HEADER HYDROLASE/ANTIBIOTIC 08-JUN-04 1TK2 TITLE CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN ALKALINE PROTEINASE TITLE 2 SAVINASE AND GRAMICIDIN S AT 1.5A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUBTILISIN SAVINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKALINE PROTEASE; COMPND 5 EC: 3.4.21.62; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GRAMICIDIN S; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: GRAMICIDIN SOVIET; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LENTUS; SOURCE 3 ORGANISM_TAXID: 1467; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 ORGANISM_SCIENTIFIC: BREVIBACILLUS BREVIS; SOURCE 7 ORGANISM_TAXID: 1393 KEYWDS GRAMICIDIN, ANTIBIOTIC, ANTIFUNGAL, ANTIBACTERIAL, CYCLIC GRAMICIDIN, KEYWDS 2 MEMBRANE ION CHANNEL, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.S.BHATT,P.KAUR,S.KLUPSCH,C.BETZEL,S.BRENNER,T.P.SINGH REVDAT 5 23-AUG-23 1TK2 1 REMARK LINK REVDAT 4 27-JUL-11 1TK2 1 REMARK REVDAT 3 13-JUL-11 1TK2 1 VERSN REVDAT 2 24-FEB-09 1TK2 1 VERSN REVDAT 1 22-JUN-04 1TK2 0 JRNL AUTH V.S.BHATT,P.KAUR,S.KLUPSCH,C.BETZEL,S.BRENNER,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN ALKALINE JRNL TITL 2 PROTEINASE SAVINASE AND GRAMICIDIN S AT 1.5A RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31702 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 + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1038 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2163 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1770 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1961 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60000 REMARK 3 B22 (A**2) : -0.42000 REMARK 3 B33 (A**2) : -0.18000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.679 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1994 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1774 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2717 ; 1.821 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4128 ; 0.973 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 273 ; 5.594 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 305 ;18.589 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 318 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2290 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 367 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 445 ; 0.368 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1644 ; 0.220 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2 ; 0.102 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 143 ; 0.146 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.267 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 22 ; 0.327 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.200 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1369 ; 1.010 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2167 ; 1.922 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 625 ; 3.107 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 550 ; 4.805 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1TK2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-91 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.5 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) : 1.009 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : OSCILLATION CAMERA REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31702 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1SVN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.33M NACL, 10% PEG 4000, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 38.12500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.44500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.44500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.12500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.67000 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 300 REMARK: THE BIOLOGICAL UNIT IS MONOMER 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 GRAMICIDIN S IS A CYCLODECAPEPTIDE, CONSTRUCTED AS TWO REMARK 400 IDENTICAL PENTAPEPTIDES JOINED HEAD TO TAIL, PRODUCED BY REMARK 400 THE GRAM POSITIVE BACTERIUM BACILLUS BREVIS REMARK 400 HERE, GRAMICIDIN S IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 THE GRAMICIDIN S IS CYCLIC PEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: GRAMICIDIN S REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: GRAMICIDIN S IS A DECAPEPTIDE, RESIDUES 1 AND 10 REMARK 400 FORM A PEPTIDE BOND RESULTING IN CYCLIZATION. 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 DPN B 9 CB DPN B 9 CG -0.118 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 LEU B 3 CB - CA - C ANGL. DEV. = 13.1 DEGREES REMARK 500 LEU B 3 CA - CB - CG ANGL. DEV. = -14.5 DEGREES REMARK 500 DPN B 9 CB - CG - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 PRO B 10 C - N - CA ANGL. DEV. = -9.6 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 ASP A 32 -150.42 -163.08 REMARK 500 ALA A 73 24.73 -146.48 REMARK 500 ASN A 77 -150.98 -157.12 REMARK 500 VAL A 81 -161.49 -119.79 REMARK 500 THR A 213 -164.26 -128.83 REMARK 500 PRO B 5 9.86 -64.12 REMARK 500 LEU B 8 110.11 160.86 REMARK 500 DPN B 9 -178.36 58.14 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 VAL B 1 ORN B 2 -148.15 REMARK 500 ORN B 7 LEU B 8 -146.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 DPN B 9 15.73 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 CA A1277 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 2 OE1 REMARK 620 2 ASP A 41 OD1 150.6 REMARK 620 3 ASP A 41 OD2 156.1 50.0 REMARK 620 4 LEU A 75 O 77.5 82.7 102.3 REMARK 620 5 ILE A 79 O 92.5 101.0 92.3 163.2 REMARK 620 6 VAL A 81 O 80.9 119.4 75.2 86.4 105.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1276 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 169 O REMARK 620 2 TYR A 171 O 97.2 REMARK 620 3 ALA A 174 O 104.6 91.1 REMARK 620 4 HOH A2114 O 94.1 96.5 158.9 REMARK 620 5 HOH A2137 O 123.1 138.1 89.3 72.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF GRAMICIDIN S REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XDC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A FROM CRYSTALS GROWN IN A LIPID REMARK 900 CUBIC PHASE. RELATED ENTRIES REMARK 900 RELATED ID: 1AV2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE REMARK 900 RELATED ID: 1BDW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A FROM BACILLUS BREVIS REMARK 900 RELATED ID: 1C4D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE REMARK 900 RELATED ID: 1GMK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLRXED WITH POTASSIUM REMARK 900 THIOCYANATE REMARK 900 RELATED ID: 1GRM RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE GRAMICIDIN A REMARK 900 RELATED ID: 1JNO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1KQE RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A IN BENZENE/ REMARK 900 ACETONE 10:1 REMARK 900 RELATED ID: 1MAG RELATED DB: PDB REMARK 900 SOLID STATE NMR STRUCTURE OF GRAMICIDIN A IN HYDRATED DMPC BILAYERS, REMARK 900 RELATED ID: 1MIC RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN METHANOL IN THE PRESENCE OF REMARK 900 CACL REMARK 900 RELATED ID: 1NG8 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A (W15G) IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1NRM RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE REMARK 900 MICELLES REMARK 900 RELATED ID: 1NRU RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE REMARK 900 MICELLES IN THE PRESENCE OF EXCESS NA+ REMARK 900 RELATED ID: 1NT5 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A (V1F) IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1JO3 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN B IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1JO4 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN C IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1NT6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1TKQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN A IN A REMARK 900 MEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE, IN THE PRESENCE OF CSCL REMARK 900 RELATED ID: 1W5U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL REMARK 900 RELATED ID: 2IZQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH KI IN METHANOL REMARK 900 RELATED ID: 3L8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH NAI REMARK 900 RELATED ID: 1AL4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN N-PROPANOL REMARK 900 RELATED ID: 1ALX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN METHANOL REMARK 900 RELATED ID: 1ALZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL DBREF 1TK2 A 1 269 UNP P29600 SUBS_BACLE 1 269 DBREF 1TK2 B 1 10 NOR NOR00249 NOR00249 1 10 SEQRES 1 A 269 ALA GLN SER VAL PRO TRP GLY ILE SER ARG VAL GLN ALA SEQRES 2 A 269 PRO ALA ALA HIS ASN ARG GLY LEU THR GLY SER GLY VAL SEQRES 3 A 269 LYS VAL ALA VAL LEU ASP THR GLY ILE SER THR HIS PRO SEQRES 4 A 269 ASP LEU ASN ILE ARG GLY GLY ALA SER PHE VAL PRO GLY SEQRES 5 A 269 GLU PRO SER THR GLN ASP GLY ASN GLY HIS GLY THR HIS SEQRES 6 A 269 VAL ALA GLY THR ILE ALA ALA LEU ASN ASN SER ILE GLY SEQRES 7 A 269 VAL LEU GLY VAL ALA PRO SER ALA GLU LEU TYR ALA VAL SEQRES 8 A 269 LYS VAL LEU GLY ALA SER GLY SER GLY SER VAL SER SER SEQRES 9 A 269 ILE ALA GLN GLY LEU GLU TRP ALA GLY ASN ASN GLY MET SEQRES 10 A 269 HIS VAL ALA ASN LEU SER LEU GLY SER PRO SER PRO SER SEQRES 11 A 269 ALA THR LEU GLU GLN ALA VAL ASN SER ALA THR SER ARG SEQRES 12 A 269 GLY VAL LEU VAL VAL ALA ALA SER GLY ASN SER GLY ALA SEQRES 13 A 269 GLY SER ILE SER TYR PRO ALA ARG TYR ALA ASN ALA MET SEQRES 14 A 269 ALA VAL GLY ALA THR ASP GLN ASN ASN ASN ARG ALA SER SEQRES 15 A 269 PHE SER GLN TYR GLY ALA GLY LEU ASP ILE VAL ALA PRO SEQRES 16 A 269 GLY VAL ASN VAL GLN SER THR TYR PRO GLY SER THR TYR SEQRES 17 A 269 ALA SER LEU ASN GLY THR SER MET ALA THR PRO HIS VAL SEQRES 18 A 269 ALA GLY ALA ALA ALA LEU VAL LYS GLN LYS ASN PRO SER SEQRES 19 A 269 TRP SER ASN VAL GLN ILE ARG ASN HIS LEU LYS ASN THR SEQRES 20 A 269 ALA THR SER LEU GLY SER THR ASN LEU TYR GLY SER GLY SEQRES 21 A 269 LEU VAL ASN ALA GLU ALA ALA THR ARG SEQRES 1 B 10 VAL ORN LEU DPN PRO VAL ORN LEU DPN PRO HET ORN B 2 8 HET DPN B 4 11 HET ORN B 7 8 HET DPN B 9 11 HET CA A1276 1 HET CA A1277 1 HETNAM ORN L-ORNITHINE HETNAM DPN D-PHENYLALANINE HETNAM CA CALCIUM ION FORMUL 2 ORN 2(C5 H12 N2 O2) FORMUL 2 DPN 2(C9 H11 N O2) FORMUL 3 CA 2(CA 2+) FORMUL 5 HOH *192(H2 O) HELIX 1 1 PRO A 5 VAL A 11 1 7 HELIX 2 2 GLN A 12 ASN A 18 1 7 HELIX 3 3 GLY A 63 ALA A 74 1 12 HELIX 4 4 SER A 103 ASN A 117 1 15 HELIX 5 5 SER A 132 ARG A 145 1 14 HELIX 6 6 GLY A 219 ASN A 238 1 20 HELIX 7 7 SER A 242 THR A 253 1 12 HELIX 8 8 SER A 259 GLY A 264 1 6 HELIX 9 9 ASN A 269 THR A 274 1 6 SHEET 1 AA 7 ILE A 44 SER A 49 0 SHEET 2 AA 7 GLU A 89 LYS A 94 1 O LEU A 90 N ARG A 45 SHEET 3 AA 7 LYS A 27 ASP A 32 1 O VAL A 28 N TYR A 91 SHEET 4 AA 7 VAL A 121 LEU A 124 1 O VAL A 121 N ALA A 29 SHEET 5 AA 7 LEU A 148 ALA A 152 1 O LEU A 148 N ALA A 122 SHEET 6 AA 7 ALA A 174 THR A 180 1 O MET A 175 N ALA A 151 SHEET 7 AA 7 ILE A 198 PRO A 201 1 O ILE A 198 N GLY A 178 SHEET 1 AB 2 VAL A 205 TYR A 209 0 SHEET 2 AB 2 THR A 213 LEU A 217 -1 O THR A 213 N TYR A 209 SHEET 1 BA 2 ORN B 2 LEU B 3 0 SHEET 2 BA 2 VAL B 6 ORN B 7 -1 O VAL B 6 N LEU B 3 LINK C VAL B 1 N ORN B 2 1555 1555 1.33 LINK N VAL B 1 C PRO B 10 1555 1555 1.32 LINK C ORN B 2 N LEU B 3 1555 1555 1.32 LINK C LEU B 3 N DPN B 4 1555 1555 1.35 LINK C DPN B 4 N PRO B 5 1555 1555 1.34 LINK C VAL B 6 N ORN B 7 1555 1555 1.32 LINK C ORN B 7 N LEU B 8 1555 1555 1.30 LINK C LEU B 8 N DPN B 9 1555 1555 1.28 LINK C DPN B 9 N PRO B 10 1555 1555 1.32 LINK OE1 GLN A 2 CA CA A1277 1555 1555 2.30 LINK OD1 ASP A 41 CA CA A1277 1555 1555 2.52 LINK OD2 ASP A 41 CA CA A1277 1555 1555 2.48 LINK O LEU A 75 CA CA A1277 1555 1555 2.46 LINK O ILE A 79 CA CA A1277 1555 1555 2.22 LINK O VAL A 81 CA CA A1277 1555 1555 2.37 LINK O ALA A 169 CA CA A1276 1555 1555 2.29 LINK O TYR A 171 CA CA A1276 1555 1555 2.32 LINK O ALA A 174 CA CA A1276 1555 1555 2.32 LINK CA CA A1276 O HOH A2114 1555 1555 2.73 LINK CA CA A1276 O HOH A2137 1555 1555 2.32 CISPEP 1 TYR A 167 PRO A 168 0 6.44 SITE 1 AC1 5 ALA A 169 TYR A 171 ALA A 174 HOH A2114 SITE 2 AC1 5 HOH A2137 SITE 1 AC2 6 GLN A 2 ASP A 41 LEU A 75 ASN A 77 SITE 2 AC2 6 ILE A 79 VAL A 81 SITE 1 AC3 16 LEU A 96 GLY A 100 GLY A 102 ILE A 107 SITE 2 AC3 16 LEU A 126 GLY A 127 SER A 128 PRO A 129 SITE 3 AC3 16 SER A 130 GLY A 154 ASN A 155 SER A 166 SITE 4 AC3 16 GLN A 191 SER A 240 HOH A2127 HOH B2001 CRYST1 76.250 73.340 40.890 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 0.013115 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024456 0.00000