HEADER CELL ADHESION 20-FEB-17 5N7I 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, B; 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 3 17-JAN-24 5N7I 1 REMARK REVDAT 2 18-OCT-17 5N7I 1 JRNL REMARK REVDAT 1 12-JUL-17 5N7I 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. 2.88 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) : 2.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 7259 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.410 REMARK 3 FREE R VALUE TEST SET COUNT : 538 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) : 2.88 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.22 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.78 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2021 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2304 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1871 REMARK 3 BIN R VALUE (WORKING SET) : 0.2295 REMARK 3 BIN FREE R VALUE : 0.2429 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.42 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 150 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 : 1663 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 97.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 116.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.57490 REMARK 3 B22 (A**2) : -8.57490 REMARK 3 B33 (A**2) : 17.14980 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) : 0.410 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.920 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.321 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 1.004 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.329 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 : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1692 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2261 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 640 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 57 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 229 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1692 ; 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 : 208 ; 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 : 2008 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.98 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.24 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.32 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 21.5098 10.0111 5.4364 REMARK 3 T TENSOR REMARK 3 T11: -0.4617 T22: -0.1208 REMARK 3 T33: -0.3997 T12: 0.1721 REMARK 3 T13: 0.0197 T23: -0.2187 REMARK 3 L TENSOR REMARK 3 L11: 4.9707 L22: 8.0565 REMARK 3 L33: 4.1053 L12: 0.8659 REMARK 3 L13: 0.1996 L23: -1.3123 REMARK 3 S TENSOR REMARK 3 S11: -0.2082 S12: -0.4425 S13: 1.2312 REMARK 3 S21: -0.0315 S22: 0.1524 S23: 0.9052 REMARK 3 S31: -0.4474 S32: -1.1590 S33: 0.0558 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 39.0191 3.2917 11.2114 REMARK 3 T TENSOR REMARK 3 T11: -0.2903 T22: -0.1833 REMARK 3 T33: -0.2665 T12: -0.0175 REMARK 3 T13: 0.0073 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 7.9796 L22: 0.9494 REMARK 3 L33: 3.3307 L12: 1.3557 REMARK 3 L13: -0.7892 L23: 0.3457 REMARK 3 S TENSOR REMARK 3 S11: 0.5431 S12: -0.1539 S13: 0.4853 REMARK 3 S21: 0.6812 S22: -0.3154 S23: -0.5618 REMARK 3 S31: 0.0731 S32: -0.1050 S33: -0.2276 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5N7I 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_1200003610. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-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 : 7271 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.879 REMARK 200 RESOLUTION RANGE LOW (A) : 47.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 1.33200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.330 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: 5N7H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8.5% (W/V) PEG4000, 20% 2-PROPANOL, REMARK 280 0.1 M HEPES-NAOH PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z+1/2 REMARK 290 4555 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 0.00000 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 17.30750 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 17.30750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 SER A 499 REMARK 465 ARG A 500 REMARK 465 GLN A 501 REMARK 465 GLU A 502 REMARK 465 HIS A 503 REMARK 465 GLU A 504 REMARK 465 ALA A 505 REMARK 465 ILE A 506 REMARK 465 SER A 507 REMARK 465 ARG A 508 REMARK 465 ILE A 509 REMARK 465 MET A 550 REMARK 465 ASN A 551 REMARK 465 HIS B 495 REMARK 465 HIS B 496 REMARK 465 SER B 497 REMARK 465 GLU B 498 REMARK 465 SER B 499 REMARK 465 ARG B 500 REMARK 465 GLN B 501 REMARK 465 GLU B 502 REMARK 465 HIS B 503 REMARK 465 MET B 550 REMARK 465 ASN B 551 DBREF 5N7I A 439 551 UNP Q8N4S9 MALD2_HUMAN 439 551 DBREF 5N7I B 439 551 UNP Q8N4S9 MALD2_HUMAN 439 551 SEQADV 5N7I GLY A 437 UNP Q8N4S9 EXPRESSION TAG SEQADV 5N7I SER A 438 UNP Q8N4S9 EXPRESSION TAG SEQADV 5N7I ALA A 457 UNP Q8N4S9 ARG 457 ENGINEERED MUTATION SEQADV 5N7I ALA A 505 UNP Q8N4S9 ARG 505 ENGINEERED MUTATION SEQADV 5N7I GLY B 437 UNP Q8N4S9 EXPRESSION TAG SEQADV 5N7I SER B 438 UNP Q8N4S9 EXPRESSION TAG SEQADV 5N7I ALA B 457 UNP Q8N4S9 ARG 457 ENGINEERED MUTATION SEQADV 5N7I ALA B 505 UNP Q8N4S9 ARG 505 ENGINEERED MUTATION 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 ALA 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 ALA 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 SEQRES 1 B 115 GLY SER MET PRO ASP TYR VAL ALA LYS TYR PRO VAL ILE SEQRES 2 B 115 GLN THR ASP ASP GLU ARG GLU ALA TYR LYS ALA VAL PHE SEQRES 3 B 115 GLN ASP GLN PHE SER GLU TYR LYS GLU LEU SER ALA GLU SEQRES 4 B 115 VAL GLN ALA VAL LEU ARG LYS PHE ASP GLU LEU ASP ALA SEQRES 5 B 115 VAL MET SER ARG LEU PRO HIS HIS SER GLU SER ARG GLN SEQRES 6 B 115 GLU HIS GLU ALA ILE SER ARG ILE HIS GLU GLU PHE LYS SEQRES 7 B 115 LYS LYS LYS ASN ASP PRO THR PHE LEU GLU LYS LYS GLU SEQRES 8 B 115 ARG CYS ASP TYR LEU LYS ASN LYS LEU SER HIS ILE LYS SEQRES 9 B 115 GLN ARG ILE GLN GLU TYR ASP LYS VAL MET ASN HELIX 1 AA1 PRO A 440 TYR A 446 1 7 HELIX 2 AA2 THR A 451 MET A 490 1 40 HELIX 3 AA3 GLU A 511 ASN A 518 1 8 HELIX 4 AA4 ASP A 519 VAL A 549 1 31 HELIX 5 AA5 PRO B 440 TYR B 446 1 7 HELIX 6 AA6 THR B 451 ARG B 492 1 42 HELIX 7 AA7 ALA B 505 ASN B 518 1 14 HELIX 8 AA8 ASP B 519 VAL B 549 1 31 CRYST1 95.711 95.711 34.615 90.00 90.00 90.00 P 42 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 0.010448 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010448 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028889 0.00000