HEADER PROTON TRANSPORT 11-FEB-02 1L0M TITLE SOLUTION STRUCTURE OF BACTERIORHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIORHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE, CORRESPONDING TO DIFFERENT SECONDARY SOURCE 4 STRUCTURE ELEMENTS, WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS SOURCE 5 PEPTIDE IS NATURALLY FOUND IN HALOBACTERIUM HALOBIUM. KEYWDS BACTERIORHODOPSIN, ALTERNATIVE METHOD FOR STRUCTURE DETERMINATION, KEYWDS 2 PROTON TRANSPORT EXPDTA SOLUTION NMR AUTHOR M.KATRAGADDA,J.L.ALDERFER,P.L.YEAGLE REVDAT 3 23-FEB-22 1L0M 1 REMARK REVDAT 2 24-FEB-09 1L0M 1 VERSN REVDAT 1 27-MAR-02 1L0M 0 JRNL AUTH M.KATRAGADDA,J.L.ALDERFER,P.L.YEAGLE JRNL TITL ASSEMBLY OF A POLYTOPIC MEMBRANE PROTEIN STRUCTURE FROM THE JRNL TITL 2 SOLUTION STRUCTURES OF OVERLAPPING PEPTIDE FRAGMENTS OF JRNL TITL 3 BACTERIORHODOPSIN. JRNL REF BIOPHYS.J. V. 81 1029 2001 JRNL REFN ISSN 0006-3495 JRNL PMID 11463644 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97.1, SYBYL 6.6 REMARK 3 AUTHORS : TRIPOS, INC. (SYBYL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING REMARK 4 REMARK 4 1L0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015534. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : CHMEICALLY SYNTHESIZED PEPTIDES REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DIANA, SYBYL 6.6 REMARK 210 METHOD USED : REFINED USING 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: 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: 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 NE1 TRP A 182 CD2 TYR A 185 2.19 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 TRP A 182 CG TRP A 182 CD2 0.523 REMARK 500 TRP A 182 CG TRP A 182 CD1 0.366 REMARK 500 TRP A 182 CD1 TRP A 182 NE1 0.526 REMARK 500 TRP A 182 NE1 TRP A 182 CE2 0.569 REMARK 500 TRP A 182 CE2 TRP A 182 CD2 0.448 REMARK 500 TYR A 185 CG TYR A 185 CD2 0.080 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 A 28 CB - CG - CD1 ANGL. DEV. = 12.3 DEGREES REMARK 500 ALA A 39 CB - CA - C ANGL. DEV. = 12.3 DEGREES REMARK 500 ILE A 52 CA - CB - CG2 ANGL. DEV. = 12.6 DEGREES REMARK 500 ARG A 82 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 PHE A 88 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 PRO A 91 C - N - CD ANGL. DEV. = -13.1 DEGREES REMARK 500 ASP A 96 C - N - CA ANGL. DEV. = 18.6 DEGREES REMARK 500 VAL A 124 CA - CB - CG1 ANGL. DEV. = 11.2 DEGREES REMARK 500 TYR A 131 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 SER A 132 CB - CA - C ANGL. DEV. = 14.6 DEGREES REMARK 500 TYR A 133 CB - CA - C ANGL. DEV. = 14.3 DEGREES REMARK 500 TYR A 133 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 PHE A 135 C - N - CA ANGL. DEV. = 20.4 DEGREES REMARK 500 PHE A 156 CB - CG - CD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 TRP A 182 NE1 - CE2 - CZ2 ANGL. DEV. = 7.4 DEGREES REMARK 500 TRP A 182 CD2 - CE2 - CZ2 ANGL. DEV. = -7.6 DEGREES REMARK 500 TYR A 185 CA - CB - CG ANGL. DEV. = 16.8 DEGREES REMARK 500 TYR A 185 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 TYR A 185 CB - CG - CD1 ANGL. DEV. = -8.2 DEGREES REMARK 500 TYR A 185 CG - CD2 - CE2 ANGL. DEV. = -19.7 DEGREES REMARK 500 PHE A 208 CB - CG - CD2 ANGL. DEV. = -6.6 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 PRO A 8 130.58 -39.91 REMARK 500 ILE A 11 -38.09 -142.44 REMARK 500 ALA A 14 -68.91 -162.93 REMARK 500 THR A 17 -60.11 -10.33 REMARK 500 LEU A 19 -42.22 -130.25 REMARK 500 LEU A 22 -43.42 114.26 REMARK 500 THR A 24 39.88 -77.06 REMARK 500 PHE A 27 61.97 -109.05 REMARK 500 MET A 32 -81.46 -13.64 REMARK 500 ALA A 39 -102.33 26.38 REMARK 500 LYS A 40 -44.99 -168.01 REMARK 500 LYS A 41 13.57 -10.26 REMARK 500 LEU A 48 -56.58 -132.63 REMARK 500 PRO A 50 -9.93 -50.39 REMARK 500 ILE A 52 57.47 -67.29 REMARK 500 ALA A 53 -30.10 -178.88 REMARK 500 LEU A 58 -71.78 -146.49 REMARK 500 LEU A 62 58.67 -119.53 REMARK 500 TYR A 64 -4.11 -141.15 REMARK 500 LEU A 66 -97.81 91.72 REMARK 500 MET A 68 -64.50 -146.43 REMARK 500 ASN A 76 -51.73 128.02 REMARK 500 PRO A 77 86.89 -63.26 REMARK 500 ILE A 78 -51.17 -126.47 REMARK 500 TRP A 80 98.18 -60.36 REMARK 500 ALA A 84 52.80 -169.79 REMARK 500 ASP A 85 -41.61 -157.49 REMARK 500 TRP A 86 54.05 -117.00 REMARK 500 PHE A 88 81.15 71.54 REMARK 500 THR A 89 -81.85 -98.89 REMARK 500 THR A 90 -68.93 74.97 REMARK 500 LEU A 95 -54.80 -169.64 REMARK 500 ASP A 96 157.77 33.46 REMARK 500 ALA A 98 58.12 -119.43 REMARK 500 LEU A 100 50.64 -163.63 REMARK 500 VAL A 101 72.60 -7.69 REMARK 500 GLN A 105 4.85 48.21 REMARK 500 THR A 107 -113.26 135.48 REMARK 500 ILE A 108 -131.52 58.92 REMARK 500 ASP A 115 -106.53 -81.09 REMARK 500 ILE A 117 -93.53 -69.72 REMARK 500 MET A 118 30.64 -99.89 REMARK 500 LYS A 129 43.83 -86.63 REMARK 500 VAL A 130 -62.53 -142.71 REMARK 500 TYR A 131 -79.77 -103.65 REMARK 500 SER A 132 -158.60 49.59 REMARK 500 TYR A 133 39.08 -86.69 REMARK 500 PHE A 135 -176.58 125.67 REMARK 500 VAL A 136 58.11 -67.36 REMARK 500 THR A 142 37.34 -90.13 REMARK 500 REMARK 500 THIS ENTRY HAS 78 RAMACHANDRAN OUTLIERS. 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 LEU A 15 GLY A 16 -148.88 REMARK 500 MET A 20 GLY A 21 136.68 REMARK 500 LEU A 22 GLY A 23 139.66 REMARK 500 THR A 24 LEU A 25 147.74 REMARK 500 PHE A 27 LEU A 28 30.70 REMARK 500 LEU A 28 VAL A 29 131.84 REMARK 500 VAL A 29 LYS A 30 138.37 REMARK 500 LYS A 30 GLY A 31 135.05 REMARK 500 PRO A 37 ASP A 38 133.46 REMARK 500 LYS A 40 LYS A 41 -123.43 REMARK 500 TYR A 43 ALA A 44 -97.11 REMARK 500 ILE A 45 THR A 46 -126.46 REMARK 500 THR A 46 THR A 47 59.54 REMARK 500 MET A 56 TYR A 57 -138.53 REMARK 500 MET A 60 LEU A 61 148.60 REMARK 500 LEU A 62 GLY A 63 -38.78 REMARK 500 PRO A 77 ILE A 78 142.80 REMARK 500 TYR A 79 TRP A 80 129.74 REMARK 500 ALA A 81 ARG A 82 -50.17 REMARK 500 THR A 89 THR A 90 79.54 REMARK 500 PRO A 91 LEU A 92 149.16 REMARK 500 ASP A 96 LEU A 97 97.72 REMARK 500 ALA A 98 LEU A 99 132.74 REMARK 500 LEU A 100 VAL A 101 50.23 REMARK 500 ASP A 104 GLN A 105 147.52 REMARK 500 GLY A 106 THR A 107 -139.30 REMARK 500 THR A 107 ILE A 108 143.31 REMARK 500 VAL A 124 GLY A 125 -143.28 REMARK 500 VAL A 130 TYR A 131 -91.92 REMARK 500 SER A 132 TYR A 133 -63.61 REMARK 500 VAL A 136 TRP A 137 141.01 REMARK 500 THR A 142 ALA A 143 141.07 REMARK 500 TYR A 150 VAL A 151 147.51 REMARK 500 PHE A 153 PHE A 154 148.81 REMARK 500 PHE A 154 GLY A 155 146.65 REMARK 500 GLY A 155 PHE A 156 -48.35 REMARK 500 PHE A 156 THR A 157 141.95 REMARK 500 ARG A 164 PRO A 165 144.89 REMARK 500 GLU A 166 VAL A 167 -121.71 REMARK 500 TRP A 182 SER A 183 133.08 REMARK 500 TRP A 189 LEU A 190 135.87 REMARK 500 ILE A 198 VAL A 199 -135.71 REMARK 500 ILE A 203 GLU A 204 136.19 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 TYR A 26 0.20 SIDE CHAIN REMARK 500 PHE A 27 0.17 SIDE CHAIN REMARK 500 PHE A 42 0.16 SIDE CHAIN REMARK 500 TYR A 43 0.09 SIDE CHAIN REMARK 500 TYR A 64 0.08 SIDE CHAIN REMARK 500 TYR A 79 0.10 SIDE CHAIN REMARK 500 ARG A 82 0.13 SIDE CHAIN REMARK 500 PHE A 88 0.12 SIDE CHAIN REMARK 500 TYR A 131 0.16 SIDE CHAIN REMARK 500 TYR A 133 0.10 SIDE CHAIN REMARK 500 TYR A 150 0.07 SIDE CHAIN REMARK 500 PHE A 156 0.14 SIDE CHAIN REMARK 500 ARG A 164 0.09 SIDE CHAIN REMARK 500 TYR A 185 0.26 SIDE CHAIN REMARK 500 PHE A 208 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1L0M A 7 218 UNP P02945 BACR_HALN1 20 231 SEQRES 1 A 212 ARG PRO GLU TRP ILE TRP LEU ALA LEU GLY THR ALA LEU SEQRES 2 A 212 MET GLY LEU GLY THR LEU TYR PHE LEU VAL LYS GLY MET SEQRES 3 A 212 GLY VAL SER ASP PRO ASP ALA LYS LYS PHE TYR ALA ILE SEQRES 4 A 212 THR THR LEU VAL PRO ALA ILE ALA PHE THR MET TYR LEU SEQRES 5 A 212 SER MET LEU LEU GLY TYR GLY LEU THR MET VAL PRO PHE SEQRES 6 A 212 GLY GLY GLU GLN ASN PRO ILE TYR TRP ALA ARG TYR ALA SEQRES 7 A 212 ASP TRP LEU PHE THR THR PRO LEU LEU LEU LEU ASP LEU SEQRES 8 A 212 ALA LEU LEU VAL ASP ALA ASP GLN GLY THR ILE LEU ALA SEQRES 9 A 212 LEU VAL GLY ALA ASP GLY ILE MET ILE GLY THR GLY LEU SEQRES 10 A 212 VAL GLY ALA LEU THR LYS VAL TYR SER TYR ARG PHE VAL SEQRES 11 A 212 TRP TRP ALA ILE SER THR ALA ALA MET LEU TYR ILE LEU SEQRES 12 A 212 TYR VAL LEU PHE PHE GLY PHE THR SER LYS ALA GLU SER SEQRES 13 A 212 MET ARG PRO GLU VAL ALA SER THR PHE LYS VAL LEU ARG SEQRES 14 A 212 ASN VAL THR VAL VAL LEU TRP SER ALA TYR PRO VAL VAL SEQRES 15 A 212 TRP LEU ILE GLY SER GLU GLY ALA GLY ILE VAL PRO LEU SEQRES 16 A 212 ASN ILE GLU THR LEU LEU PHE MET VAL LEU ASP VAL SER SEQRES 17 A 212 ALA LYS VAL GLY HELIX 1 1 LEU A 19 THR A 24 1 6 HELIX 2 2 LEU A 58 LEU A 62 5 5 HELIX 3 3 MET A 68 GLY A 73 1 6 HELIX 4 4 THR A 107 VAL A 112 1 6 HELIX 5 5 ILE A 119 LEU A 123 5 5 HELIX 6 6 TRP A 137 THR A 142 1 6 HELIX 7 7 ILE A 148 PHE A 153 1 6 HELIX 8 8 GLU A 166 TRP A 182 1 17 HELIX 9 9 PHE A 208 VAL A 217 1 10 CISPEP 1 PRO A 8 GLU A 9 0 6.85 CISPEP 2 LEU A 25 TYR A 26 0 -13.49 CISPEP 3 VAL A 34 SER A 35 0 4.20 CISPEP 4 ALA A 39 LYS A 40 0 -24.37 CISPEP 5 PHE A 42 TYR A 43 0 28.88 CISPEP 6 ALA A 44 ILE A 45 0 -18.44 CISPEP 7 LEU A 87 PHE A 88 0 -14.04 CISPEP 8 PHE A 88 THR A 89 0 21.26 CISPEP 9 LEU A 95 ASP A 96 0 -23.22 CISPEP 10 LEU A 127 THR A 128 0 16.77 CISPEP 11 TYR A 131 SER A 132 0 -3.54 CISPEP 12 ARG A 134 PHE A 135 0 -8.59 CISPEP 13 GLU A 194 GLY A 195 0 -9.46 CISPEP 14 GLY A 197 ILE A 198 0 0.59 CISPEP 15 PRO A 200 LEU A 201 0 1.08 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