HEADER LYASE 03-JAN-23 8FOQ TITLE CRYSTAL STRUCTURE OF KEMP ELIMINASE 1A53-CORE WITH BOUND TRANSITION TITLE 2 STATE ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: KEMP ELIMINASE 1A53-CORE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD DE3 KEYWDS ISOMERASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR N.ZARIFI,P.ASTHANA,J.S.FRASER,R.A.CHICA REVDAT 1 10-JAN-24 8FOQ 0 JRNL AUTH N.ZARIFI,P.ASTHANA,J.S.FRASER,R.A.CHICA JRNL TITL CRYSTAL STRUCTURE OF KEMP ELIMINASE 1A53-CORE WITH BOUND JRNL TITL 2 TRANSITION STATE ANALOGUE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 34621 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 1659 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 48.4800 - 3.6700 1.00 2986 150 0.1541 0.1672 REMARK 3 2 3.6700 - 2.9100 1.00 2848 165 0.1467 0.1707 REMARK 3 3 2.9100 - 2.5500 1.00 2824 124 0.1485 0.1861 REMARK 3 4 2.5400 - 2.3100 1.00 2795 133 0.1422 0.1572 REMARK 3 5 2.3100 - 2.1500 1.00 2791 146 0.1452 0.1675 REMARK 3 6 2.1500 - 2.0200 1.00 2781 132 0.1500 0.1823 REMARK 3 7 2.0200 - 1.9200 1.00 2810 104 0.1617 0.2190 REMARK 3 8 1.9200 - 1.8400 1.00 2711 161 0.1786 0.2334 REMARK 3 9 1.8300 - 1.7600 1.00 2827 120 0.2069 0.2864 REMARK 3 10 1.7600 - 1.7000 0.97 2617 154 0.2312 0.2812 REMARK 3 11 1.7000 - 1.6500 0.94 2575 146 0.2657 0.2923 REMARK 3 12 1.6500 - 1.6000 0.88 2397 124 0.3122 0.3263 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) : 0.189 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.375 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.02 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 : 0.012 2179 REMARK 3 ANGLE : 1.179 2954 REMARK 3 CHIRALITY : 0.066 325 REMARK 3 PLANARITY : 0.007 384 REMARK 3 DIHEDRAL : 15.031 859 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 8FOQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000270938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 1.115870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34679 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 48.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 8.250 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.13300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM MES, PH 6, 40% V/V PEG400, 5% REMARK 280 W/V PEG3000, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K 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 40.65900 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 81.31800 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 81.31800 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 40.65900 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: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 249 REMARK 465 SER A 250 REMARK 465 ILE A 251 REMARK 465 GLU A 252 REMARK 465 GLY A 253 REMARK 465 ARG A 254 REMARK 465 GLY A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 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 HH22 ARG A 238 O HOH A 603 1.40 REMARK 500 O HOH A 664 O HOH A 722 2.00 REMARK 500 O ILE A 232 O HOH A 601 2.07 REMARK 500 OE2 GLU A 143 O HOH A 602 2.13 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 ARG A 54 -68.33 -107.48 REMARK 500 TYR A 76 -37.05 -134.05 REMARK 500 SER A 214 -3.92 -141.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FOQ A 2 261 PDB 8FOQ 8FOQ 2 261 SEQRES 1 A 260 PRO ARG TYR LEU LYS GLY TRP LEU LYS ASP VAL VAL GLN SEQRES 2 A 260 LEU SER LEU ARG ARG PRO SER PHE ARG ALA SER ARG GLN SEQRES 3 A 260 ARG PRO ILE ILE SER LEU ASN GLU ARG ILE LEU GLU PHE SEQRES 4 A 260 ASN LYS ARG ASN ILE THR ALA ILE ILE ALA ALA TYR ARG SEQRES 5 A 260 ARG LYS SER PRO SER GLY LEU ASP VAL GLU ARG ASP PRO SEQRES 6 A 260 ILE GLU TYR SER LYS PHE MET GLU ARG TYR ALA VAL GLY SEQRES 7 A 260 LEU ALA VAL ALA THR GLU GLU LYS TYR PHE ASN GLY SER SEQRES 8 A 260 TYR GLU THR LEU ARG LYS ILE ALA SER SER VAL SER ILE SEQRES 9 A 260 PRO ILE LEU MET TRP ASP PHE ILE VAL LYS GLU SER GLN SEQRES 10 A 260 ILE ASP ASP ALA TYR ASN LEU GLY ALA ASP THR VAL ALA SEQRES 11 A 260 LEU ILE VAL LYS ILE LEU THR GLU ARG GLU LEU GLU SER SEQRES 12 A 260 LEU LEU GLU TYR ALA ARG SER TYR GLY MET GLU PRO TYR SEQRES 13 A 260 ILE VAL ILE ASN ASP GLU ASN ASP LEU ASP ILE ALA LEU SEQRES 14 A 260 ARG ILE GLY ALA ARG PHE ILE GLU ILE CYS SER ARG ASP SEQRES 15 A 260 LEU GLU THR LEU GLU ILE ASN LYS GLU ASN GLN ARG LYS SEQRES 16 A 260 LEU ILE SER MET ILE PRO SER ASN VAL VAL LYS VAL ALA SEQRES 17 A 260 TRP GLY GLY ILE SER GLU ARG ASN GLU ILE GLU GLU LEU SEQRES 18 A 260 ARG LYS LEU GLY VAL ASN ALA PHE GLY ILE GLY SER SER SEQRES 19 A 260 LEU LEU ARG ASN PRO GLU LYS ILE LYS GLU PHE ILE LEU SEQRES 20 A 260 GLY SER ILE GLU GLY ARG GLY HIS HIS HIS HIS HIS HIS HET PO4 A 501 5 HET 3NY A 502 16 HETNAM PO4 PHOSPHATE ION HETNAM 3NY 5-NITRO-1H-BENZOTRIAZOLE FORMUL 2 PO4 O4 P 3- FORMUL 3 3NY C6 H4 N4 O2 FORMUL 4 HOH *169(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 ARG A 75 1 11 HELIX 4 AA4 SER A 92 VAL A 103 1 12 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 SER A 199 1 10 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 LEU A 248 1 8 SHEET 1 AA1 9 ILE A 48 TYR A 52 0 SHEET 2 AA1 9 GLY A 79 ALA A 83 1 O ALA A 81 N TYR A 52 SHEET 3 AA1 9 ILE A 107 TRP 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 TYR A 157 ILE A 160 1 O VAL A 159 N LEU A 132 SHEET 6 AA1 9 PHE A 176 CYS A 180 1 O GLU A 178 N ILE A 160 SHEET 7 AA1 9 VAL A 206 TRP A 210 1 O VAL A 208 N ILE A 179 SHEET 8 AA1 9 ALA A 229 ILE A 232 1 O GLY 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 61.003 61.003 121.977 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 0.016393 0.009464 0.000000 0.00000 SCALE2 0.000000 0.018929 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008198 0.00000