HEADER TRANSFERASE 23-FEB-18 6CI2 TITLE CRYSTAL STRUCTURE OF THE FORMYLTRANSFERASE PSEJ FROM ANOXYBACILLUS TITLE 2 KAMCHATKENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FORMYLTRANSFERASE PSEJ; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANOXYBACILLUS KAMCHATKENSIS G10; SOURCE 3 ORGANISM_TAXID: 1212546; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FORMYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.REIMER,J.JIANG,I.HARB,T.M.SCHMEING REVDAT 5 04-OCT-23 6CI2 1 REMARK REVDAT 4 08-JAN-20 6CI2 1 REMARK REVDAT 3 28-NOV-18 6CI2 1 JRNL REVDAT 2 07-NOV-18 6CI2 1 JRNL REVDAT 1 17-OCT-18 6CI2 0 JRNL AUTH J.M.REIMER,I.HARB,O.G.OVCHINNIKOVA,J.JIANG,C.WHITFIELD, JRNL AUTH 2 T.M.SCHMEING JRNL TITL STRUCTURAL INSIGHT INTO A NOVEL FORMYLTRANSFERASE AND JRNL TITL 2 EVOLUTION TO A NONRIBOSOMAL PEPTIDE SYNTHETASE TAILORING JRNL TITL 3 DOMAIN. JRNL REF ACS CHEM. BIOL. V. 13 3161 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 30346688 JRNL DOI 10.1021/ACSCHEMBIO.8B00739 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3042 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 21296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2132 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 31.3400 - 4.8200 0.93 1227 135 0.1688 0.2029 REMARK 3 2 4.8200 - 3.8200 0.99 1276 144 0.1482 0.1763 REMARK 3 3 3.8200 - 3.3400 1.00 1318 145 0.1806 0.2164 REMARK 3 4 3.3400 - 3.0400 1.00 1286 135 0.1846 0.2496 REMARK 3 5 3.0400 - 2.8200 1.00 1275 145 0.2113 0.2584 REMARK 3 6 2.8200 - 2.6500 1.00 1296 144 0.2010 0.2721 REMARK 3 7 2.6500 - 2.5200 1.00 1262 144 0.1898 0.2190 REMARK 3 8 2.5200 - 2.4100 1.00 1308 136 0.1831 0.2379 REMARK 3 9 2.4100 - 2.3200 1.00 1256 151 0.1794 0.2539 REMARK 3 10 2.3200 - 2.2400 1.00 1294 140 0.1883 0.2273 REMARK 3 11 2.2400 - 2.1700 1.00 1288 139 0.1900 0.2568 REMARK 3 12 2.1700 - 2.1100 1.00 1259 152 0.1807 0.2129 REMARK 3 13 2.1100 - 2.0500 1.00 1272 137 0.1921 0.1966 REMARK 3 14 2.0500 - 2.0000 1.00 1298 132 0.1961 0.2490 REMARK 3 15 2.0000 - 1.9600 0.98 1249 153 0.2012 0.2363 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) : 0.208 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.395 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.03 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 : 0.017 1638 REMARK 3 ANGLE : 1.330 2218 REMARK 3 CHIRALITY : 0.092 234 REMARK 3 PLANARITY : 0.009 276 REMARK 3 DIHEDRAL : 20.456 975 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 6CI2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21304 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 59.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12400 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 REMARK 200 STARTING MODEL: 5ES6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M MES PH REMARK 280 6.6, 30.67% PEG5000 MME, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.81500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.81500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.75500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 531 LIES ON A SPECIAL POSITION. 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 ASN A 215 REMARK 465 ASN A 216 REMARK 465 GLU A 217 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 GLN A 88 13.00 58.47 REMARK 500 ILE A 95 51.12 -92.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 DBREF 6CI2 A 26 217 PDB 6CI2 6CI2 26 217 SEQRES 1 A 192 GLY LYS ILE LEU LEU LEU GLY PRO GLU ARG LYS TRP LEU SEQRES 2 A 192 ARG ASP PHE LEU GLU SER PHE GLU ASP GLU VAL THR GLN SEQRES 3 A 192 TYR GLN ASP LYS LEU ASP LYS LYS SER ALA ILE LEU ASN SEQRES 4 A 192 ASN VAL ASP PHE ILE ILE SER TYR GLY TYR ARG TYR ILE SEQRES 5 A 192 ILE HIS PRO ASP ILE VAL GLU ARG PHE LYS GLN ARG ALA SEQRES 6 A 192 ILE ASN LEU HIS ILE SER TYR LEU PRO TRP ASN LYS GLY SEQRES 7 A 192 ALA ASP PRO ASN LEU TRP SER PHE LEU GLU ASP SER PRO SEQRES 8 A 192 LYS GLY VAL THR ILE HIS TYR ILE ASP SER GLY LEU ASP SEQRES 9 A 192 THR GLY GLU ILE ILE VAL GLN ARG GLU VAL THR TYR TYR SEQRES 10 A 192 GLU ASN ASP THR LEU ARG THR THR TYR GLU ARG LEU THR SEQRES 11 A 192 GLN THR ILE GLU LYS LEU PHE MET GLU TYR TRP PRO LEU SEQRES 12 A 192 ILE ARG LEU GLY LYS ILE ARG GLY ILE PRO GLN PRO LYS SEQRES 13 A 192 GLY GLY SER TYR HIS LYS LEU LYS ASP LYS GLU LYS TYR SEQRES 14 A 192 LEU TYR LEU LEU THR ASP GLY TRP ASP THR PRO VAL GLN SEQRES 15 A 192 LYS LEU ILE GLY LYS ALA GLN ASN ASN GLU HET MES A 301 12 HET SO4 A 302 5 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM SO4 SULFATE ION FORMUL 2 MES C6 H13 N O4 S FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *132(H2 O) HELIX 1 AA1 ARG A 35 SER A 44 1 10 HELIX 2 AA2 SER A 60 ASN A 64 5 5 HELIX 3 AA3 HIS A 79 PHE A 86 1 8 HELIX 4 AA4 ASP A 105 GLU A 113 1 9 HELIX 5 AA5 THR A 146 LEU A 171 1 26 HELIX 6 AA6 LYS A 187 LEU A 198 5 12 HELIX 7 AA7 ASP A 200 THR A 204 5 5 HELIX 8 AA8 PRO A 205 ILE A 210 5 6 SHEET 1 AA1 6 GLU A 48 TYR A 52 0 SHEET 2 AA1 6 LYS A 27 LEU A 31 1 N LEU A 30 O THR A 50 SHEET 3 AA1 6 PHE A 68 SER A 71 1 O PHE A 68 N LEU A 29 SHEET 4 AA1 6 ALA A 90 HIS A 94 1 O ILE A 91 N SER A 71 SHEET 5 AA1 6 GLY A 118 TYR A 123 -1 O THR A 120 N HIS A 94 SHEET 6 AA1 6 ILE A 133 GLU A 138 -1 O ILE A 134 N ILE A 121 SHEET 1 AA2 2 LYS A 102 GLY A 103 0 SHEET 2 AA2 2 TYR A 185 HIS A 186 1 O HIS A 186 N LYS A 102 CISPEP 1 LEU A 98 PRO A 99 0 7.45 SITE 1 AC1 8 ASN A 64 ASP A 105 ASN A 107 LEU A 108 SITE 2 AC1 8 TYR A 151 TRP A 202 HOH A 467 HOH A 488 SITE 1 AC2 2 LYS A 36 TRP A 37 CRYST1 95.630 77.510 41.730 90.00 103.84 90.00 C 1 2 1 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 0.010457 0.000000 0.002576 0.00000 SCALE2 0.000000 0.012902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024680 0.00000