HEADER STRUCTURAL PROTEIN 31-MAR-23 8OMW TITLE CRYSTAL STRUCTURE OF THE TITIN DOMAIN FN3-20 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TITIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CONNECTIN,RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.14; COMPND 5 EC: 2.7.11.1; COMPND 6 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: TTN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS TITIN FIBRONECTIN TYPE III A-BAND STRUCTURAL PROTEIN, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.REES,M.GAUTEL REVDAT 2 30-AUG-23 8OMW 1 JRNL REVDAT 1 23-AUG-23 8OMW 0 JRNL AUTH M.REES,R.NIKOOPOUR,A.ALEXANDROVICH,M.PFUHL,L.R.LOPES, JRNL AUTH 2 M.M.AKHTAR,P.SYRRIS,P.ELLIOTT,G.CARR-WHITE,M.GAUTEL JRNL TITL STRUCTURE DETERMINATION AND ANALYSIS OF TITIN A-BAND JRNL TITL 2 FIBRONECTIN TYPE III DOMAINS PROVIDES INSIGHTS FOR JRNL TITL 3 DISEASE-LINKED VARIANTS AND PROTEIN OLIGOMERISATION. JRNL REF J.STRUCT.BIOL. V. 215 08009 2023 JRNL REFN ESSN 1095-8657 JRNL PMID 37549721 JRNL DOI 10.1016/J.JSB.2023.108009 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 47521 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) : 0.149 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.240 REMARK 3 FREE R VALUE TEST SET COUNT : 2014 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 31.0900 - 2.5300 0.99 3404 151 0.1886 0.2219 REMARK 3 2 2.5300 - 2.0100 0.99 3324 146 0.1597 0.2011 REMARK 3 3 2.0100 - 1.7500 1.00 3323 146 0.1446 0.1615 REMARK 3 4 1.7500 - 1.5900 0.99 3317 147 0.1349 0.1515 REMARK 3 5 1.5900 - 1.4800 0.99 3294 146 0.1298 0.1697 REMARK 3 6 1.4800 - 1.3900 0.99 3285 146 0.1233 0.1503 REMARK 3 7 1.3900 - 1.3200 0.99 3265 143 0.1240 0.1314 REMARK 3 8 1.3200 - 1.2600 0.99 3274 142 0.1249 0.1567 REMARK 3 9 1.2600 - 1.2200 0.99 3292 147 0.1217 0.1319 REMARK 3 10 1.2200 - 1.1700 0.99 3232 144 0.1191 0.1521 REMARK 3 11 1.1700 - 1.1400 0.98 3232 145 0.1238 0.1482 REMARK 3 12 1.1400 - 1.1000 0.99 3252 144 0.1198 0.1362 REMARK 3 13 1.1000 - 1.0700 0.98 3227 141 0.1277 0.1765 REMARK 3 14 1.0700 - 1.0500 0.85 2786 126 0.1810 0.2074 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.078 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.211 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.65 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 : 0.010 888 REMARK 3 ANGLE : 1.273 1224 REMARK 3 CHIRALITY : 0.097 128 REMARK 3 PLANARITY : 0.010 164 REMARK 3 DIHEDRAL : 6.837 131 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 8OMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292129376. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-14 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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 31.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : 0.62680 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 163.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM TRIS-HCL PH 7.5 50MM NACL 0.5MM REMARK 280 DTT 0.1M TBG PH 9.0 25% W/V PEG 1500, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 24.51700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.13150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 24.51700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.13150 REMARK 290 SMTRY3 4 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 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 A 325 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 GLY A 1 REMARK 465 SER A 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 442 O HOH A 506 4545 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 106 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 106 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 544 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 545 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 546 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 547 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 548 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A 549 DISTANCE = 8.31 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4O00 RELATED DB: PDB REMARK 900 PDB ENTRY FOR SAME CITATION REMARK 900 RELATED ID: 8OIY RELATED DB: PDB REMARK 900 PDB ENTRY FOR SAME CITATION DBREF 8OMW A 4 109 UNP Q8WZ42 TITIN_HUMAN 16525 16630 SEQADV 8OMW GLY A 1 UNP Q8WZ42 EXPRESSION TAG SEQADV 8OMW SER A 2 UNP Q8WZ42 EXPRESSION TAG SEQADV 8OMW SER A 3 UNP Q8WZ42 EXPRESSION TAG SEQRES 1 A 109 GLY SER SER LEU PRO GLY PRO PRO GLY LYS PRO LYS VAL SEQRES 2 A 109 LEU ALA ARG THR LYS GLY SER MET LEU VAL SER TRP THR SEQRES 3 A 109 PRO PRO LEU ASP ASN GLY GLY SER PRO ILE THR GLY TYR SEQRES 4 A 109 TRP LEU GLU LYS ARG GLU GLU GLY SER PRO TYR TRP SER SEQRES 5 A 109 ARG VAL SER ARG ALA PRO ILE THR LYS VAL GLY LEU LYS SEQRES 6 A 109 GLY VAL GLU PHE ASN VAL PRO ARG LEU LEU GLU GLY VAL SEQRES 7 A 109 LYS TYR GLN PHE ARG ALA MET ALA ILE ASN ALA ALA GLY SEQRES 8 A 109 ILE GLY PRO PRO SER GLU PRO SER ASP PRO GLU VAL ALA SEQRES 9 A 109 GLY ASP PRO ILE PHE HET CL A 201 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *249(H2 O) SHEET 1 AA1 3 LYS A 12 THR A 17 0 SHEET 2 AA1 3 SER A 20 TRP A 25 -1 O LEU A 22 N LEU A 14 SHEET 3 AA1 3 VAL A 67 VAL A 71 -1 O VAL A 71 N MET A 21 SHEET 1 AA2 4 SER A 52 ARG A 53 0 SHEET 2 AA2 4 GLY A 38 GLU A 45 -1 N LYS A 43 O SER A 52 SHEET 3 AA2 4 LYS A 79 ASN A 88 -1 O ARG A 83 N GLU A 42 SHEET 4 AA2 4 GLY A 91 ILE A 92 -1 O GLY A 91 N ASN A 88 SHEET 1 AA3 4 SER A 52 ARG A 53 0 SHEET 2 AA3 4 GLY A 38 GLU A 45 -1 N LYS A 43 O SER A 52 SHEET 3 AA3 4 LYS A 79 ASN A 88 -1 O ARG A 83 N GLU A 42 SHEET 4 AA3 4 GLU A 102 VAL A 103 -1 O GLU A 102 N TYR A 80 CRYST1 49.034 34.263 63.081 90.00 99.68 90.00 C 1 2 1 4 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 0.020394 0.000000 0.003479 0.00000 SCALE2 0.000000 0.029186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016082 0.00000