HEADER STRUCTURAL PROTEIN 19-JUL-20 7JGT TITLE CRYSTAL STRUCTURE OF FN3TT COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN TYPE-III DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FN3-LIKE DOMAIN, RESIDUES 1458-1547; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CALDANAEROBACTER SUBTERRANEUS SUBSP. SOURCE 3 TENGCONGENSIS (STRAIN DSM 15242 / JCM 11007 / NBRC 100824 / MB4); SOURCE 4 ORGANISM_TAXID: 273068; SOURCE 5 STRAIN: DSM 15242 / JCM 11007 / NBRC 100824 / MB4; SOURCE 6 GENE: TTE0165; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS HYPERTHERMAL STABILITY, SURFACE SALT BRIDGES, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LUO,T.J.MALIA REVDAT 4 03-APR-24 7JGT 1 REMARK REVDAT 3 22-DEC-21 7JGT 1 JRNL REVDAT 2 08-SEP-21 7JGT 1 JRNL REVDAT 1 21-JUL-21 7JGT 0 JRNL AUTH L.BOUCHER,S.SOMANI,C.NEGRON,W.MA,S.JACOBS,W.CHAN,T.MALIA, JRNL AUTH 2 G.OBMOLOVA,A.TEPLYAKOV,G.L.GILLILAND,J.LUO JRNL TITL SURFACE SALT BRIDGES CONTRIBUTE TO THE EXTREME THERMAL JRNL TITL 2 STABILITY OF AN FN3-LIKE DOMAIN FROM A THERMOPHILIC JRNL TITL 3 BACTERIUM. JRNL REF PROTEINS V. 90 270 2022 JRNL REFN ESSN 1097-0134 JRNL PMID 34405904 JRNL DOI 10.1002/PROT.26218 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3855 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 6681 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 673 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 31.1100 - 3.2500 1.00 1318 148 0.1648 0.2103 REMARK 3 2 3.2500 - 2.5800 1.00 1224 136 0.1872 0.2201 REMARK 3 3 2.5800 - 2.2500 1.00 1200 133 0.1871 0.2890 REMARK 3 4 2.2500 - 2.0500 1.00 1188 131 0.1819 0.2531 REMARK 3 5 2.0500 - 1.9000 0.91 1078 125 0.1865 0.2699 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.89 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7JGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMICTM VARIMAXTM CONFOCAL REMARK 200 OPTICS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6681 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 31.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 24.13 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.7 REMARK 200 DATA REDUNDANCY IN SHELL : 14.54 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.850 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: ROSETTA GENERATED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, 28% PEG 3350, PH REMARK 280 7.5, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 52.73000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.26500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.36500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.26500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.26500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.09500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.26500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.26500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.36500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.26500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.26500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 79.09500 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 52.73000 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: 5300 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 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 172 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 93 REMARK 465 HIS A 94 REMARK 465 HIS A 95 REMARK 465 HIS A 96 REMARK 465 HIS A 97 REMARK 465 HIS A 98 REMARK 465 HIS A 99 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 SER A 41 OG REMARK 470 ASP A 42 CG OD1 OD2 REMARK 470 SER A 43 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 27 O HOH A 101 2.08 REMARK 500 NZ LYS A 53 O HOH A 102 2.11 REMARK 500 OD1 ASN A 64 O HOH A 103 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 174 O HOH A 184 5445 1.96 REMARK 500 O HOH A 186 O HOH A 187 7565 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 7JGT A 2 91 UNP Q8RD81 Q8RD81_CALS4 1458 1547 SEQADV 7JGT MET A 1 UNP Q8RD81 INITIATING METHIONINE SEQADV 7JGT CYS A 68 UNP Q8RD81 THR 1524 ENGINEERED MUTATION SEQADV 7JGT GLY A 92 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGT GLY A 93 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGT HIS A 94 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGT HIS A 95 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGT HIS A 96 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGT HIS A 97 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGT HIS A 98 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGT HIS A 99 UNP Q8RD81 EXPRESSION TAG SEQRES 1 A 99 MET THR VAL PRO ASP GLU PRO VAL GLY PHE TRP VAL GLU SEQRES 2 A 99 SER ILE PRO GLY ASN ASP HIS THR LEU ARG LEU ARG TRP SEQRES 3 A 99 SER GLU THR LYS GLY ALA LYS TYR TYR GLU ILE TYR LEU SEQRES 4 A 99 VAL SER ASP SER THR TYR LYS PHE ILE ALA SER THR ASP SEQRES 5 A 99 LYS LEU GLU TYR TYR VAL THR ASN LEU SER PRO ASN THR SEQRES 6 A 99 LYS TYR CYS PHE ALA LEU ARG ALA VAL ASN GLU LEU GLY SEQRES 7 A 99 PRO SER ASN PHE VAL THR ALA SER SER THR THR ASP ARG SEQRES 8 A 99 GLY GLY HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *88(H2 O) SHEET 1 AA1 3 TRP A 11 SER A 14 0 SHEET 2 AA1 3 LEU A 22 ARG A 25 -1 O ARG A 23 N GLU A 13 SHEET 3 AA1 3 GLU A 55 VAL A 58 -1 O TYR A 56 N LEU A 24 SHEET 1 AA2 4 THR A 44 THR A 51 0 SHEET 2 AA2 4 TYR A 34 SER A 41 -1 N SER A 41 O THR A 44 SHEET 3 AA2 4 LYS A 66 ASN A 75 -1 O CYS A 68 N VAL A 40 SHEET 4 AA2 4 GLY A 78 PRO A 79 -1 O GLY A 78 N ASN A 75 SHEET 1 AA3 4 THR A 44 THR A 51 0 SHEET 2 AA3 4 TYR A 34 SER A 41 -1 N SER A 41 O THR A 44 SHEET 3 AA3 4 LYS A 66 ASN A 75 -1 O CYS A 68 N VAL A 40 SHEET 4 AA3 4 VAL A 83 THR A 88 -1 O SER A 87 N TYR A 67 CRYST1 38.530 38.530 105.460 90.00 90.00 90.00 P 41 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 0.025954 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025954 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009482 0.00000