HEADER LYASE 23-APR-14 4PEK TITLE CRYSTAL STRUCTURE OF A COMPUTATIONALLY DESIGNED RETRO-ALDOLASE, TITLE 2 RA114.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETRO-ALDOLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPUTATIONALLY DESIGNED ENZYME, FLUORESCENT PROBE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR G.BHABHA,X.ZHANG,Y.LIU,D.C.EKIERT REVDAT 2 27-SEP-23 4PEK 1 SOURCE REMARK REVDAT 1 08-APR-15 4PEK 0 JRNL AUTH Y.LIU,X.ZHANG,Y.L.TAN,G.BHABHA,D.C.EKIERT,Y.KIPNIS,S.BJELIC, JRNL AUTH 2 D.BAKER,J.W.KELLY JRNL TITL DE NOVO-DESIGNED ENZYMES AS SMALL-MOLECULE-REGULATED JRNL TITL 2 FLUORESCENCE IMAGING TAGS AND FLUORESCENT REPORTERS. JRNL REF J.AM.CHEM.SOC. V. 136 13102 2014 JRNL REFN ESSN 1520-5126 JRNL PMID 25209927 JRNL DOI 10.1021/JA5056356 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1593) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 42440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 37.4803 - 3.8549 0.99 3061 151 0.1498 0.1771 REMARK 3 2 3.8549 - 3.0602 1.00 2968 147 0.1491 0.1755 REMARK 3 3 3.0602 - 2.6735 1.00 2905 143 0.1550 0.1957 REMARK 3 4 2.6735 - 2.4291 1.00 2897 144 0.1445 0.1845 REMARK 3 5 2.4291 - 2.2550 1.00 2883 143 0.1348 0.2204 REMARK 3 6 2.2550 - 2.1221 1.00 2876 142 0.1221 0.1558 REMARK 3 7 2.1221 - 2.0158 1.00 2881 143 0.1227 0.1713 REMARK 3 8 2.0158 - 1.9281 1.00 2857 140 0.1253 0.1807 REMARK 3 9 1.9281 - 1.8538 1.00 2863 142 0.1380 0.1950 REMARK 3 10 1.8538 - 1.7899 1.00 2862 142 0.1560 0.2304 REMARK 3 11 1.7899 - 1.7339 1.00 2848 141 0.1612 0.2180 REMARK 3 12 1.7339 - 1.6843 1.00 2838 140 0.1758 0.2428 REMARK 3 13 1.6843 - 1.6400 1.00 2867 141 0.1982 0.2753 REMARK 3 14 1.6400 - 1.6000 1.00 2835 140 0.2374 0.3029 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.014 2228 REMARK 3 ANGLE : 1.369 3024 REMARK 3 CHIRALITY : 0.076 337 REMARK 3 PLANARITY : 0.007 399 REMARK 3 DIHEDRAL : 14.765 897 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 4PEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000201241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3TC7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 CITRATE, PH 5.6 AND 30 % (W/V) PEG 4000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.53500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.54000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.53500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.54000 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 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 GLU A 248 REMARK 465 GLY A 249 REMARK 465 SER A 250 REMARK 465 LEU A 251 REMARK 465 GLU A 252 REMARK 465 HIS A 253 REMARK 465 HIS A 254 REMARK 465 HIS A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 REMARK 465 HIS A 258 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 TYR A 76 -38.79 -131.48 REMARK 500 ALA A 181 -74.99 -88.79 REMARK 500 GLU A 185 -52.90 167.00 REMARK 500 GLU A 211 176.28 60.84 REMARK 500 GLU A 211 176.28 60.80 REMARK 500 SER A 214 -1.91 -160.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PEJ RELATED DB: PDB DBREF 4PEK A 1 258 PDB 4PEK 4PEK 1 258 SEQRES 1 A 258 MET PRO ARG TYR LEU LYS GLY TRP LEU GLU ASP VAL VAL SEQRES 2 A 258 GLN LEU SER LEU ARG ARG PRO SER VAL ARG ALA SER ARG SEQRES 3 A 258 GLN ARG PRO ILE ILE SER LEU ASN GLU ARG ILE LEU GLU SEQRES 4 A 258 PHE ASN LYS ARG ASN ILE THR ALA ILE ILE ALA GLU TYR SEQRES 5 A 258 LYS ARG LYS ASP PRO SER GLY LEU ASP VAL GLU ARG ASP SEQRES 6 A 258 PRO ILE GLU TYR ALA LYS PHE MET GLU ARG TYR ALA VAL SEQRES 7 A 258 GLY LEU PHE ILE SER THR GLU GLU LYS TYR PHE ASN GLY SEQRES 8 A 258 SER TYR GLU THR LEU ARG LYS ILE ALA SER SER VAL SER SEQRES 9 A 258 ILE PRO ILE LEU MET TYR ASP PHE ILE VAL LYS GLU SER SEQRES 10 A 258 GLN ILE ASP ASP ALA TYR ASN LEU GLY ALA ASP THR VAL SEQRES 11 A 258 ALA LEU ILE VAL LYS ILE LEU THR GLU ARG GLU LEU GLU SEQRES 12 A 258 SER LEU LEU GLU TYR ALA ARG SER TYR GLY MET GLU PRO SEQRES 13 A 258 LEU ILE ILE ILE ASN ASP GLU ASN ASP LEU ASP ILE ALA SEQRES 14 A 258 LEU ARG ILE GLY ALA ARG PHE ILE GLY ILE ALA ALA ARG SEQRES 15 A 258 ASP TRP GLU THR GLY GLU ILE ASN LYS GLU ASN GLN ARG SEQRES 16 A 258 LYS LEU ILE SER MET ILE PRO SER ASN VAL VAL LYS VAL SEQRES 17 A 258 ALA LYS GLU GLY ILE SER GLU ARG ASN GLU ILE GLU GLU SEQRES 18 A 258 LEU ARG LYS LEU GLY VAL ASN ALA PHE LEU ILE GLY SER SEQRES 19 A 258 SER LEU MET ARG ASN PRO GLU LYS ILE LYS GLU LEU ILE SEQRES 20 A 258 GLU GLY SER LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *140(H2 O) HELIX 1 AA1 LYS A 6 ARG A 18 1 13 HELIX 2 AA2 SER A 32 ARG A 43 1 12 HELIX 3 AA3 ASP A 65 GLU A 74 1 10 HELIX 4 AA4 SER A 92 SER A 101 1 10 HELIX 5 AA5 LYS A 115 GLY A 126 1 12 HELIX 6 AA6 LYS A 135 LEU A 137 5 3 HELIX 7 AA7 THR A 138 TYR A 152 1 15 HELIX 8 AA8 ASP A 162 ILE A 172 1 11 HELIX 9 AA9 ASN A 190 MET A 200 1 11 HELIX 10 AB1 GLU A 215 LEU A 225 1 11 HELIX 11 AB2 GLY A 233 ASN A 239 1 7 HELIX 12 AB3 GLU A 241 ILE A 247 1 7 SHEET 1 AA1 9 ILE A 48 TYR A 52 0 SHEET 2 AA1 9 GLY A 79 SER A 83 1 O PHE A 81 N TYR A 52 SHEET 3 AA1 9 ILE A 107 TYR A 110 1 O LEU A 108 N LEU A 80 SHEET 4 AA1 9 THR A 129 ILE A 133 1 O THR A 129 N MET A 109 SHEET 5 AA1 9 LEU A 157 ILE A 160 1 O ILE A 159 N LEU A 132 SHEET 6 AA1 9 PHE A 176 ALA A 180 1 O PHE A 176 N ILE A 158 SHEET 7 AA1 9 VAL A 206 LYS A 210 1 O VAL A 208 N ILE A 179 SHEET 8 AA1 9 ALA A 229 ILE A 232 1 O LEU A 231 N ALA A 209 SHEET 9 AA1 9 ILE A 48 TYR A 52 1 N ILE A 49 O PHE A 230 CRYST1 53.800 63.080 93.070 90.00 90.00 90.00 P 21 21 21 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 0.018587 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010745 0.00000