 5N7H GLY A 437 UNP Q8N4S9 EXPRESSION TAG SEQADV 5N7H SER A 438 UNP Q8N4S9 EXPRESSION TAG SEQRES 1 A 115 GLY SER MET PRO ASP TYR VAL ALA LYS TYR PRO VAL ILE SEQRES 2 A 115 GLN THR ASP ASP GLU ARG GLU ARG TYR LYS ALA VAL PHE SEQRES 3 A 115 GLN ASP GLN PHE SER GLU TYR LYS GLU LEU SER ALA GLU SEQRES 4 A 115 VAL GLN ALA VAL LEU ARG LYS PHE ASP GLU LEU ASP ALA SEQRES 5 A 115 VAL MET SER ARG LEU PRO HIS HIS SER GLU SER ARG GLN SEQRES 6 A 115 GLU HIS GLU ARG ILE SER ARG ILE HIS GLU GLU PHE LYS SEQRES 7 A 115 LYS LYS LYS ASN ASP PRO THR PHE LEU GLU LYS LYS GLU SEQRES 8 A 115 ARG CYS ASP TYR LEU LYS ASN LYS LEU SER HIS ILE LYS SEQRES 9 A 115 GLN ARG ILE GLN GLU TYR ASP LYS VAL MET ASN FORMUL 2 HOH *17(H2 O) HELIX 1 AA1 ASP A 441 TYR A 446 1 6 HELIX 2 AA2 THR A 451 ALA A 488 1 38 HELIX 3 AA3 ARG A 500 ASN A 518 1 19 HELIX 4 AA4 ASP A 519 MET A 550 1 32 CRYST1 44.039 44.039 202.843 90.00 90.00 120.00 P 62 2 2 12 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 0.022707 0.013110 0.000000 0.00000 SCALE2 0.000000 0.026220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004930 0.00000