HEADER TRANSFERASE 29-JUL-21 7FHC TITLE STRUCTURE OF PRENYLTRANSFERASE MUTANT V49W FROM STREPTOMYCES SP. TITLE 2 (STRAIN CL190) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRENYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. (STRAIN CL190); SOURCE 3 ORGANISM_TAXID: 93372; SOURCE 4 STRAIN: CL190; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSY5CDF KEYWDS PT-BARREL, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.XUE,K.J.H.LIM,Y.D.HARTONO,M.D.K.GO,H.FAN,W.S.YEW REVDAT 2 29-NOV-23 7FHC 1 REMARK REVDAT 1 22-JUN-22 7FHC 0 JRNL AUTH K.J.H.LIM,Y.D.HARTONO,B.XUE,M.K.GO,H.FAN,W.S.YEW JRNL TITL STRUCTURE-GUIDED ENGINEERING OF PRENYLTRANSFERASE NPHB FOR JRNL TITL 2 HIGH-YIELD AND REGIOSELECTIVE CANNABINOID PRODUCTION. JRNL REF ACS CATALYSIS V. 12 4628 2022 JRNL REFN ESSN 2155-5435 JRNL DOI 10.1021/ACSCATAL.2C00786 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19226 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 985 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 42.8000 - 3.9300 1.00 2752 155 0.1771 0.1878 REMARK 3 2 3.9300 - 3.1200 1.00 2626 148 0.1569 0.2193 REMARK 3 3 3.1200 - 2.7300 1.00 2611 143 0.1968 0.2530 REMARK 3 4 2.7300 - 2.4800 1.00 2592 108 0.2075 0.2760 REMARK 3 5 2.4800 - 2.3000 1.00 2587 136 0.1926 0.2484 REMARK 3 6 2.3000 - 2.1700 1.00 2571 150 0.1978 0.2551 REMARK 3 7 2.1700 - 2.0600 0.99 2502 145 0.2184 0.2956 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.02 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 : 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 7FHC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023581. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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) : 0.95373 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19285 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 44.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.34000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.60 REMARK 200 R MERGE FOR SHELL (I) : 1.84200 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 2.8.3 REMARK 200 STARTING MODEL: 1ZB6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE PH 5.0, 18% W/V PEG 20,000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K 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 22.16950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.80200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.80200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.16950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.37500 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 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 LEU A 305 REMARK 465 GLU A 306 REMARK 465 ASP A 307 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 73 104.94 -30.79 REMARK 500 LYS A 118 -18.79 -146.49 REMARK 500 ASN A 128 48.83 -152.47 REMARK 500 ASP A 158 -70.55 -120.61 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FHC A 1 307 UNP Q4R2T2 Q4R2T2_STRC1 1 307 SEQADV 7FHC GLY A -1 UNP Q4R2T2 EXPRESSION TAG SEQADV 7FHC PRO A 0 UNP Q4R2T2 EXPRESSION TAG SEQADV 7FHC TRP A 49 UNP Q4R2T2 VAL 49 ENGINEERED MUTATION SEQRES 1 A 309 GLY PRO MET SER GLU ALA ALA ASP VAL GLU ARG VAL TYR SEQRES 2 A 309 ALA ALA MET GLU GLU ALA ALA GLY LEU LEU GLY VAL ALA SEQRES 3 A 309 CYS ALA ARG ASP LYS ILE TYR PRO LEU LEU SER THR PHE SEQRES 4 A 309 GLN ASP THR LEU VAL GLU GLY GLY SER VAL VAL TRP PHE SEQRES 5 A 309 SER MET ALA SER GLY ARG HIS SER THR GLU LEU ASP PHE SEQRES 6 A 309 SER ILE SER VAL PRO THR SER HIS GLY ASP PRO TYR ALA SEQRES 7 A 309 THR VAL VAL GLU LYS GLY LEU PHE PRO ALA THR GLY HIS SEQRES 8 A 309 PRO VAL ASP ASP LEU LEU ALA ASP THR GLN LYS HIS LEU SEQRES 9 A 309 PRO VAL SER MET PHE ALA ILE ASP GLY GLU VAL THR GLY SEQRES 10 A 309 GLY PHE LYS LYS THR TYR ALA PHE PHE PRO THR ASP ASN SEQRES 11 A 309 MET PRO GLY VAL ALA GLU LEU SER ALA ILE PRO SER MET SEQRES 12 A 309 PRO PRO ALA VAL ALA GLU ASN ALA GLU LEU PHE ALA ARG SEQRES 13 A 309 TYR GLY LEU ASP LYS VAL GLN MET THR SER MET ASP TYR SEQRES 14 A 309 LYS LYS ARG GLN VAL ASN LEU TYR PHE SER GLU LEU SER SEQRES 15 A 309 ALA GLN THR LEU GLU ALA GLU SER VAL LEU ALA LEU VAL SEQRES 16 A 309 ARG GLU LEU GLY LEU HIS VAL PRO ASN GLU LEU GLY LEU SEQRES 17 A 309 LYS PHE CYS LYS ARG SER PHE SER VAL TYR PRO THR LEU SEQRES 18 A 309 ASN TRP GLU THR GLY LYS ILE ASP ARG LEU CYS PHE ALA SEQRES 19 A 309 VAL ILE SER ASN ASP PRO THR LEU VAL PRO SER SER ASP SEQRES 20 A 309 GLU GLY ASP ILE GLU LYS PHE HIS ASN TYR ALA THR LYS SEQRES 21 A 309 ALA PRO TYR ALA TYR VAL GLY GLU LYS ARG THR LEU VAL SEQRES 22 A 309 TYR GLY LEU THR LEU SER PRO LYS GLU GLU TYR TYR LYS SEQRES 23 A 309 LEU GLY ALA TYR TYR HIS ILE THR ASP VAL GLN ARG GLY SEQRES 24 A 309 LEU LEU LYS ALA PHE ASP SER LEU GLU ASP FORMUL 2 HOH *219(H2 O) HELIX 1 AA1 GLY A -1 LEU A 20 1 22 HELIX 2 AA2 ALA A 26 PHE A 37 1 12 HELIX 3 AA3 PHE A 37 GLY A 44 1 8 HELIX 4 AA4 GLY A 55 SER A 58 5 4 HELIX 5 AA5 SER A 70 GLY A 72 5 3 HELIX 6 AA6 ASP A 73 LYS A 81 1 9 HELIX 7 AA7 PRO A 90 LEU A 102 1 13 HELIX 8 AA8 GLY A 131 SER A 136 1 6 HELIX 9 AA9 PRO A 142 ASN A 148 1 7 HELIX 10 AB1 ASN A 148 TYR A 155 1 8 HELIX 11 AB2 SER A 180 GLU A 185 1 6 HELIX 12 AB3 GLU A 185 GLY A 197 1 13 HELIX 13 AB4 ASN A 202 ARG A 211 1 10 HELIX 14 AB5 ASP A 245 ALA A 259 1 15 HELIX 15 AB6 THR A 292 ASP A 303 1 12 SHEET 1 AA111 VAL A 48 ALA A 53 0 SHEET 2 AA111 ASP A 62 PRO A 68 -1 O ASP A 62 N SER A 51 SHEET 3 AA111 MET A 106 GLU A 112 -1 O PHE A 107 N VAL A 67 SHEET 4 AA111 GLY A 116 PHE A 123 -1 O GLY A 116 N GLU A 112 SHEET 5 AA111 VAL A 160 ASP A 166 -1 O MET A 165 N THR A 120 SHEET 6 AA111 GLN A 171 PHE A 176 -1 O GLN A 171 N ASP A 166 SHEET 7 AA111 SER A 214 ASN A 220 -1 O LEU A 219 N VAL A 172 SHEET 8 AA111 ARG A 228 SER A 235 -1 O ALA A 232 N SER A 214 SHEET 9 AA111 LEU A 270 LEU A 276 -1 O LEU A 276 N LEU A 229 SHEET 10 AA111 GLU A 281 HIS A 290 -1 O GLY A 286 N VAL A 271 SHEET 11 AA111 VAL A 48 ALA A 53 -1 N PHE A 50 O ALA A 287 CRYST1 44.339 78.750 85.604 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 0.022554 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012698 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011682 0.00000