HEADER STRUCTURAL PROTEIN 19-JUL-20 7JGU TITLE STRUCTURE OF FN3TT MUT COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN TYPE-III DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: 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 KEYWDS FN3-LIKE DOMAIN, HYPERTHERMAL STABILITY, SURFACE SALT BRIDGES, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LUO,L.E.BOUCHER REVDAT 3 18-OCT-23 7JGU 1 REMARK REVDAT 2 02-FEB-22 7JGU 1 JRNL REVDAT 1 21-JUL-21 7JGU 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 34158 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1707 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 27.3600 - 2.7500 0.98 2761 145 0.1495 0.1901 REMARK 3 2 2.7500 - 2.1800 0.99 2710 142 0.1502 0.1715 REMARK 3 3 2.1800 - 1.9000 0.98 2684 142 0.1246 0.1474 REMARK 3 4 1.9000 - 1.7300 0.99 2726 143 0.1206 0.1426 REMARK 3 5 1.7300 - 1.6100 1.00 2697 142 0.1190 0.1458 REMARK 3 6 1.6100 - 1.5100 1.00 2732 144 0.1245 0.1540 REMARK 3 7 1.5100 - 1.4400 1.00 2698 142 0.1296 0.1574 REMARK 3 8 1.4400 - 1.3700 1.00 2698 142 0.1469 0.1980 REMARK 3 9 1.3700 - 1.3200 0.99 2680 141 0.1984 0.2545 REMARK 3 10 1.3200 - 1.2800 0.99 2695 142 0.2598 0.3093 REMARK 3 11 1.2800 - 1.2400 0.99 2673 140 0.2857 0.3040 REMARK 3 12 1.2400 - 1.2000 0.99 2697 142 0.2960 0.3264 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.70 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 7JGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250769. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34160 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.184 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3900 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) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.92 REMARK 200 R MERGE FOR SHELL (I) : 0.92300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.550 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: 7JGT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2M SODIUM DI-HYDROGEN REMARK 280 PHOSPHATE, PH 7.5, EVAPORATION, TEMPERATURE 298K 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 53.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.15500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.00000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.15500 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 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 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 227 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 MET A 1 REMARK 465 GLY A 92 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 ASP A 42 CG OD1 OD2 REMARK 470 ARG A 91 CG CD NE CZ NH1 NH2 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 HG SER A 27 O HOH A 201 1.49 REMARK 500 OG SER A 27 O HOH A 201 1.67 REMARK 500 O HOH A 222 O HOH A 283 2.07 REMARK 500 O HOH A 222 O HOH A 262 2.10 REMARK 500 O HOH A 277 O HOH A 293 2.13 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 236 O HOH A 236 2555 2.02 REMARK 500 O HOH A 288 O HOH A 293 2555 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 89 36.04 -96.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7JGT RELATED DB: PDB DBREF 7JGU A 2 91 UNP Q8RD81 Q8RD81_CALS4 1458 1547 SEQADV 7JGU MET A 1 UNP Q8RD81 INITIATING METHIONINE SEQADV 7JGU LEU A 23 UNP Q8RD81 ARG 1479 CONFLICT SEQADV 7JGU THR A 25 UNP Q8RD81 ARG 1481 CONFLICT SEQADV 7JGU ILE A 72 UNP Q8RD81 ARG 1528 CONFLICT SEQADV 7JGU GLY A 92 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGU GLY A 93 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGU HIS A 94 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGU HIS A 95 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGU HIS A 96 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGU HIS A 97 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGU HIS A 98 UNP Q8RD81 EXPRESSION TAG SEQADV 7JGU 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 LEU LEU THR 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 THR PHE ALA LEU ILE 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 HET 1PE A 101 38 HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 1PE C10 H22 O6 FORMUL 3 HOH *97(H2 O) SHEET 1 AA1 3 TRP A 11 ILE A 15 0 SHEET 2 AA1 3 ASN A 18 THR A 25 -1 O LEU A 23 N GLU A 13 SHEET 3 AA1 3 GLU A 55 VAL A 58 -1 O VAL A 58 N LEU A 22 SHEET 1 AA2 4 THR A 44 THR A 51 0 SHEET 2 AA2 4 TYR A 34 SER A 41 -1 N LEU A 39 O LYS A 46 SHEET 3 AA2 4 LYS A 66 ASN A 75 -1 O THR 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 LEU A 39 O LYS A 46 SHEET 3 AA3 4 LYS A 66 ASN A 75 -1 O THR 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 SITE 1 AC1 5 TYR A 38 TYR A 57 ILE A 72 HOH A 207 SITE 2 AC1 5 HOH A 252 CRYST1 106.000 38.310 28.180 90.00 103.88 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 0.009434 0.000000 0.002331 0.00000 SCALE2 0.000000 0.026103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036554 0.00000