HEADER TRANSFERASE 26-FEB-25 9NIL TITLE STRUCTURE OF A Y1216F MUTANT OF THE ACYLTRANSFERASE DOMAIN OF NCDE, A TITLE 2 MULTI-DOMAIN NRPS PROTEIN FROM NOCARDICHELIN BIOSYNTHESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NCDE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ACYLTRANSFERASE DOMAIN; COMPND 5 EC: 2.3.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: N-TERMINAL GLY HIS REMAIN FOLLOWING CLEAVAGE OF COMPND 9 HISTIDINE TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOCARDIA CARNEA; SOURCE 3 ORGANISM_TAXID: 1206726; SOURCE 4 STRAIN: NBRC 14403; SOURCE 5 GENE: NCDE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ACYLTRANSFERASE, GNAT, SIDEROPHORE BIOSYNTHESIS, NRPS INDEPENDENT KEYWDS 2 SIDEROPHORES, NCDE-ATX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.B.FISK,A.M.GULICK,J.BARRERA RAMIREZ REVDAT 1 09-JUL-25 9NIL 0 JRNL AUTH M.B.FISK,J.BARRERA RAMIREZ,C.E.MERRICK,T.A.WENCEWICZ, JRNL AUTH 2 A.M.GULICK JRNL TITL IDENTIFICATION AND CHARACTERIZATION OF THE BIOSYNTHESIS OF JRNL TITL 2 THE HYBRID NRPS-NIS SIDEROPHORE NOCARDICHELIN. JRNL REF ACS CHEM.BIOL. V. 20 1435 2025 JRNL REFN ESSN 1554-8937 JRNL PMID 40479602 JRNL DOI 10.1021/ACSCHEMBIO.5C00286 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1545 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 36.7600 - 3.2100 1.00 2694 146 0.1503 0.1482 REMARK 3 2 3.2100 - 2.5500 1.00 2646 137 0.1529 0.1801 REMARK 3 3 2.5500 - 2.2200 1.00 2636 140 0.1477 0.1749 REMARK 3 4 2.2200 - 2.0200 1.00 2648 144 0.1423 0.1696 REMARK 3 5 2.0200 - 1.8800 1.00 2626 137 0.1455 0.1577 REMARK 3 6 1.8800 - 1.7600 1.00 2595 146 0.1548 0.1878 REMARK 3 7 1.7600 - 1.6800 1.00 2637 137 0.1620 0.1845 REMARK 3 8 1.6800 - 1.6000 1.00 2658 131 0.1609 0.1658 REMARK 3 9 1.6000 - 1.5400 1.00 2624 154 0.1637 0.2187 REMARK 3 10 1.5400 - 1.4900 1.00 2636 128 0.1663 0.1838 REMARK 3 11 1.4900 - 1.4400 1.00 2610 145 0.1928 0.2372 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.128 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.291 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.59 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 : 0.007 1544 REMARK 3 ANGLE : 0.972 2094 REMARK 3 CHIRALITY : 0.074 221 REMARK 3 PLANARITY : 0.010 278 REMARK 3 DIHEDRAL : 5.763 228 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 9NIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92019 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30580 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 70.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.300 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 (%): 35.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 8000 AND 0.1M HEPES PH 7.5 REMARK 280 ADJUSTED WITH NAOH (10.23 MG/ML PROTEIN), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 35.00400 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 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 1133 REMARK 465 HIS A 1134 REMARK 465 MET A 1135 REMARK 465 ALA A 1136 REMARK 465 GLU A 1137 REMARK 465 VAL A 1138 REMARK 465 GLY A 1139 REMARK 465 ASN A 1140 REMARK 465 GLY A 1141 REMARK 465 ALA A 1142 REMARK 465 THR A 1143 REMARK 465 GLY A 1329 REMARK 465 GLU A 1330 REMARK 465 VAL A 1331 REMARK 465 GLU A 1332 REMARK 465 SER A 1333 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A1247 CG CD OE1 OE2 REMARK 470 ARG A1272 CG CD NE CZ NH1 NH2 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 OE1 GLU A 1277 O HOH A 1501 2.00 REMARK 500 O HOH A 1629 O HOH A 1675 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1520 O HOH A 1670 2545 2.11 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 GLU A1277 53.93 -143.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9NIJ RELATED DB: PDB REMARK 900 WILDTYPE STRUCTURE DBREF 9NIL A 1133 1333 PDB 9NIL 9NIL 1133 1333 SEQRES 1 A 201 GLY HIS MET ALA GLU VAL GLY ASN GLY ALA THR THR TYR SEQRES 2 A 201 HIS PHE GLN SER ARG ARG ILE ASP VAL ASP ARG ASP LEU SEQRES 3 A 201 GLU SER VAL HIS ARG TRP LEU GLY HIS PRO LYS SER HIS SEQRES 4 A 201 TYR TRP ASP MET LEU ASN SER SER LEU ALA ASP VAL GLU SEQRES 5 A 201 LYS LEU ILE ARG ASP ALA GLY ALA ASP PRO ASP PRO ARG SEQRES 6 A 201 PHE GLY MET ARG ILE GLY TYR PHE GLU GLY GLU ARG GLN SEQRES 7 A 201 PHE LEU PHE GLU LEU PHE ASN PRO LEU THR SER ASP LEU SEQRES 8 A 201 ALA ARG PRO GLY THR GLY TYR VAL TYR GLU THR GLY ASP SEQRES 9 A 201 ILE GLY MET HIS LEU LEU VAL SER SER SER GLU ARG ARG SEQRES 10 A 201 LEU PRO GLY PHE THR GLY ALA VAL MET LEU HIS ILE MET SEQRES 11 A 201 ARG THR ALA PHE PHE GLU ALA GLY ALA ARG ARG VAL VAL SEQRES 12 A 201 VAL GLU PRO ASP VAL ARG ASN ALA ASP VAL GLN ARG LEU SEQRES 13 A 201 ASN ALA ALA VAL GLY PHE ARG VAL ALA GLY ASP PHE PRO SEQRES 14 A 201 VAL PRO GLY LYS THR ALA ARG LEU SER TYR CYS THR ARG SEQRES 15 A 201 GLU ASP PHE ALA ARG ALA THR ASP ASN GLY ARG THR LEU SEQRES 16 A 201 ALA GLY GLU VAL GLU SER HET EPE A1401 33 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S FORMUL 3 HOH *185(H2 O) HELIX 1 AA1 ASP A 1153 HIS A 1167 1 15 HELIX 2 AA2 PRO A 1168 ASP A 1174 5 7 HELIX 3 AA3 SER A 1179 GLY A 1191 1 13 HELIX 4 AA4 ASN A 1217 ARG A 1225 5 9 HELIX 5 AA5 GLY A 1252 GLU A 1268 1 17 HELIX 6 AA6 ASN A 1282 VAL A 1292 1 11 HELIX 7 AA7 ARG A 1314 ASP A 1322 1 9 SHEET 1 AA1 7 GLN A1148 ARG A1151 0 SHEET 2 AA1 7 GLY A1199 PHE A1205 -1 O TYR A1204 N GLN A1148 SHEET 3 AA1 7 GLU A1208 PHE A1216 -1 O PHE A1213 N ARG A1201 SHEET 4 AA1 7 ASP A1236 VAL A1243 -1 O LEU A1242 N LEU A1212 SHEET 5 AA1 7 ARG A1273 VAL A1276 1 O VAL A1275 N ILE A1237 SHEET 6 AA1 7 LYS A1305 THR A1313 -1 O CYS A1312 N VAL A1274 SHEET 7 AA1 7 ARG A1295 VAL A1302 -1 N ALA A1297 O LEU A1309 CRYST1 33.489 70.008 37.099 90.00 97.72 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 0.029861 0.000000 0.004048 0.00000 SCALE2 0.000000 0.014284 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027201 0.00000 CONECT 2924 2925 2929 2933 CONECT 2925 2924 2926 2939 2940 CONECT 2926 2925 2927 2941 2942 CONECT 2927 2926 2928 2930 CONECT 2928 2927 2929 2943 2944 CONECT 2929 2924 2928 2945 2946 CONECT 2930 2927 2931 2947 2948 CONECT 2931 2930 2932 2949 2950 CONECT 2932 2931 2951 CONECT 2933 2924 2934 2952 2953 CONECT 2934 2933 2935 2954 2955 CONECT 2935 2934 2936 2937 2938 CONECT 2936 2935 CONECT 2937 2935 CONECT 2938 2935 2956 CONECT 2939 2925 CONECT 2940 2925 CONECT 2941 2926 CONECT 2942 2926 CONECT 2943 2928 CONECT 2944 2928 CONECT 2945 2929 CONECT 2946 2929 CONECT 2947 2930 CONECT 2948 2930 CONECT 2949 2931 CONECT 2950 2931 CONECT 2951 2932 CONECT 2952 2933 CONECT 2953 2933 CONECT 2954 2934 CONECT 2955 2934 CONECT 2956 2938 MASTER 273 0 1 7 7 0 0 6 1666 1 33 16 END