HEADER HYDROLASE 13-DEC-18 6Q7Q TITLE CRYSTAL STRUCTURE OF OE1.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OE1.3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: PH0459; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPUTATIONALLY DESIGNED ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.W.LEVY REVDAT 3 24-JAN-24 6Q7Q 1 REMARK REVDAT 2 26-JUN-19 6Q7Q 1 JRNL REVDAT 1 05-JUN-19 6Q7Q 0 JRNL AUTH A.J.BURKE,S.L.LOVELOCK,A.FRESE,R.CRAWSHAW,M.ORTMAYER, JRNL AUTH 2 M.DUNSTAN,C.LEVY,A.P.GREEN JRNL TITL DESIGN AND EVOLUTION OF AN ENZYME WITH A NON-CANONICAL JRNL TITL 2 ORGANOCATALYTIC MECHANISM. JRNL REF NATURE V. 570 219 2019 JRNL REFN ESSN 1476-4687 JRNL PMID 31132786 JRNL DOI 10.1038/S41586-019-1262-8 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3304 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 18669 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 864 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 49.8400 - 3.4500 1.00 3025 140 0.1504 0.1905 REMARK 3 2 3.4500 - 2.7400 1.00 2985 143 0.1776 0.2348 REMARK 3 3 2.7400 - 2.3900 1.00 2970 145 0.1961 0.2502 REMARK 3 4 2.3900 - 2.1700 1.00 2957 140 0.1955 0.2245 REMARK 3 5 2.1700 - 2.0200 1.00 2966 138 0.2065 0.2703 REMARK 3 6 2.0200 - 1.9000 0.98 2902 158 0.2340 0.2777 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) : 0.182 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.53 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 1905 REMARK 3 ANGLE : 0.711 2562 REMARK 3 CHIRALITY : 0.050 271 REMARK 3 PLANARITY : 0.005 331 REMARK 3 DIHEDRAL : 13.835 1157 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -13.2005 1.0218 10.0006 REMARK 3 T TENSOR REMARK 3 T11: 0.1617 T22: 0.2427 REMARK 3 T33: 0.2280 T12: 0.0136 REMARK 3 T13: -0.0007 T23: -0.0562 REMARK 3 L TENSOR REMARK 3 L11: 0.6865 L22: 1.3939 REMARK 3 L33: 1.3839 L12: 0.0011 REMARK 3 L13: -0.1375 L23: -0.6978 REMARK 3 S TENSOR REMARK 3 S11: 0.0118 S12: -0.1513 S13: 0.0728 REMARK 3 S21: 0.0244 S22: -0.0405 S23: -0.0338 REMARK 3 S31: -0.0267 S32: 0.0456 S33: 0.0355 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 6Q7Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18693 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.280 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: 2UW6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M CALCIUM CHLORIDE DIHYDRATE 0.1 REMARK 280 M SODIUM ACETATE PH 4.6, 30 % V/V MPD, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.56250 REMARK 290 SMTRY3 2 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11230 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 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 VAL A 183 REMARK 465 GLY A 231 REMARK 465 GLN A 232 REMARK 465 GLY A 233 REMARK 465 SER A 234 REMARK 465 LEU A 235 REMARK 465 GLU A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 HIS A 241 REMARK 465 HIS A 242 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 O HOH A 416 O HOH A 445 2.08 REMARK 500 O HOH A 434 O HOH A 443 2.10 REMARK 500 O HOH A 407 O HOH A 418 2.13 REMARK 500 O PRO A 182 O HOH A 301 2.13 REMARK 500 O HOH A 390 O HOH A 455 2.15 REMARK 500 O HOH A 314 O HOH A 334 2.16 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 ASP A 185 -80.69 -96.19 REMARK 500 ALA A 186 70.76 -62.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Q7Q A 1 232 UNP O58216 O58216_PYRHO 1 232 SEQADV 6Q7Q SER A 9 UNP O58216 PHE 9 CONFLICT SEQADV 6Q7Q PRO A 10 UNP O58216 VAL 10 CONFLICT SEQADV 6Q7Q ASN A 14 UNP O58216 LEU 14 CONFLICT SEQADV 6Q7Q HIS A 19 UNP O58216 GLU 19 CONFLICT SEQADV 6Q7Q MET A 22 UNP O58216 THR 22 CONFLICT SEQADV 6Q7Q ASN A 46 UNP O58216 GLU 46 CONFLICT SEQADV 6Q7Q GLY A 63 UNP O58216 PRO 63 CONFLICT SEQADV 6Q7Q LEU A 64 UNP O58216 ILE 64 CONFLICT SEQADV 6Q7Q LEU A 68 UNP O58216 GLU 68 CONFLICT SEQADV 6Q7Q SER A 91 UNP O58216 HIS 91 CONFLICT SEQADV 6Q7Q SER A 95 UNP O58216 HIS 95 CONFLICT SEQADV 6Q7Q GLY A 125 UNP O58216 ASP 125 CONFLICT SEQADV 6Q7Q GLN A 128 UNP O58216 TYR 128 CONFLICT SEQADV 6Q7Q ALA A 129 UNP O58216 LEU 129 CONFLICT SEQADV 6Q7Q PHE A 132 UNP O58216 HIS 132 CONFLICT SEQADV 6Q7Q ALA A 186 UNP O58216 CYS 186 CONFLICT SEQADV 6Q7Q ALA A 212 UNP O58216 CYS 212 CONFLICT SEQADV 6Q7Q GLY A 233 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q SER A 234 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q LEU A 235 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q GLU A 236 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q HIS A 237 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q HIS A 238 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q HIS A 239 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q HIS A 240 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q HIS A 241 UNP O58216 EXPRESSION TAG SEQADV 6Q7Q HIS A 242 UNP O58216 EXPRESSION TAG SEQRES 1 A 242 MET ILE ARG ALA VAL PHE PHE ASP SER PRO GLY THR LEU SEQRES 2 A 242 ASN SER VAL GLU GLY HIS ALA LYS MET MHS LEU LYS ILE SEQRES 3 A 242 MET GLU GLU VAL LEU GLY ASP TYR PRO LEU ASN PRO LYS SEQRES 4 A 242 THR LEU LEU ASP GLU TYR ASN LYS LEU THR ARG GLU ALA SEQRES 5 A 242 PHE SER ASN TYR ALA GLY LYS PRO TYR ARG GLY LEU ARG SEQRES 6 A 242 ASP ILE LEU GLU GLU VAL MET ARG LYS LEU ALA GLU LYS SEQRES 7 A 242 TYR GLY PHE LYS TYR PRO GLU ASN PHE TRP GLU ILE SER SEQRES 8 A 242 LEU ARG MET SER GLN ARG TYR GLY GLU LEU TYR PRO GLU SEQRES 9 A 242 VAL VAL GLU VAL LEU LYS SER LEU LYS GLY LYS TYR HIS SEQRES 10 A 242 VAL GLY MET ILE THR ASP SER GLY THR GLU GLN ALA MET SEQRES 11 A 242 ALA PHE LEU ASP ALA LEU GLY ILE LYS ASP LEU PHE ASP SEQRES 12 A 242 SER ILE THR THR SER GLU GLU ALA GLY PHE PHE LYS PRO SEQRES 13 A 242 HIS PRO ARG ILE PHE GLU LEU ALA LEU LYS LYS ALA GLY SEQRES 14 A 242 VAL LYS GLY GLU GLU ALA VAL TYR VAL GLY ASP ASN PRO SEQRES 15 A 242 VAL LYS ASP ALA GLY GLY SER LYS ASN LEU GLY MET THR SEQRES 16 A 242 SER ILE LEU LEU ASP ARG LYS GLY GLU LYS ARG GLU PHE SEQRES 17 A 242 TRP ASP LYS ALA ASP PHE ILE VAL SER ASP LEU ARG GLU SEQRES 18 A 242 VAL ILE LYS ILE VAL ASP GLU LEU ASN GLY GLN GLY SER SEQRES 19 A 242 LEU GLU HIS HIS HIS HIS HIS HIS MODRES 6Q7Q MHS A 23 HIS MODIFIED RESIDUE HET MHS A 23 19 HETNAM MHS N1-METHYLATED HISTIDINE FORMUL 1 MHS C7 H11 N3 O2 FORMUL 2 HOH *172(H2 O) HELIX 1 AA1 SER A 15 GLY A 32 1 18 HELIX 2 AA2 ASN A 37 ALA A 57 1 21 HELIX 3 AA3 GLY A 63 GLY A 80 1 18 HELIX 4 AA4 ASN A 86 GLY A 99 1 14 HELIX 5 AA5 GLU A 104 LYS A 113 1 10 HELIX 6 AA6 GLY A 125 LEU A 136 1 12 HELIX 7 AA7 ILE A 138 PHE A 142 5 5 HELIX 8 AA8 SER A 148 GLY A 152 1 5 HELIX 9 AA9 HIS A 157 GLY A 169 1 13 HELIX 10 AB1 LYS A 171 GLU A 173 5 3 HELIX 11 AB2 GLY A 187 LEU A 192 1 6 HELIX 12 AB3 LYS A 205 ALA A 212 5 8 HELIX 13 AB4 LEU A 219 ASN A 230 1 12 SHEET 1 AA1 6 SER A 144 THR A 147 0 SHEET 2 AA1 6 HIS A 117 THR A 122 1 N MET A 120 O THR A 146 SHEET 3 AA1 6 ALA A 4 SER A 9 1 N VAL A 5 O HIS A 117 SHEET 4 AA1 6 ALA A 175 GLY A 179 1 O VAL A 176 N PHE A 6 SHEET 5 AA1 6 THR A 195 LEU A 199 1 O LEU A 199 N GLY A 179 SHEET 6 AA1 6 PHE A 214 VAL A 216 1 O PHE A 214 N LEU A 198 LINK C MET A 22 N MHS A 23 1555 1555 1.32 LINK C MHS A 23 N LEU A 24 1555 1555 1.33 CISPEP 1 SER A 9 PRO A 10 0 3.72 CISPEP 2 LYS A 155 PRO A 156 0 2.62 CRYST1 33.952 71.125 51.922 90.00 106.33 90.00 P 1 21 1 2 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 0.029453 0.000000 0.008631 0.00000 SCALE2 0.000000 0.014060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020070 0.00000