HEADER LIGASE 06-SEP-13 2MD9 TITLE SOLUTION STRUCTURE OF AN ACTIVE SITE MUTANT PEPITDYL CARRIER PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROCIDINE SYNTHASE 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THIRD PCP DOMAIN OF TYCC (UNP RESIDUES 3032-3113); COMPND 5 SYNONYM: TYROCIDINE SYNTHASE III, ATP-DEPENDENT ASPARAGINE ADENYLASE, COMPND 6 ASNA, ASPARAGINE ACTIVASE, ATP-DEPENDENT GLUTAMINE ADENYLASE, GLNA, COMPND 7 GLUTAMINE ACTIVASE, ATP-DEPENDENT TYROSINE ADENYLASE, TYRA, TYROSINE COMPND 8 ACTIVASE, ATP-DEPENDENT VALINE ADENYLASE, VALA, VALINE ACTIVASE, ATP- COMPND 9 DEPENDENT ORNITHINE ADENYLASE, ORNA, ORNITHINE ACTIVASE, ATP- COMPND 10 DEPENDENT LEUCINE ADENYLASE, LEUA, LEUCINE ACTIVASE; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BREVIBACILLUS PARABREVIS; SOURCE 3 ORGANISM_TAXID: 54914; SOURCE 4 STRAIN: ATCC 8185; SOURCE 5 GENE: TYCC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PREP4; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PQE70 KEYWDS PROTEIN, CARRIER PROTEIN, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.TUFAR,S.RAHIGHI,F.I.KRAAS,D.K.KIRCHNER,F.LOEHR,E.HENRICH,J.KOEPKE, AUTHOR 2 I.DIKIC,P.GUENTERT,M.A.MARAHIEL,V.DOETSCH REVDAT 4 14-JUN-23 2MD9 1 REMARK SEQADV REVDAT 3 29-NOV-17 2MD9 1 HELIX REVDAT 2 14-MAY-14 2MD9 1 JRNL REVDAT 1 23-APR-14 2MD9 0 JRNL AUTH P.TUFAR,S.RAHIGHI,F.I.KRAAS,D.K.KIRCHNER,F.LOHR,E.HENRICH, JRNL AUTH 2 J.KOPKE,I.DIKIC,P.GUNTERT,M.A.MARAHIEL,V.DOTSCH JRNL TITL CRYSTAL STRUCTURE OF A PCP/SFP COMPLEX REVEALS THE JRNL TITL 2 STRUCTURAL BASIS FOR CARRIER PROTEIN POSTTRANSLATIONAL JRNL TITL 3 MODIFICATION. JRNL REF CHEM.BIOL. V. 21 552 2014 JRNL REFN ISSN 1074-5521 JRNL PMID 24704508 JRNL DOI 10.1016/J.CHEMBIOL.2014.02.014 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TALOS, OPALP 1.4 REMARK 3 AUTHORS : CORNILESCU, DELAGLIO AND BAX (TALOS), LUGINBUHL, REMARK 3 GUNTERT, BILLETER AND WUTHRICH (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000103499. 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 : 0.7 MM [U-100% 13C; U-100% 15N] REMARK 210 PCP, 50 MM SODIUM PHOSPHATE, REMARK 210 0.15 MM DSS, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCACB; 3D H(CCCO) REMARK 210 NH-TOCSY; 3D (H)C(CCO)NH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.114, TOPSPIN 3.0, CYANA REMARK 210 3.96 REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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 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 4 PRO A 2 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 13 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 3.5 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 VAL A 3 -11.78 -158.29 REMARK 500 2 HIS A 87 92.79 -57.75 REMARK 500 3 VAL A 3 -169.04 -76.18 REMARK 500 3 ILE A 41 29.64 -75.86 REMARK 500 3 HIS A 90 67.63 -100.67 REMARK 500 5 GLU A 5 7.75 56.29 REMARK 500 5 TYR A 8 131.66 -38.77 REMARK 500 5 HIS A 87 -160.13 -128.55 REMARK 500 5 HIS A 88 -74.96 -119.36 REMARK 500 6 HIS A 88 72.01 41.37 REMARK 500 7 GLU A 5 13.90 59.26 REMARK 500 8 VAL A 3 161.89 -49.76 REMARK 500 8 SER A 85 4.30 -67.61 REMARK 500 10 HIS A 89 -69.12 -154.16 REMARK 500 11 GLU A 5 10.60 55.26 REMARK 500 11 SER A 85 34.93 -83.81 REMARK 500 11 HIS A 87 -34.26 -150.21 REMARK 500 12 GLU A 5 1.48 -65.50 REMARK 500 12 HIS A 90 32.43 -76.20 REMARK 500 13 LEU A 63 79.67 -116.19 REMARK 500 14 SER A 85 38.73 -83.10 REMARK 500 17 GLU A 5 4.39 -64.88 REMARK 500 17 SER A 85 36.49 -77.94 REMARK 500 18 VAL A 3 75.45 58.05 REMARK 500 18 ILE A 41 29.36 -78.46 REMARK 500 18 LEU A 63 78.71 -114.76 REMARK 500 18 HIS A 88 30.41 -140.26 REMARK 500 19 HIS A 88 105.30 -59.42 REMARK 500 19 HIS A 90 -15.44 -140.18 REMARK 500 20 HIS A 89 46.01 -74.79 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 8 TYR A 59 0.10 SIDE CHAIN REMARK 500 9 ARG A 84 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GDY RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE B. BREVIS TYCC3-PCP IN A-STATE REMARK 900 RELATED ID: 2GDX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE B. BREVIS TYCC3-PCP IN H-STATE REMARK 900 RELATED ID: 2GDW RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE B. BREVIS TYCC3-PCP IN A/H-STATE REMARK 900 RELATED ID: 2GE1 RELATED DB: PDB REMARK 900 PROTEIN COMPLEX OF A-STATE TYCC3-APO-PCP WITH THE PPTASE SFP (MODEL) REMARK 900 RELATED ID: 1DNY RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF PCP, A PROTOTYPE FOR THE PEPTIDYL CARRIER REMARK 900 DOMAINS OF MODULAR PEPTIDE SNTHETASES REMARK 900 RELATED ID: 19479 RELATED DB: BMRB REMARK 900 RELATED ID: 4MRT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SAME PCP IN COMPLEX WITH SFP DBREF 2MD9 A 2 83 UNP O30409 TYCC_BREPA 3032 3113 SEQADV 2MD9 ALA A 45 UNP O30409 SER 3075 ENGINEERED MUTATION SEQADV 2MD9 ARG A 84 UNP O30409 CLONING ARTIFACT SEQADV 2MD9 SER A 85 UNP O30409 CLONING ARTIFACT SEQADV 2MD9 HIS A 86 UNP O30409 EXPRESSION TAG SEQADV 2MD9 HIS A 87 UNP O30409 EXPRESSION TAG SEQADV 2MD9 HIS A 88 UNP O30409 EXPRESSION TAG SEQADV 2MD9 HIS A 89 UNP O30409 EXPRESSION TAG SEQADV 2MD9 HIS A 90 UNP O30409 EXPRESSION TAG SEQADV 2MD9 HIS A 91 UNP O30409 EXPRESSION TAG SEQRES 1 A 90 PRO VAL THR GLU ALA GLN TYR VAL ALA PRO THR ASN ALA SEQRES 2 A 90 VAL GLU SER LYS LEU ALA GLU ILE TRP GLU ARG VAL LEU SEQRES 3 A 90 GLY VAL SER GLY ILE GLY ILE LEU ASP ASN PHE PHE GLN SEQRES 4 A 90 ILE GLY GLY HIS ALA LEU LYS ALA MET ALA VAL ALA ALA SEQRES 5 A 90 GLN VAL HIS ARG GLU TYR GLN VAL GLU LEU PRO LEU LYS SEQRES 6 A 90 VAL LEU PHE ALA GLN PRO THR ILE LYS ALA LEU ALA GLN SEQRES 7 A 90 TYR VAL ALA THR ARG SER HIS HIS HIS HIS HIS HIS HELIX 1 1 GLU A 16 LEU A 27 1 12 HELIX 2 2 ALA A 45 GLU A 58 1 14 HELIX 3 3 LEU A 65 LEU A 68 1 4 HELIX 4 4 ILE A 74 ALA A 82 1 9 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