HEADER HYDROLASE/ANTIBIOTIC 18-NOV-05 2C77 TITLE EF-TU COMPLEXED WITH A GTP ANALOG AND THE ANTIBIOTIC GE2270 A CAVEAT 2C77 PRO B 14 HAS WRONG CHIRALITY FOR AN L-AMINO ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGATION FACTOR TU-B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ELONGATION FACTOR TU, EF-TU-B; COMPND 5 EC: 3.1.5.1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: TUFA GENE; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: THIOCILLIN GE2270; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: GE22700A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: PLANOBISPORA ROSEA; SOURCE 9 ORGANISM_TAXID: 35762 KEYWDS HYDROLASE-ANTIBIOTIC COMPLEX, THIOPEPTIDE, ANTIBIOTIC, ANTIBACTERIAL, KEYWDS 2 THIAZOLE, OXAZOLE, HYDROLASE, GTPASE, TRANSLATION ELONGATION FACTOR, KEYWDS 3 PROTEIN SYNTHESIS, NUCLEOTIDE-BINDING, PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR A.PARMEGGIANI,I.M.KRAB,S.OKAMURA,R.C.NIELSEN,J.NYBORG,P.NISSEN REVDAT 9 13-DEC-23 2C77 1 REMARK HETSYN LINK REVDAT 8 24-JUL-19 2C77 1 REMARK REVDAT 7 10-JUL-19 2C77 1 REMARK REVDAT 6 24-APR-19 2C77 1 REMARK SEQRES LINK REVDAT 5 28-MAR-18 2C77 1 SOURCE JRNL REVDAT 4 13-JUL-11 2C77 1 VERSN REVDAT 3 15-JAN-09 2C77 1 VERSN REVDAT 2 07-JUN-06 2C77 1 JRNL REVDAT 1 16-MAR-06 2C77 0 JRNL AUTH A.PARMEGGIANI,I.M.KRAB,S.OKAMURA,R.C.NIELSEN,J.NYBORG, JRNL AUTH 2 P.NISSEN JRNL TITL STRUCTURAL BASIS OF THE ACTION OF PULVOMYCIN AND GE2270 A ON JRNL TITL 2 ELONGATION FACTOR TU. JRNL REF BIOCHEMISTRY V. 45 6846 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16734421 JRNL DOI 10.1021/BI0525122 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1741200.150 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 57219 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1702 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5286 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 179 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3225 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.11000 REMARK 3 B22 (A**2) : -0.94000 REMARK 3 B33 (A**2) : -1.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.04 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.04 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.610 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.750 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 32.89 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : LIGANDS2.PAR REMARK 3 PARAMETER FILE 4 : MG.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : LIGANDS2.TOP REMARK 3 TOPOLOGY FILE 3 : MG.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: N-TERMINAL REGION IS INVOLVED IN REMARK 3 CRYSTAL PACKING AND ADOPTS AN UNUSUAL STRUCTURE. N-TERMINAL REMARK 3 RESIDUE IS DISORDERED AND HAS NOT BEEN MODELLED. REMARK 4 REMARK 4 2C77 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1290026463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8133 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1EFT REMARK 200 REMARK 200 REMARK: DATA WERE LIMITED TO 1.6 A RESOLUTION DUE TO A POWDER RING REMARK 200 IN THE DIFFRACTION PATTERN. MR PHASES WERE EXTENDED FROM 03 TO REMARK 200 1.6 A RESOLUTION BY SOLVENT FLIPPING REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-23% PEG6000, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 21.66000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.19000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.19000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.66000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.29000 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 400 REMARK 400 COMPOUND REMARK 400 GEA2270A IS A MEMBER OF A CLASS OF SULPHUR-RICH HETEROCYCLIC REMARK 400 PEPTIDES. ALL MEMBERS SHARE A MACROCYLIC CORE, CONSISTING OF A REMARK 400 NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO REMARK 400 ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING REMARK 400 THIAZOLES, THIAZOLINES AND OXAZOLES. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: GEA2270A REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 15 REMARK 400 DESCRIPTION: GEA2270A IS A THIOPEPTIDE CONSISTING OF ONE REMARK 400 PYRIDINE, ONE OXAZOLE AND FIVE THIAZOLE RINGS. REMARK 400 THE OBSERVED C-TERMINAL AMINO GROUP NH2(15) IS REMARK 400 LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMARK 400 REMNANT OF A SER C-TERMINAL RESIDUE. REMARK 400 REMARK 400 THE GE2270A IS THIOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: GE2270A REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: GEA2270A IS A THIOPEPTIDE CONSISTING OF ONE PYRIDINE, REMARK 400 ONE OXAZOLE AND FIVE THIAZOLE RINGS. THE OBSERVED C- REMARK 400 TERMINAL AMINO GROUP NH2(15) IS LIKELY TO BE A POST- REMARK 400 TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C- REMARK 400 TERMINAL RESIDUE. 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 ALA A 1 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 BB9 B 12 C SER B 13 N 0.160 REMARK 500 REMARK 500 REMARK: NULL 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 SER B 13 C - N - CA ANGL. DEV. = -15.9 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 LEU A 258 -45.62 62.39 REMARK 500 ARG A 345 -121.31 50.11 REMARK 500 VAL B 5 -38.14 -151.33 REMARK 500 SER B 13 137.98 123.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 13 PRO B 14 119.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1407 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 25 OG1 REMARK 620 2 THR A 62 OG1 86.5 REMARK 620 3 GNP A1406 O1G 171.8 92.2 REMARK 620 4 GNP A1406 O2B 92.1 172.0 90.3 REMARK 620 5 HOH A2042 O 89.6 85.1 98.3 87.0 REMARK 620 6 HOH A2082 O 82.8 92.9 89.2 94.7 172.3 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 1406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 1409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF THIOCILLIN GE2270 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D8T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-MGGDP COMPLEXED REMARK 900 WITH THE THIOPEPTIDE GE2270A. REMARK 900 RELATED ID: 1E9W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THIOPEPTIDE THIOSTREPTON REMARK 900 RELATED ID: 1OLN RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THIOPEPTIDE THIOSTREPTON BINDING TO L11 REMARK 900 SUBSTRATE FROM 50S RIBOSOMAL RNA REMARK 900 RELATED ID: 2JQ7 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE COMPLEX OF THIOPEPTIDE THIOSTREPTON AND REMARK 900 RIBOSOMAL L11-RNA REMARK 900 RELATED ID: 2ZJP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NOSIHEPTIDE COMPLEXED WITH THE LARGE RIBOSOMAL REMARK 900 SUBUNIT OF DEINOCOCCUS RADIODURANS REMARK 900 RELATED ID: 3CF5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBOSOMAL L11-RNA COMPLEXED WITH THE REMARK 900 THIOPEPTIDE THIOSTREPTON REMARK 900 RELATED ID: 2C78 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTUE OF EF-TU COMPLEXED WITH A GTP ANALOG AND THE REMARK 900 ANTIBIOTIC PULVOMYCIN DBREF 2C77 A 1 405 UNP P60339 EFTU2_THET8 1 405 DBREF 2C77 B 1 14 UNP Q7M0J8 THCL_PLARO 1 14 SEQADV 2C77 TYR A 33 UNP P60339 PHE 33 CONFLICT SEQRES 1 A 405 ALA LYS GLY GLU PHE ILE ARG THR LYS PRO HIS VAL ASN SEQRES 2 A 405 VAL GLY THR ILE GLY HIS VAL ASP HIS GLY LYS THR THR SEQRES 3 A 405 LEU THR ALA ALA LEU THR TYR VAL THR ALA ALA GLU ASN SEQRES 4 A 405 PRO ASN VAL GLU VAL LYS ASP TYR GLY ASP ILE ASP LYS SEQRES 5 A 405 ALA PRO GLU GLU ARG ALA ARG GLY ILE THR ILE ASN THR SEQRES 6 A 405 ALA HIS VAL GLU TYR GLU THR ALA LYS ARG HIS TYR SER SEQRES 7 A 405 HIS VAL ASP CYS PRO GLY HIS ALA ASP TYR ILE LYS ASN SEQRES 8 A 405 MET ILE THR GLY ALA ALA GLN MET ASP GLY ALA ILE LEU SEQRES 9 A 405 VAL VAL SER ALA ALA ASP GLY PRO MET PRO GLN THR ARG SEQRES 10 A 405 GLU HIS ILE LEU LEU ALA ARG GLN VAL GLY VAL PRO TYR SEQRES 11 A 405 ILE VAL VAL PHE MET ASN LYS VAL ASP MET VAL ASP ASP SEQRES 12 A 405 PRO GLU LEU LEU ASP LEU VAL GLU MET GLU VAL ARG ASP SEQRES 13 A 405 LEU LEU ASN GLN TYR GLU PHE PRO GLY ASP GLU VAL PRO SEQRES 14 A 405 VAL ILE ARG GLY SER ALA LEU LEU ALA LEU GLU GLN MET SEQRES 15 A 405 HIS ARG ASN PRO LYS THR ARG ARG GLY GLU ASN GLU TRP SEQRES 16 A 405 VAL ASP LYS ILE TRP GLU LEU LEU ASP ALA ILE ASP GLU SEQRES 17 A 405 TYR ILE PRO THR PRO VAL ARG ASP VAL ASP LYS PRO PHE SEQRES 18 A 405 LEU MET PRO VAL GLU ASP VAL PHE THR ILE THR GLY ARG SEQRES 19 A 405 GLY THR VAL ALA THR GLY ARG ILE GLU ARG GLY LYS VAL SEQRES 20 A 405 LYS VAL GLY ASP GLU VAL GLU ILE VAL GLY LEU ALA PRO SEQRES 21 A 405 GLU THR ARG LYS THR VAL VAL THR GLY VAL GLU MET HIS SEQRES 22 A 405 ARG LYS THR LEU GLN GLU GLY ILE ALA GLY ASP ASN VAL SEQRES 23 A 405 GLY VAL LEU LEU ARG GLY VAL SER ARG GLU GLU VAL GLU SEQRES 24 A 405 ARG GLY GLN VAL LEU ALA LYS PRO GLY SER ILE THR PRO SEQRES 25 A 405 HIS THR LYS PHE GLU ALA SER VAL TYR VAL LEU LYS LYS SEQRES 26 A 405 GLU GLU GLY GLY ARG HIS THR GLY PHE PHE SER GLY TYR SEQRES 27 A 405 ARG PRO GLN PHE TYR PHE ARG THR THR ASP VAL THR GLY SEQRES 28 A 405 VAL VAL GLN LEU PRO PRO GLY VAL GLU MET VAL MET PRO SEQRES 29 A 405 GLY ASP ASN VAL THR PHE THR VAL GLU LEU ILE LYS PRO SEQRES 30 A 405 VAL ALA LEU GLU GLU GLY LEU ARG PHE ALA ILE ARG GLU SEQRES 31 A 405 GLY GLY ARG THR VAL GLY ALA GLY VAL VAL THR LYS ILE SEQRES 32 A 405 LEU GLU SEQRES 1 B 15 SER BB9 MEN BB6 VAL BB7 GLY BB8 BB9 BB9 MH6 BB9 SER SEQRES 2 B 15 PRO NH2 MODRES 2C77 BB9 B 2 CYS MODRES 2C77 MEN B 3 ASN N-METHYL ASPARAGINE MODRES 2C77 BB6 B 4 CYS (2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID MODRES 2C77 BB7 B 6 CYS MODRES 2C77 BB8 B 8 PHE (2S,3S)-BETA-HYDROXY-PHENYLALANINE MODRES 2C77 BB9 B 9 CYS MODRES 2C77 BB9 B 10 CYS MODRES 2C77 MH6 B 11 SER 3-HYDROXY-2-IMINOPROPANOIC ACID MODRES 2C77 BB9 B 12 CYS HET BB9 B 2 6 HET MEN B 3 8 HET BB6 B 4 7 HET BB7 B 6 9 HET BB8 B 8 11 HET BB9 B 9 5 HET BB9 B 10 5 HET MH6 B 11 4 HET BB9 B 12 5 HET NH2 B 15 1 HET GNP A1406 32 HET MG A1407 1 HET PEG A1409 7 HETNAM BB9 (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID HETNAM MEN N-METHYL ASPARAGINE HETNAM BB6 (2Z)-2-AMINO-3-SULFANYLBUT-2-ENOIC ACID HETNAM BB7 (2Z)-2-AMINO-4-METHOXY-3-SULFANYLBUT-2-ENOIC ACID HETNAM BB8 (2S,3S)-BETA-HYDROXY-PHENYLALANINE HETNAM MH6 3-HYDROXY-2-IMINOPROPANOIC ACID HETNAM NH2 AMINO GROUP HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN BB8 BETA-HYDROXY-PHENYLALANINE; THREO-BETA-HYDROXY-L- HETSYN 2 BB8 PHENYLALANINE; (BETAS)-BETA-HYDROXY-L-PHENYLALANINE; HETSYN 3 BB8 L-THREO-3-PHENYLSERINE; L-THREO-BETA-PHENYLSERINE; 3- HETSYN 4 BB8 HYDROXY-L-PHENYLALANINE FORMUL 2 BB9 4(C3 H5 N O2 S) FORMUL 2 MEN C5 H10 N2 O3 FORMUL 2 BB6 C4 H7 N O2 S FORMUL 2 BB7 C5 H9 N O3 S FORMUL 2 BB8 C9 H11 N O3 FORMUL 2 MH6 C3 H5 N O3 FORMUL 2 NH2 H2 N FORMUL 3 GNP C10 H17 N6 O13 P3 FORMUL 4 MG MG 2+ FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *370(H2 O) HELIX 1 1 GLY A 23 ASN A 39 1 17 HELIX 2 2 ASP A 46 ASP A 51 1 6 HELIX 3 3 ALA A 53 GLY A 60 1 8 HELIX 4 4 HIS A 85 ASP A 87 5 3 HELIX 5 5 TYR A 88 ALA A 97 1 10 HELIX 6 6 MET A 113 GLY A 127 1 15 HELIX 7 7 LYS A 137 VAL A 141 5 5 HELIX 8 8 ASP A 143 TYR A 161 1 19 HELIX 9 9 SER A 174 ASN A 185 1 12 HELIX 10 10 ASN A 193 ILE A 210 1 18 HELIX 11 11 SER A 294 VAL A 298 5 5 HELIX 12 12 LYS A 324 GLY A 328 5 5 SHEET 1 AA 6 ALA A 66 GLU A 71 0 SHEET 2 AA 6 HIS A 76 ASP A 81 -1 O TYR A 77 N TYR A 70 SHEET 3 AA 6 HIS A 11 ILE A 17 1 O VAL A 12 N SER A 78 SHEET 4 AA 6 ALA A 102 SER A 107 1 O ILE A 103 N ILE A 17 SHEET 5 AA 6 ILE A 131 ASN A 136 1 O VAL A 132 N LEU A 104 SHEET 6 AA 6 VAL A 170 ARG A 172 1 O ILE A 171 N MET A 135 SHEET 1 AB 5 LEU A 222 PRO A 224 0 SHEET 2 AB 5 VAL A 303 ALA A 305 -1 O LEU A 304 N MET A 223 SHEET 3 AB 5 GLU A 252 VAL A 256 -1 O GLU A 254 N ALA A 305 SHEET 4 AB 5 ARG A 263 MET A 272 -1 O ARG A 263 N ILE A 255 SHEET 5 AB 5 LYS A 275 THR A 276 -1 O LYS A 275 N MET A 272 SHEET 1 AC 7 LEU A 222 PRO A 224 0 SHEET 2 AC 7 VAL A 303 ALA A 305 -1 O LEU A 304 N MET A 223 SHEET 3 AC 7 GLU A 252 VAL A 256 -1 O GLU A 254 N ALA A 305 SHEET 4 AC 7 ARG A 263 MET A 272 -1 O ARG A 263 N ILE A 255 SHEET 5 AC 7 ASN A 285 LEU A 290 -1 O GLY A 287 N GLU A 271 SHEET 6 AC 7 GLY A 235 ARG A 241 -1 O THR A 236 N LEU A 290 SHEET 7 AC 7 ASP A 227 ILE A 231 -1 O ASP A 227 N THR A 239 SHEET 1 AD 2 LYS A 275 THR A 276 0 SHEET 2 AD 2 ARG A 263 MET A 272 -1 O MET A 272 N LYS A 275 SHEET 1 AE 2 LYS A 246 VAL A 247 0 SHEET 2 AE 2 GLY A 280 ILE A 281 -1 O GLY A 280 N VAL A 247 SHEET 1 AF 7 THR A 311 VAL A 322 0 SHEET 2 AF 7 ASN A 367 LEU A 380 -1 O VAL A 368 N VAL A 320 SHEET 3 AF 7 THR A 347 GLN A 354 -1 O THR A 350 N ILE A 375 SHEET 4 AF 7 GLN A 341 PHE A 344 -1 O PHE A 342 N VAL A 349 SHEET 5 AF 7 ARG A 385 GLU A 390 -1 O ALA A 387 N TYR A 343 SHEET 6 AF 7 ARG A 393 ILE A 403 -1 O ARG A 393 N GLU A 390 SHEET 7 AF 7 THR A 311 VAL A 322 -1 O GLU A 317 N THR A 401 SHEET 1 AG 2 PHE A 334 PHE A 335 0 SHEET 2 AG 2 MET A 361 VAL A 362 -1 O VAL A 362 N PHE A 334 LINK C SER B 1 N BB9 B 2 1555 1555 1.32 LINK C SER B 1 SG BB9 B 2 1555 1555 1.67 LINK CA SER B 1 C BB9 B 10 1555 1555 1.47 LINK CB SER B 1 CB MH6 B 11 1555 1555 1.41 LINK C BB9 B 2 N MEN B 3 1555 1555 1.33 LINK C MEN B 3 N BB6 B 4 1555 1555 1.31 LINK C MEN B 3 SG BB6 B 4 1555 1555 1.71 LINK C BB6 B 4 N VAL B 5 1555 1555 1.35 LINK C VAL B 5 SG BB7 B 6 1555 1555 1.70 LINK C VAL B 5 N BB7 B 6 1555 1555 1.31 LINK C BB7 B 6 N GLY B 7 1555 1555 1.34 LINK C GLY B 7 N BB8 B 8 1555 1555 1.33 LINK C BB8 B 8 SG BB9 B 9 1555 1555 1.72 LINK C BB8 B 8 N BB9 B 9 1555 1555 1.32 LINK C BB9 B 9 SG BB9 B 10 1555 1555 1.71 LINK C BB9 B 9 N BB9 B 10 1555 1555 1.30 LINK C BB9 B 10 N MH6 B 11 1555 1555 1.33 LINK C MH6 B 11 SG BB9 B 12 1555 1555 1.71 LINK C MH6 B 11 N BB9 B 12 1555 1555 1.31 LINK C BB9 B 12 OG SER B 13 1555 1555 1.35 LINK C BB9 B 12 N SER B 13 1555 1555 1.50 LINK C PRO B 14 N NH2 B 15 1555 1555 1.35 LINK OG1 THR A 25 MG MG A1407 1555 1555 2.08 LINK OG1 THR A 62 MG MG A1407 1555 1555 2.11 LINK O1G GNP A1406 MG MG A1407 1555 1555 2.01 LINK O2B GNP A1406 MG MG A1407 1555 1555 2.10 LINK MG MG A1407 O HOH A2042 1555 1555 2.13 LINK MG MG A1407 O HOH A2082 1555 1555 2.11 SITE 1 AC1 27 VAL A 20 ASP A 21 HIS A 22 GLY A 23 SITE 2 AC1 27 LYS A 24 THR A 25 THR A 26 TYR A 47 SITE 3 AC1 27 ILE A 61 THR A 62 GLY A 84 ASN A 136 SITE 4 AC1 27 LYS A 137 ASP A 139 MET A 140 SER A 174 SITE 5 AC1 27 ALA A 175 LEU A 176 MG A1407 HOH A2015 SITE 6 AC1 27 HOH A2042 HOH A2057 HOH A2082 HOH A2359 SITE 7 AC1 27 HOH A2360 HOH A2361 HOH A2362 SITE 1 AC2 5 THR A 25 THR A 62 GNP A1406 HOH A2042 SITE 2 AC2 5 HOH A2082 SITE 1 AC3 12 ASP A 143 GLU A 145 LEU A 146 LEU A 149 SITE 2 AC3 12 THR A 230 THR A 236 VAL A 293 SER A 294 SITE 3 AC3 12 ARG A 295 HOH A2256 HOH A2257 HOH A2363 SITE 1 AC4 2 SER B 13 PRO B 14 SITE 1 AC5 27 GLU A 4 PHE A 5 HIS A 67 VAL A 68 SITE 2 AC5 27 SER A 78 GLN A 98 GLU A 226 ASP A 227 SITE 3 AC5 27 PHE A 229 ARG A 234 THR A 239 THR A 268 SITE 4 AC5 27 GLY A 269 GLU A 271 HIS A 273 ARG A 274 SITE 5 AC5 27 ASN A 285 VAL A 286 GLY A 287 LEU A 289 SITE 6 AC5 27 HOH A2236 HOH A2248 NH2 B 15 HOH B2003 SITE 7 AC5 27 HOH B2004 HOH B2005 HOH B2006 CRYST1 43.320 94.580 104.380 90.00 90.00 90.00 P 21 21 21 4 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 0.023084 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009580 0.00000