HEADER LUMINESCENT PROTEIN 11-JUL-19 6S97 TITLE FRAGMENT TRANSPLANTATION ONTO A HYPERSTABLE ANCESTOR OF HALOALKANE TITLE 2 DEHALOGENASES AND RENILLA LUCIFERASE (ANC-FT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRAGMENT TRANSPLANTATION ONTO HYPERSTABLE ANCESTOR OF COMPND 3 HALOALKANE DEHALOGENASES AND RENILLA LUCIFERASE (ANC-FT); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RENILLA RENIFORMIS; SOURCE 3 ORGANISM_TAXID: 6136; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI #1/H766; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1354003 KEYWDS FRAGMENT TRANSPLANTATION, ANCESTRAL ENZYME, BIOLUMINSCENCE, KEYWDS 2 COELENTERAZINE-UTILIZING ENZYME, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SCHENKMAYEROVA,J.DAMBORSKY,M.MAREK REVDAT 3 19-JUN-24 6S97 1 REMARK REVDAT 2 08-SEP-21 6S97 1 JRNL REVDAT 1 26-AUG-20 6S97 0 JRNL AUTH A.SCHENKMAYEROVA,G.P.PINTO,M.TOUL,M.MAREK,L.HERNYCHOVA, JRNL AUTH 2 J.PLANAS-IGLESIAS,V.DANIEL LISKOVA,D.PLUSKAL,M.VASINA, JRNL AUTH 3 S.EMOND,M.DORR,R.CHALOUPKOVA,D.BEDNAR,Z.PROKOP,F.HOLLFELDER, JRNL AUTH 4 U.T.BORNSCHEUER,J.DAMBORSKY JRNL TITL ENGINEERING THE PROTEIN DYNAMICS OF AN ANCESTRAL LUCIFERASE. JRNL REF NAT COMMUN V. 12 3616 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34127663 JRNL DOI 10.1038/S41467-021-23450-Z REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 33321 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.293 REMARK 3 R VALUE (WORKING SET) : 0.291 REMARK 3 FREE R VALUE : 0.330 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1633 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 43.7780 - 4.4701 1.00 2793 150 0.3108 0.3166 REMARK 3 2 4.4701 - 3.5486 1.00 2688 139 0.2790 0.2828 REMARK 3 3 3.5486 - 3.1001 1.00 2641 163 0.2812 0.3355 REMARK 3 4 3.1001 - 2.8167 1.00 2637 136 0.2982 0.3149 REMARK 3 5 2.8167 - 2.6149 1.00 2643 122 0.2895 0.3492 REMARK 3 6 2.6149 - 2.4607 1.00 2643 128 0.2930 0.3622 REMARK 3 7 2.4607 - 2.3375 1.00 2616 129 0.2836 0.3807 REMARK 3 8 2.3375 - 2.2357 1.00 2606 135 0.2924 0.3563 REMARK 3 9 2.2357 - 2.1497 1.00 2637 126 0.2812 0.3742 REMARK 3 10 2.1497 - 2.0755 1.00 2575 140 0.2866 0.3760 REMARK 3 11 2.0755 - 2.0106 1.00 2600 136 0.2858 0.3822 REMARK 3 12 2.0106 - 1.9531 0.99 2609 129 0.2934 0.3606 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.55 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 6S97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292103259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33369 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 43.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 19.90 REMARK 200 R MERGE FOR SHELL (I) : 1.44000 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 2.8.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM ACETATE, TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -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 34.04167 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 68.08333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.08333 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 34.04167 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: 12080 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 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 LEU A 27 -126.46 46.63 REMARK 500 SER A 29 -162.07 -127.62 REMARK 500 ASP A 37 79.95 -155.12 REMARK 500 ASP A 37 78.22 -156.37 REMARK 500 LYS A 42 -165.43 -76.45 REMARK 500 PRO A 52 49.16 -107.75 REMARK 500 THR A 53 -157.21 -101.26 REMARK 500 ASP A 118 -129.03 54.59 REMARK 500 ARG A 182 -60.17 -120.90 REMARK 500 LYS A 224 98.46 -54.40 REMARK 500 PHE A 259 -67.15 -137.81 REMARK 500 LEU A 282 -132.55 -97.56 REMARK 500 PHE A 284 56.29 -90.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6S6E RELATED DB: PDB DBREF 6S97 A 12 305 PDB 6S97 6S97 12 305 SEQRES 1 A 294 ALA THR GLY ASP GLU TRP TRP ALA LYS CYS LYS GLN VAL SEQRES 2 A 294 ASP VAL LEU ASP SER GLU MET SER TYR TYR ASP SER ASP SEQRES 3 A 294 PRO GLY LYS HIS LYS ASN THR VAL ILE PHE LEU HIS GLY SEQRES 4 A 294 ASN PRO THR SER SER TYR LEU TRP ARG ASN VAL ILE PRO SEQRES 5 A 294 HIS VAL GLU PRO LEU ALA ARG CYS LEU ALA PRO ASP LEU SEQRES 6 A 294 ILE GLY MET GLY LYS SER GLY LYS LEU PRO ASN HIS SER SEQRES 7 A 294 TYR ARG PHE VAL ASP HIS TYR ARG TYR LEU SER ALA TRP SEQRES 8 A 294 PHE ASP SER VAL ASN LEU PRO GLU LYS VAL THR ILE VAL SEQRES 9 A 294 CYS HIS ASP TRP GLY SER GLY LEU GLY PHE HIS TRP CYS SEQRES 10 A 294 ASN GLU HIS ARG ASP ARG VAL LYS GLY ILE VAL HIS MET SEQRES 11 A 294 GLU SER VAL VAL ASP VAL ILE GLU SER TRP ASP GLU TRP SEQRES 12 A 294 PRO ASP ILE GLU GLU ASP ILE ALA LEU ILE LYS SER GLU SEQRES 13 A 294 ALA GLY GLU GLU MET VAL LEU LYS LYS ASN PHE PHE ILE SEQRES 14 A 294 GLU ARG LEU LEU PRO SER SER ILE MET ARG LYS LEU SER SEQRES 15 A 294 GLU GLU GLU MET ASP ALA TYR ARG GLU PRO PHE VAL GLU SEQRES 16 A 294 PRO GLY GLU SER ARG ARG PRO THR LEU THR TRP PRO ARG SEQRES 17 A 294 GLU ILE PRO ILE LYS GLY ASP GLY PRO GLU ASP VAL ILE SEQRES 18 A 294 GLU ILE VAL LYS SER TYR ASN LYS TRP LEU SER THR SER SEQRES 19 A 294 LYS ASP ILE PRO LYS LEU PHE ILE ASN ALA ASP PRO GLY SEQRES 20 A 294 PHE PHE SER ASN ALA ILE LYS LYS VAL THR LYS ASN TRP SEQRES 21 A 294 PRO ASN GLN LYS THR VAL THR VAL LYS GLY LEU HIS PHE SEQRES 22 A 294 LEU GLN GLU ASP SER PRO GLU GLU ILE GLY GLU ALA ILE SEQRES 23 A 294 ALA ASP PHE LEU ASN GLU LEU THR FORMUL 2 HOH *140(H2 O) HELIX 1 AA1 THR A 13 LYS A 20 1 8 HELIX 2 AA2 SER A 54 ARG A 59 5 6 HELIX 3 AA3 VAL A 61 ALA A 69 5 9 HELIX 4 AA4 ARG A 91 ASP A 104 1 14 HELIX 5 AA5 ASP A 118 HIS A 131 1 14 HELIX 6 AA6 SER A 150 TRP A 154 5 5 HELIX 7 AA7 ILE A 157 SER A 166 1 10 HELIX 8 AA8 SER A 166 LYS A 175 1 10 HELIX 9 AA9 ASN A 177 ARG A 182 1 6 HELIX 10 AB1 ARG A 182 SER A 187 1 6 HELIX 11 AB2 SER A 193 GLU A 202 1 10 HELIX 12 AB3 PRO A 203 VAL A 205 5 3 HELIX 13 AB4 GLY A 208 SER A 210 5 3 HELIX 14 AB5 ARG A 211 GLU A 220 1 10 HELIX 15 AB6 PRO A 228 SER A 243 1 16 HELIX 16 AB7 PHE A 260 THR A 268 1 9 HELIX 17 AB8 PHE A 284 ASP A 288 5 5 HELIX 18 AB9 SER A 289 THR A 305 1 17 SHEET 1 AA1 8 LYS A 22 VAL A 26 0 SHEET 2 AA1 8 SER A 29 ASP A 35 -1 O TYR A 33 N LYS A 22 SHEET 3 AA1 8 ARG A 70 PRO A 74 -1 O ALA A 73 N TYR A 34 SHEET 4 AA1 8 THR A 44 LEU A 48 1 N PHE A 47 O LEU A 72 SHEET 5 AA1 8 VAL A 112 HIS A 117 1 O VAL A 115 N LEU A 48 SHEET 6 AA1 8 VAL A 135 MET A 141 1 O LYS A 136 N VAL A 112 SHEET 7 AA1 8 LYS A 250 PRO A 257 1 O LEU A 251 N ILE A 138 SHEET 8 AA1 8 GLN A 274 GLY A 281 1 O VAL A 277 N ASN A 254 CISPEP 1 ASN A 51 PRO A 52 0 -1.26 CISPEP 2 GLY A 227 PRO A 228 0 -12.92 CISPEP 3 ASP A 256 PRO A 257 0 5.64 CRYST1 87.556 87.556 102.125 90.00 90.00 120.00 P 31 2 1 6 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 0.011421 0.006594 0.000000 0.00000 SCALE2 0.000000 0.013188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009792 0.00000