HEADER TRANSFERASE 26-FEB-25 9NIM TITLE STRUCTURE OF A K1305A 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 9NIM 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) : 34.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1589 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 34.9100 - 3.2100 1.00 2773 153 0.1496 0.1690 REMARK 3 2 3.2100 - 2.5500 1.00 2731 152 0.1566 0.1788 REMARK 3 3 2.5500 - 2.2200 1.00 2753 124 0.1500 0.1553 REMARK 3 4 2.2200 - 2.0200 1.00 2761 125 0.1513 0.1997 REMARK 3 5 2.0200 - 1.8800 1.00 2720 142 0.1524 0.1981 REMARK 3 6 1.8800 - 1.7600 1.00 2708 149 0.1711 0.2116 REMARK 3 7 1.7600 - 1.6800 1.00 2723 147 0.1813 0.2197 REMARK 3 8 1.6800 - 1.6000 1.00 2721 148 0.1897 0.2203 REMARK 3 9 1.6000 - 1.5400 1.00 2698 140 0.2041 0.2201 REMARK 3 10 1.5400 - 1.4900 1.00 2734 156 0.2196 0.2694 REMARK 3 11 1.4900 - 1.4400 0.99 2687 153 0.2659 0.2971 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) : 0.148 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.006 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.36 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 1551 REMARK 3 ANGLE : 0.978 2105 REMARK 3 CHIRALITY : 0.080 221 REMARK 3 PLANARITY : 0.010 280 REMARK 3 DIHEDRAL : 5.578 231 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 9NIM 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_1000293014. 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 : 31624 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 69.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.81000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 8000 AND 0.1M HEPES PH 7.5 REMARK 280 ADJUSTED BY NAOH (7.16 MG/ML PROTEIN), VAPOR DIFFUSION, HANGING REMARK 280 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 34.91000 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 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 ARG A1248 CG CD NE CZ NH1 NH2 REMARK 470 ASN A1323 CG OD1 ND2 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 HH21 ARG A 1263 O HOH A 1502 1.49 REMARK 500 O HOH A 1553 O HOH A 1642 2.01 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 58.23 -144.32 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 9NIM A 1133 1333 PDB 9NIM 9NIM 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 TYR 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 ALA 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 *169(H2 O) HELIX 1 AA1 ASP A 1153 GLY A 1166 1 14 HELIX 2 AA2 HIS A 1167 ASP A 1174 5 8 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 TYR A1216 -1 O GLN A1210 N GLY A1203 SHEET 4 AA1 7 ASP A1236 VAL A1243 -1 O GLY A1238 N TYR A1216 SHEET 5 AA1 7 ARG A1273 VAL A1276 1 O VAL A1275 N ILE A1237 SHEET 6 AA1 7 ALA 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 33.689 69.820 38.140 90.00 96.51 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 0.029683 0.000000 0.003387 0.00000 SCALE2 0.000000 0.014323 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026389 0.00000 CONECT 2933 2934 2938 2942 CONECT 2934 2933 2935 2948 2949 CONECT 2935 2934 2936 2950 2951 CONECT 2936 2935 2937 2939 CONECT 2937 2936 2938 2952 2953 CONECT 2938 2933 2937 2954 2955 CONECT 2939 2936 2940 2956 2957 CONECT 2940 2939 2941 2958 2959 CONECT 2941 2940 2960 CONECT 2942 2933 2943 2961 2962 CONECT 2943 2942 2944 2963 2964 CONECT 2944 2943 2945 2946 2947 CONECT 2945 2944 CONECT 2946 2944 CONECT 2947 2944 2965 CONECT 2948 2934 CONECT 2949 2934 CONECT 2950 2935 CONECT 2951 2935 CONECT 2952 2937 CONECT 2953 2937 CONECT 2954 2938 CONECT 2955 2938 CONECT 2956 2939 CONECT 2957 2939 CONECT 2958 2940 CONECT 2959 2940 CONECT 2960 2941 CONECT 2961 2942 CONECT 2962 2942 CONECT 2963 2943 CONECT 2964 2943 CONECT 2965 2947 MASTER 253 0 1 7 7 0 0 6 1652 1 33 16 END