HEADER LIGASE 31-AUG-15 2N6Z TITLE SOLUTION STRUCTURE OF THE SALICYLATE-LOADED ARCP FROM YERSINIABACTIN TITLE 2 SYNTHETASE CAVEAT 2N6Z CHIRALITY ERRORS AT CA ATOM OF RESIDUE 4HJ IN MODELS 12, 15, CAVEAT 2 2N6Z AND 18. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HMWP2 NONRIBOSOMAL PEPTIDE SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 14-93; COMPND 5 SYNONYM: YERSINIABACTIN BIOSYNTHETIC PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 GENE: IRP2, Y2399, YPO1911; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-DUET-1 KEYWDS CARRIER PROTEIN, SUBSTRATE-LOADED, NONRIBOSOMAL PEPTIDE SYNTHETASE, KEYWDS 2 YERSINIABACTIN, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.C.GOODRICH,B.J.HARDEN,D.P.FRUEH REVDAT 4 14-JUN-23 2N6Z 1 REMARK DBREF SEQADV LINK REVDAT 3 07-OCT-15 2N6Z 1 JRNL REVDAT 2 30-SEP-15 2N6Z 1 JRNL REVDAT 1 23-SEP-15 2N6Z 0 JRNL AUTH A.C.GOODRICH,B.J.HARDEN,D.P.FRUEH JRNL TITL SOLUTION STRUCTURE OF A NONRIBOSOMAL PEPTIDE SYNTHETASE JRNL TITL 2 CARRIER PROTEIN LOADED WITH ITS SUBSTRATE REVEALS TRANSIENT, JRNL TITL 3 WELL-DEFINED CONTACTS. JRNL REF J.AM.CHEM.SOC. V. 137 12100 2015 JRNL REFN ISSN 0002-7863 JRNL PMID 26334259 JRNL DOI 10.1021/JACS.5B07772 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CNS REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000104500. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3-0.4 MM [U-99% 15N] LOADED REMARK 210 -ARCP, 50 MM ACES, 0.5 MM TCEP, REMARK 210 150 MM SODIUM CHLORIDE, 1 MM REMARK 210 MAGNESIUM CHLORIDE, 0.1 MM DSS, REMARK 210 90% H2O/10% D2O; 0.3-0.4 MM [U- REMARK 210 99% 13C; U-99% 15N] LOADED-ARCP, REMARK 210 50 MM ACES, 0.5 MM TCEP, 150 MM REMARK 210 SODIUM CHLORIDE, 1 MM MAGNESIUM REMARK 210 CHLORIDE, 0.1 MM DSS, 2 MM ATP, REMARK 210 2 MM SODIUM SALICYLATE, 0.02- REMARK 210 0.10 UM ADENYLATION DOMAIN YBTE, REMARK 210 90% H2O/10% D2O; 0.3-0.4 MM [U- REMARK 210 99% 13C; U-99% 15N] LOADED-ARCP, REMARK 210 50 MM ACES, 0.5 MM TCEP, 150 MM REMARK 210 SODIUM CHLORIDE, 1 MM MAGNESIUM REMARK 210 CHLORIDE, 0.1 MM DSS, 2 MM ATP, REMARK 210 0.5 MM [U-100% 13C] SODIUM REMARK 210 SALICYLATE, 0.02-0.10 UM REMARK 210 ADENYLATION DOMAIN YBTE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HNCACB; 3D H(CCO)NH; 3D REMARK 210 HN(CA)CO; 3D 1H-15N NOESY; 2D 1H- REMARK 210 13C HSQC; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 12 REMARK 465 THR A 13 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HH12 ARG A 90 O GLU A 93 1.57 REMARK 500 OE2 GLU A 31 HH12 ARG A 57 1.59 REMARK 500 HG1 THR A 70 OE1 GLU A 73 1.60 REMARK 500 HH22 ARG A 63 OE2 GLU A 93 1.60 REMARK 500 OD2 ASP A 51 HH11 ARG A 54 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 16 SER A 89 CA SER A 89 CB -0.105 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 1 LEU A 69 149.32 -171.54 REMARK 500 1 ARG A 90 -67.28 48.21 REMARK 500 1 SER A 91 105.34 150.30 REMARK 500 1 PRO A 92 -83.58 -0.89 REMARK 500 2 ASN A 15 -154.36 41.82 REMARK 500 2 PRO A 36 -4.69 -57.83 REMARK 500 2 SER A 91 76.78 32.84 REMARK 500 2 PRO A 92 105.15 -57.13 REMARK 500 3 ARG A 90 -56.73 64.26 REMARK 500 4 ARG A 90 68.79 -10.79 REMARK 500 4 SER A 91 -55.39 -154.30 REMARK 500 5 ARG A 90 -76.75 64.38 REMARK 500 5 SER A 91 84.20 -159.98 REMARK 500 6 ASN A 44 106.02 -38.17 REMARK 500 6 ARG A 90 -26.79 61.86 REMARK 500 6 SER A 91 82.38 71.23 REMARK 500 6 PRO A 92 -56.25 -11.79 REMARK 500 7 ASP A 51 -133.47 -130.37 REMARK 500 7 4HJ A 52 -74.01 -99.99 REMARK 500 7 ARG A 90 -55.64 69.46 REMARK 500 8 ASN A 15 178.50 179.48 REMARK 500 8 ARG A 90 -65.77 66.71 REMARK 500 8 SER A 91 76.39 -159.03 REMARK 500 9 ASN A 15 -130.21 -155.28 REMARK 500 9 ASP A 51 -138.44 -114.18 REMARK 500 9 4HJ A 52 -74.03 -95.87 REMARK 500 9 ILE A 53 -39.38 -37.55 REMARK 500 9 ARG A 90 -33.44 69.66 REMARK 500 10 ALA A 18 -16.01 -42.95 REMARK 500 10 TYR A 67 108.50 -58.01 REMARK 500 10 ARG A 90 -16.45 68.19 REMARK 500 10 SER A 91 88.99 68.07 REMARK 500 10 PRO A 92 148.41 -37.40 REMARK 500 11 ASN A 15 -90.18 -139.59 REMARK 500 11 ASP A 51 -141.20 -128.71 REMARK 500 11 4HJ A 52 -68.25 -94.27 REMARK 500 11 ARG A 90 -25.10 70.65 REMARK 500 11 SER A 91 -54.30 -136.14 REMARK 500 12 ALA A 18 -14.28 -45.55 REMARK 500 12 ASP A 51 -146.00 -130.28 REMARK 500 12 4HJ A 52 -70.54 -94.58 REMARK 500 12 ARG A 90 59.93 21.15 REMARK 500 12 SER A 91 -65.38 -159.33 REMARK 500 13 ASN A 15 87.41 -168.57 REMARK 500 13 ASN A 33 70.86 55.62 REMARK 500 13 ASP A 51 -155.81 -126.05 REMARK 500 13 ARG A 68 90.07 -64.68 REMARK 500 13 ARG A 90 68.20 -19.60 REMARK 500 13 SER A 91 -61.72 -164.84 REMARK 500 14 ASN A 33 70.71 56.39 REMARK 500 REMARK 500 THIS ENTRY HAS 70 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 ARG A 25 0.07 SIDE CHAIN REMARK 500 4 ARG A 90 0.12 SIDE CHAIN REMARK 500 6 ARG A 90 0.10 SIDE CHAIN REMARK 500 7 ARG A 90 0.10 SIDE CHAIN REMARK 500 9 ARG A 27 0.09 SIDE CHAIN REMARK 500 11 ARG A 25 0.09 SIDE CHAIN REMARK 500 12 ARG A 57 0.11 SIDE CHAIN REMARK 500 13 ARG A 27 0.09 SIDE CHAIN REMARK 500 17 ARG A 90 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 7 4HJ A 52 -12.26 REMARK 500 9 4HJ A 52 -12.21 REMARK 500 11 4HJ A 52 -12.04 REMARK 500 12 4HJ A 52 -12.47 REMARK 500 20 4HJ A 52 -13.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25787 RELATED DB: BMRB REMARK 900 RELATED ID: 2N6Y RELATED DB: PDB DBREF 2N6Z A 14 93 UNP Q7CI41 Q7CI41_YERPE 14 93 SEQADV 2N6Z GLY A 12 UNP Q7CI41 EXPRESSION TAG SEQADV 2N6Z THR A 13 UNP Q7CI41 EXPRESSION TAG SEQRES 1 A 82 GLY THR ASP ASN ARG HIS ALA ALA ASP TYR GLN GLN LEU SEQRES 2 A 82 ARG GLU ARG LEU ILE GLN GLU LEU ASN LEU THR PRO GLN SEQRES 3 A 82 GLN LEU HIS GLU GLU SER ASN LEU ILE GLN ALA GLY LEU SEQRES 4 A 82 ASP 4HJ ILE ARG LEU MET ARG TRP LEU HIS TRP PHE ARG SEQRES 5 A 82 LYS ASN GLY TYR ARG LEU THR LEU ARG GLU LEU TYR ALA SEQRES 6 A 82 ALA PRO THR LEU ALA ALA TRP ASN GLN LEU MET LEU SER SEQRES 7 A 82 ARG SER PRO GLU MODRES 2N6Z 4HJ A 52 SER HET 4HJ A 52 65 HETNAM 4HJ O-[(R)-HYDROXY{[(3R)-3-HYDROXY-4-{[3-({2-[(2- HETNAM 2 4HJ HYDROXYBENZOYL)SULFANYL]ETHYL}AMINO)-3- HETNAM 3 4HJ OXOPROPYL]AMINO}-2,2-DIMETHYL-4- HETNAM 4 4HJ OXOBUTYL]OXY}PHOSPHORYL]-L-SERINE FORMUL 1 4HJ C21 H32 N3 O11 P S HELIX 1 1 ASN A 15 ALA A 18 5 4 HELIX 2 2 ALA A 19 ASN A 33 1 15 HELIX 3 3 ASN A 44 ALA A 48 5 5 HELIX 4 4 ASP A 51 LYS A 64 1 14 HELIX 5 5 THR A 70 ALA A 77 1 8 HELIX 6 6 THR A 79 SER A 89 1 11 LINK C ASP A 51 N 4HJ A 52 1555 1555 1.30 LINK C 4HJ A 52 N ILE A 53 1555 1555 1.30 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1