HEADER LYASE 22-JAN-18 6C7H TITLE DIRECTED EVOLUTIONARY CHANGES IN KEMP ELIMINASE KE07 - CRYSTAL 18 TITLE 2 DESIGN TRP50ALA MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: KEMP ELIMINASE KE07; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS KEMP ELIMINASE, DIRECTED EVOLUTION, KE07, DE NOVO PROTEIN, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR C.J.JACKSON,N.-S.HONG,P.D.CARR REVDAT 3 04-OCT-23 6C7H 1 REMARK REVDAT 2 13-FEB-19 6C7H 1 JRNL REVDAT 1 01-AUG-18 6C7H 0 JRNL AUTH N.S.HONG,D.PETROVIC,R.LEE,G.GRYN'OVA,M.PURG,J.SAUNDERS, JRNL AUTH 2 P.BAUER,P.D.CARR,C.Y.LIN,P.D.MABBITT,W.ZHANG,T.ALTAMORE, JRNL AUTH 3 C.EASTON,M.L.COOTE,S.C.L.KAMERLIN,C.J.JACKSON JRNL TITL THE EVOLUTION OF MULTIPLE ACTIVE SITE CONFIGURATIONS IN A JRNL TITL 2 DESIGNED ENZYME. JRNL REF NAT COMMUN V. 9 3900 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30254369 JRNL DOI 10.1038/S41467-018-06305-Y REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 846 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 46.5335 - 4.4147 1.00 2911 167 0.1753 0.2013 REMARK 3 2 4.4147 - 3.5045 0.98 2705 116 0.2255 0.3166 REMARK 3 3 3.5045 - 3.0616 1.00 2689 153 0.2535 0.3087 REMARK 3 4 3.0616 - 2.7817 1.00 2693 120 0.2726 0.3175 REMARK 3 5 2.7817 - 2.5823 1.00 2653 155 0.3322 0.3498 REMARK 3 6 2.5823 - 2.4301 1.00 2647 135 0.3283 0.3827 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1981 REMARK 3 ANGLE : 1.041 2674 REMARK 3 CHIRALITY : 0.061 309 REMARK 3 PLANARITY : 0.006 346 REMARK 3 DIHEDRAL : 17.765 738 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 6C7H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000232169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-17 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JUN 1, 2017 REMARK 200 DATA SCALING SOFTWARE : AIMLESS VERSION 1.11.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17228 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 46.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 35.40 REMARK 200 R MERGE (I) : 0.20540 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 37.90 REMARK 200 R MERGE FOR SHELL (I) : 5.87600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.570 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP VERS 11.5.05 REMARK 200 STARTING MODEL: 5D2W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 % (W/V) PEG3350, 0.1 M BIS-TRIS REMARK 280 PROPANE, PH 8.5, 0.2M NAF, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 52.26667 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 104.53333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 78.40000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 130.66667 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 26.13333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.26667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 104.53333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 130.66667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 78.40000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.13333 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 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 0 REMARK 465 ALA A 1 REMARK 465 GLU A 251 REMARK 465 GLY A 252 REMARK 465 LEU A 253 REMARK 465 GLY A 254 REMARK 465 SER A 255 REMARK 465 LEU A 256 REMARK 465 GLU A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 HIS A 262 REMARK 465 HIS A 263 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 ASN A 103 -79.24 -142.13 REMARK 500 ASN A 224 -107.15 -120.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 6C7H A 0 263 PDB 6C7H 6C7H 0 263 SEQRES 1 A 264 MET ALA LEU ALA LYS ARG ILE ILE ALA ALA LEU ILE VAL SEQRES 2 A 264 LYS ASP GLY ARG VAL VAL LYS GLY SER ASN PHE GLU ASN SEQRES 3 A 264 LEU ARG ASP SER GLY ASP PRO VAL GLU LEU GLY LYS PHE SEQRES 4 A 264 TYR SER GLU ILE GLY ILE ASP GLU LEU SER PHE ALA ASP SEQRES 5 A 264 ILE THR ALA SER VAL GLU LYS ARG LYS THR MET LEU GLU SEQRES 6 A 264 LEU VAL GLU LYS VAL ALA GLU GLN ILE ASP ILE PRO PHE SEQRES 7 A 264 THR VAL GLY GLY GLY ILE HIS ASP PHE GLU THR ALA SER SEQRES 8 A 264 GLU LEU ILE LEU ARG GLY ALA ASP LYS VAL GLU ILE ASN SEQRES 9 A 264 THR ALA ALA VAL GLU ASN PRO SER LEU ILE THR GLN ILE SEQRES 10 A 264 ALA GLN THR PHE GLY SER GLN ALA VAL VAL VAL TYR ILE SEQRES 11 A 264 ALA ALA LYS ARG VAL ASP GLY GLU PHE MET VAL PHE THR SEQRES 12 A 264 TYR SER GLY LYS LYS ASN THR GLY ILE LEU LEU ARG ASP SEQRES 13 A 264 TRP VAL VAL GLU VAL GLU LYS ARG GLY ALA GLY GLU ILE SEQRES 14 A 264 VAL LEU GLY SER ILE ASP ARG LEU GLY THR LYS SER GLY SEQRES 15 A 264 TYR ASP THR GLU MET ILE ARG PHE VAL ARG PRO LEU THR SEQRES 16 A 264 THR LEU PRO ILE ILE ALA HIS GLY GLY ALA GLY LYS MET SEQRES 17 A 264 GLU HIS PHE LEU GLU ALA PHE LEU ALA GLY ALA ASP ALA SEQRES 18 A 264 ALA LYS ALA ASN SER VAL LEU HIS PHE ARG GLU ILE ASP SEQRES 19 A 264 VAL ARG GLU LEU LYS GLU TYR LEU LYS LYS HIS GLY VAL SEQRES 20 A 264 ASN VAL ARG LEU GLU GLY LEU GLY SER LEU GLU HIS HIS SEQRES 21 A 264 HIS HIS HIS HIS FORMUL 2 HOH *64(H2 O) HELIX 1 AA1 ASP A 31 ILE A 42 1 12 HELIX 2 AA2 ALA A 54 ILE A 73 1 20 HELIX 3 AA3 ASP A 85 ARG A 95 1 11 HELIX 4 AA4 ASN A 103 ASN A 109 1 7 HELIX 5 AA5 PRO A 110 GLY A 121 1 12 HELIX 6 AA6 LEU A 153 GLY A 164 1 12 HELIX 7 AA7 ASP A 183 ARG A 191 1 9 HELIX 8 AA8 PRO A 192 THR A 194 5 3 HELIX 9 AA9 LYS A 206 GLY A 217 1 12 HELIX 10 AB1 ASN A 224 PHE A 229 1 6 HELIX 11 AB2 ASP A 233 HIS A 244 1 12 SHEET 1 AA1 8 ARG A 16 VAL A 17 0 SHEET 2 AA1 8 ARG A 5 LYS A 13 -1 N LYS A 13 O ARG A 16 SHEET 3 AA1 8 GLU A 46 ASP A 51 1 O ALA A 50 N VAL A 12 SHEET 4 AA1 8 PHE A 77 GLY A 80 1 O THR A 78 N PHE A 49 SHEET 5 AA1 8 LYS A 99 ILE A 102 1 O GLU A 101 N VAL A 79 SHEET 6 AA1 8 VAL A 125 VAL A 134 1 O VAL A 126 N VAL A 100 SHEET 7 AA1 8 GLU A 137 THR A 142 -1 O MET A 139 N LYS A 132 SHEET 8 AA1 8 LYS A 147 LEU A 152 -1 O LYS A 147 N THR A 142 SHEET 1 AA2 8 ARG A 16 VAL A 17 0 SHEET 2 AA2 8 ARG A 5 LYS A 13 -1 N LYS A 13 O ARG A 16 SHEET 3 AA2 8 ALA A 220 ALA A 223 1 O ALA A 221 N ILE A 7 SHEET 4 AA2 8 ILE A 198 HIS A 201 1 N ALA A 200 O LYS A 222 SHEET 5 AA2 8 GLU A 167 SER A 172 1 N ILE A 168 O ILE A 199 SHEET 6 AA2 8 VAL A 125 VAL A 134 1 N ILE A 129 O VAL A 169 SHEET 7 AA2 8 GLU A 137 THR A 142 -1 O MET A 139 N LYS A 132 SHEET 8 AA2 8 LYS A 147 LEU A 152 -1 O LYS A 147 N THR A 142 CRYST1 97.438 97.438 156.800 90.00 90.00 120.00 P 61 2 2 12 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 0.010263 0.005925 0.000000 0.00000 SCALE2 0.000000 0.011851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006378 0.00000