Header list of 1xt7.pdb file
Complete list - 25 201 Bytes
HEADER ANTIBIOTIC 21-OCT-04 1XT7 TITLE DAPTOMYCIN NMR STRUCTURE CAVEAT 1XT7 DSG A 3 C-ALPHA WRONG HAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DAPTOMYCIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: A21978C, CUBICIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOMYCES ROSEOSPORUS; SOURCE 4 ORGANISM_TAXID: 67294 KEYWDS DAPTOMYCIN, CUBICIN, ANTIBIOTIC, LIPOPEPTIDE, CALCIUM-DEPENDENT EXPDTA SOLUTION NMR AUTHOR L.-J.BALL,C.M.GOULT,J.A.DONARSKI,J.MICKLEFIELD,V.RAMESH REVDAT 4 27-JUL-11 1XT7 1 ATOM REMARK REVDAT 3 13-JUL-11 1XT7 1 VERSN REVDAT 2 24-FEB-09 1XT7 1 VERSN REVDAT 1 16-NOV-04 1XT7 0 JRNL AUTH L.-J.BALL,C.M.GOULT,J.A.DONARSKI,J.MICKLEFIELD,V.RAMESH JRNL TITL NMR STRUCTURE DETERMINATION AND CALCIUM BINDING EFFECTS OF JRNL TITL 2 LIPOPEPTIDE ANTIBIOTIC DAPTOMYCIN JRNL REF ORG.BIOMOL.CHEM. V. 2 1872 2004 JRNL REFN ISSN 1477-0520 JRNL PMID 15227539 JRNL DOI 10.1039/B402722A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : GUNTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 52 DISTANCE RESTRAINTS WERE REMARK 3 USED FOR NMR STRUCTURE CALCULATION. REMARK 4 REMARK 4 1XT7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-04. REMARK 100 THE RCSB ID CODE IS RCSB030740. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.05 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM DAPTOMYCIN; PH 5.05 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, NMRPIPE 1.0, SPARKY REMARK 210 3.0, DYANA 1.5 REMARK 210 METHOD USED : CONSTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 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 400 REMARK 400 COMPOUND REMARK 400 DAPTOMYCIN IS A CYCLIC TRIDECAMER LIPOPETIDE. REMARK 400 HERE, DAPTOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE REMARK 400 SEQUENCE (SEQRES) AND ONE LIGAND (HET) DKA. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: DAPTOMYCIN REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 2 TO 14 REMARK 400 COMPONENT_2: FATTY ACID RESIDUE 1 REMARK 400 DESCRIPTION: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. REMARK 400 THE SCAFFOLD IS MADE OF TWO PARTS: REMARK 400 (1) THREE RESIDUES N-TERM EXOCYCLIC PART REMARK 400 (2) A DECAPEPTIDE LACTONE RING DERIVED FROM REMARK 400 CYCLIZATION OF THR3 SIDE CHAIN ONTO THE C-TER REMARK 400 CARBOXYL GROUP REMARK 400 THE N-DECANOYL FATTY ACID IS LINKED TO THE REMARK 400 MAIN BODY OF THE MOLECULE VIA N-TERM ACYLATION. 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 OG1 THR A 5 O KYN A 14 2.18 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 ASP A 8 CG ASP A 8 OD1 0.162 REMARK 500 DSN A 12 CB DSN A 12 OG -0.168 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 ORN A 7 44.57 78.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 DSG A 3 32.8 D L WRONG HAND REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T5N RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE CALCIUM-DEPENDENT ANTIBIOTIC REMARK 900 DAPTOMYCIN REMARK 900 RELATED ID: 1T5M RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE CALCIUM-DEPENDENT ANTIBIOTIC REMARK 900 DAPTOMYCIN DBREF 1XT7 A 2 14 NOR NOR00001 NOR00001 2 14 SEQRES 1 A 13 TRP DSG ASP THR GLY ORN ASP DAL ASP GLY DSN LME KYN HET DSG A 3 14 HET ORN A 7 19 HET DAL A 9 10 HET DSN A 12 11 HET LME A 13 19 HET KYN A 14 24 HET DKA A 1 30 HETNAM DSG D-ASPARAGINE HETNAM ORN L-ORNITHINE HETNAM DAL D-ALANINE HETNAM DSN D-SERINE HETNAM LME (2S,3R)-2-AZANYL-3-METHYL-PENTANEDIOIC ACID HETNAM KYN (2S)-2-AMINO-4-(2-AMINOPHENYL)-4-OXOBUTANOIC ACID HETNAM DKA DECANOIC ACID HETSYN LME (3R)-3-METHYL-L-GLUTAMIC ACID HETSYN KYN L-KYNURENINE FORMUL 1 DSG C4 H8 N2 O3 FORMUL 1 ORN C5 H12 N2 O2 FORMUL 1 DAL C3 H7 N O2 FORMUL 1 DSN C3 H7 N O3 FORMUL 1 LME C6 H11 N O4 FORMUL 1 KYN C10 H12 N2 O3 FORMUL 2 DKA C10 H20 O2 LINK C1 DKA A 1 N TRP A 2 1555 1555 1.32 LINK C TRP A 2 N DSG A 3 1555 1555 1.32 LINK C DSG A 3 N ASP A 4 1555 1555 1.32 LINK OG1 THR A 5 C KYN A 14 1555 1555 1.36 LINK C GLY A 6 N ORN A 7 1555 1555 1.33 LINK C ORN A 7 N ASP A 8 1555 1555 1.33 LINK C ASP A 8 N DAL A 9 1555 1555 1.32 LINK C DAL A 9 N ASP A 10 1555 1555 1.32 LINK C GLY A 11 N DSN A 12 1555 1555 1.32 LINK C DSN A 12 N LME A 13 1555 1555 1.33 LINK C LME A 13 N KYN A 14 1555 1555 1.33 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
Complete list - 25 201 Bytes