HEADER PROTEIN BINDING 26-NOV-20 7B2F TITLE SOLUTION STRUCTURE OF THE PAX NRPS DOCKING DOMAIN PAXB NDD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE SYNTHETASE XPSB (MODULAR PROTEIN); COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.58,5.1.1.12; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENORHABDUS CABANILLASII JM26; SOURCE 3 ORGANISM_TAXID: 1427517; SOURCE 4 GENE: XCR1_1150011; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS PROTEIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.WATZEL,S.SARAWI,E.DUCHARDT-FERNER,H.B.BODE,J.WOEHNERT REVDAT 3 14-JUN-23 7B2F 1 REMARK REVDAT 2 16-JUN-21 7B2F 1 JRNL REVDAT 1 09-JUN-21 7B2F 0 JRNL AUTH J.WATZEL,E.DUCHARDT-FERNER,S.SARAWI,H.B.BODE,J.WOHNERT JRNL TITL COOPERATION BETWEEN A T DOMAIN AND A MINIMAL C-TERMINAL JRNL TITL 2 DOCKING DOMAIN TO ENABLE SPECIFIC ASSEMBLY IN A MULTIPROTEIN JRNL TITL 3 NRPS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 60 14171 2021 JRNL REFN ESSN 1521-3773 JRNL PMID 33876501 JRNL DOI 10.1002/ANIE.202103498 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98, OPALP REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), KORADI, REMARK 3 BILLETER AND GUNTERT (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7B2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1292112526. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT BAR REMARK 210 SAMPLE CONTENTS : 300 UM [U-15N] PAXB NDD, 50 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 5 % [U-2H] D2O, 100 UM REMARK 210 DSS, 95% H2O/5% D2O; 300 UM [U- REMARK 210 15N] PAXB NDD, 50 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 5 % [U-2H] D2O, 100 UM REMARK 210 DSS, 95% H2O/5% D2O; 300 UM [U- REMARK 210 10% 13C; U-15N] PAXB NDD, 50 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 5 % [U-2H] D2O, 100 UM REMARK 210 DSS, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D C(CO) REMARK 210 NH; 3D H(CCO)NH; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 3D 1H- REMARK 210 13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.6.2, CARA 1.8.4.2, REMARK 210 CCPNMR ANALYSIS 2.4.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 1 ARG A 16 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES 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 ALA A 24 84.95 -69.14 REMARK 500 2 ASN A 4 57.23 -147.27 REMARK 500 4 GLN A 29 -62.43 -155.58 REMARK 500 5 LYS A 25 -39.98 -152.28 REMARK 500 6 ASN A 2 16.51 -153.76 REMARK 500 8 GLU A 5 22.22 -67.78 REMARK 500 8 LYS A 25 -32.11 -135.18 REMARK 500 8 ARG A 28 32.32 -78.68 REMARK 500 9 LYS A 25 -47.04 -139.06 REMARK 500 10 ASN A 3 -12.72 68.68 REMARK 500 10 GLU A 5 20.78 -151.01 REMARK 500 11 ASN A 4 115.71 -160.71 REMARK 500 12 LYS A 25 59.26 38.83 REMARK 500 12 ARG A 28 -48.34 -144.96 REMARK 500 13 ASN A 2 -39.68 -37.13 REMARK 500 13 LYS A 25 -14.71 -149.83 REMARK 500 15 LYS A 25 44.76 -148.07 REMARK 500 16 GLU A 5 60.10 -112.37 REMARK 500 16 LYS A 25 4.73 55.63 REMARK 500 17 ASN A 4 57.02 -110.34 REMARK 500 17 GLU A 5 -43.48 -134.44 REMARK 500 17 LYS A 25 -74.61 -46.79 REMARK 500 17 SER A 27 -175.28 -68.57 REMARK 500 18 ARG A 28 -84.44 -90.79 REMARK 500 19 ALA A 24 14.17 52.12 REMARK 500 19 LYS A 25 -72.81 -69.88 REMARK 500 20 ALA A 24 6.04 54.73 REMARK 500 20 GLN A 29 -168.20 -77.03 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 6 ARG A 16 0.09 SIDE CHAIN REMARK 500 7 TYR A 31 0.07 SIDE CHAIN REMARK 500 11 ARG A 28 0.09 SIDE CHAIN REMARK 500 14 ARG A 16 0.08 SIDE CHAIN REMARK 500 16 ARG A 28 0.09 SIDE CHAIN REMARK 500 20 ARG A 28 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34576 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE PAX NRPS DOCKING DOMAIN PAXB NDD DBREF 7B2F A 1 31 PDB 7B2F 7B2F 1 31 SEQRES 1 A 31 MET ASN ASN ASN GLU LEU THR SER LEU PRO LEU ALA GLU SEQRES 2 A 31 ARG LYS ARG LEU LEU GLU LEU ALA LYS ALA ALA LYS LEU SEQRES 3 A 31 SER ARG GLN HIS TYR HELIX 1 AA1 ASN A 4 LEU A 9 5 6 HELIX 2 AA2 PRO A 10 ALA A 24 1 15 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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