HEADER PEPTIDE ANTIBIOTIC 11-AUG-88 1GMA OBSLTE 04-MAR-98 1GMA 1ALZ TITLE THREE-*DIMENSIONAL STRUCTURE AT 0.86 ANGSTROMS OF THE TITLE 2 UNCOMPLEXED FORM OF THE TRANSMEMBRANE ION CHANNEL PEPTIDE TITLE 3 GRAMICIDIN*A COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS PEPTIDE ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR D.A.LANGS REVDAT 1 15-JAN-91 1GMA 0 JRNL AUTH D.A.LANGS JRNL TITL THREE-DIMENSIONAL STRUCTURE AT 0.86 ANGSTROMS OF JRNL TITL 2 THE UNCOMPLEXED FORM OF THE TRANSMEMBRANE ION JRNL TITL 3 CHANNEL PEPTIDE GRAMICIDINA JRNL REF SCIENCE V. 241 188 1988 JRNL REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 0.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 567 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GMA COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1GMA THE WATERS IN THIS ENTRY MAY BE DISORDERED OR MAY BE REMARK 5 1GMA ETHANOL MOLECULES. 1GMA REMARK 6 REMARK 6 1GMA HYDROGEN ATOMS IN THIS ENTRY HAVE BEEN ASSIGNED NAMES REMARK 6 1GMA CONSISTENT WITH THE RECOMMENDATIONS OF THE IUPAC-IUB REMARK 6 1GMA COMMISSION ON BIOCHEMICAL NOMENCLATURE (E.G. REMARK 6 J.MOL.BIOL. 1GMA (1970) VOL.52, PP 1-17). RULE 4.4 OF THE REMARK 6 RECOMMENDATIONS 1GMA HAS BEEN FOLLOWED WITH THE FOLLOWING REMARK 6 MODIFICATION - WHEN 1GMA MORE THAN ONE HYDROGEN ATOM IS REMARK 6 BONDED TO A SINGLE 1GMA NON-HYDROGEN ATOM, THE HYDROGEN REMARK 6 ATOM NUMBER DESIGNATION IS 1GMA GIVEN AS THE FIRST REMARK 6 CHARACTER OF THE ATOM NAME RATHER THAN 1GMA AS THE LAST REMARK 6 CHARACTER (E.G. H*BETA*1 IS DENOTED AS 1HB). 1GMA REMARK 7 REMARK 7 1GMA ETHANOL 13 IS DISORDERED WITH TRP B 13, SUCH THAT WHEN REMARK 7 THE 1GMA INDOLE RING SHIFTS TO BREAK THE NE1--OA BOND TO REMARK 7 ETHANOL 13, 1GMA THE ETHANOL FLIPS END-ON-END TO EXCHANGE REMARK 7 THE OA AND CG 1GMA POSITIONS SO THAT IT CAN H-BOND TO THE REMARK 7 DISORDERED CARBONYL 1GMA OXYGEN OF RESIDUE FOR B. THE C- REMARK 7 ATOM OF THE FOR B RESIDUE 1GMA IS FULL OCCUPANCY TO BOTH REMARK 7 OXYGEN SITES. 1GMA REMARK 8 REMARK 8 1GMA THERE ARE 15 MOLECULES OF ETHANOL PER ASYMMETRIC UNIT REMARK 8 1GMA COMPUTED FROM THE MEASURED DENSITY AND CELL PARAMETERS REMARK 8 AT 1GMA ROOM TEMPERATURE. THE PRECISION OF THE DENSITY REMARK 8 MEASUREMENT 1GMA IS PROBABLY GOOD TO WITHIN A SINGLE REMARK 8 ETHANOL MOLECULE, I.E. 1GMA 15 PLUS OR MINUS 1 ETHANOLS. REMARK 8 THE REFINED STRUCTURE 1GMA ACCOUNTS FOR 12 FULL OCCUPANCY REMARK 8 AND 2 HALF OCCUPANCY SITES, 1GMA FOR 13 OF THE 15 ETHANOLS. REMARK 8 THE TWO REMAINING EOH MOLECULES 1GMA MAY BE DISORDERED IN REMARK 8 THE VICINITY OF HOH 15 AND 16. 1GMA REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 15.79750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 12.10950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.18450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 12.10950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.79750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.18450 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 C1 EOH 9 O HOH 16 1.76 REMARK 500 C1 EOH 6 O EOH 8 1.97 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP B 11 CA TRP B 11 CB -0.203 REMARK 500 TRP B 11 CG TRP B 11 CD2 0.183 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TRP B 11 N - CA - CB ANGL. DEV. = 18.1 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 LEU A 4 -139.99 92.38 REMARK 500 VAL A 6 -151.35 106.96 REMARK 500 VAL A 8 -130.42 89.29 REMARK 500 LEU A 10 -141.48 103.29 REMARK 500 LEU A 12 -137.62 102.03 REMARK 500 LEU A 14 -142.86 137.17 REMARK 500 LEU B 4 -140.29 103.90 REMARK 500 VAL B 6 -157.69 118.68 REMARK 500 VAL B 8 -144.89 118.95 REMARK 500 LEU B 10 -135.72 100.87 REMARK 500 LEU B 12 -130.81 97.81 REMARK 500 LEU B 14 -141.54 120.46 SEQRES 1 A 17 FOR VAL GLY ALA LEU ALA VAL VAL VAL TRP LEU TRP LEU SEQRES 2 A 17 TRP LEU TRP ETA SEQRES 1 B 17 FOR VAL GLY ALA LEU ALA VAL VAL VAL TRP LEU TRP LEU SEQRES 2 B 17 TRP LEU TRP ETA FTNOTE 1 RESIDUES LEU 4, VAL 6, VAL 8, LEU 10, LEU 12, AND LEU 14 FTNOTE 1 IN EACH CHAIN EXHIBIT THE D CONFIGURATION OF THE AMINO FTNOTE 1 ACID. FTNOTE 2 SEE REMARK 7. FTNOTE 3 SEE REMARK 5. HET FOR A 0 3 HET ETA A 16 9 HET FOR B 0 4 HET ETA B 16 9 HET EOH 1 3 HET EOH 2 3 HET EOH 3 3 HET EOH 4 3 HET EOH 5 3 HET EOH 6 3 HET EOH 7 3 HET EOH 8 3 HET EOH 9 3 HET EOH 10 3 HET EOH 11 3 HET EOH 12 3 HET EOH 13 3 HET EOH 14 3 HETNAM FOR FORMYL GROUP HETNAM ETA ETHANOLAMINE HETNAM EOH ETHANOL FORMUL 1 FOR 2(C H2 O) FORMUL 1 ETA 2(C2 H7 N O) FORMUL 3 EOH 14(C2 H6 O) FORMUL 17 HOH *2(H2 O1) SHEET 1 A 2 VAL A 1 TRP A 15 0 SHEET 2 A 2 VAL B 1 TRP B 15 -1 O VAL B 1 N TRP A 15 CRYST1 31.595 32.369 24.219 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 0.031651 0.000000 0.000000 0.00000 ORIGX2 0.000000 0.030894 0.000000 0.00000 ORIGX3 0.000000 0.000000 0.041290 0.00000 SCALE1 0.031651 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041290 0.00000 HETATM 1 C FOR A 0 23.776 17.737 8.612 1.00 0.08 C ANISOU 1 C FOR A 0 1619 665 106 32 148 -71 C HETATM 2 O FOR A 0 24.462 16.725 8.846 1.00 0.10 O ANISOU 2 O FOR A 0 1208 559 1261 42 106 -43 O HETATM 3 H FOR A 0 22.825 17.620 8.550 1.00 1.00 H ANISOU 3 H FOR A 0 0 0 0 0 0 0 H