HEADER PROTON TRANSPORT 16-MAR-18 5ZIL TITLE CRYSTAL STRUCTURE OF BACTERIORHODOPSIN AT 1.29 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIORHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BR,BACTERIOOPSIN,BO SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOBACTERIUM SALINARUM (STRAIN ATCC 700922 / SOURCE 3 JCM 11081 / NRC-1); SOURCE 4 ORGANISM_COMMON: HALOBACTERIUM HALOBIUM; SOURCE 5 ORGANISM_TAXID: 64091; SOURCE 6 STRAIN: ATCC 700922 / JCM 11081 / NRC-1 KEYWDS PROTON PUMP, MEMBRANE PROTEIN, PROTON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR N.HASEGAWA,H.JONOTSUKA,K.MIKI,K.TAKEDA REVDAT 3 22-NOV-23 5ZIL 1 REMARK REVDAT 2 05-MAY-21 5ZIL 1 COMPND REMARK LINK SITE REVDAT 2 2 1 ATOM REVDAT 1 10-OCT-18 5ZIL 0 JRNL AUTH N.HASEGAWA,H.JONOTSUKA,K.MIKI,K.TAKEDA JRNL TITL X-RAY STRUCTURE ANALYSIS OF BACTERIORHODOPSIN AT 1.3 JRNL TITL 2 ANGSTROM RESOLUTION. JRNL REF SCI REP V. 8 13123 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 30177765 JRNL DOI 10.1038/S41598-018-31370-0 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.152 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2887 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1766 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 186 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ZIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300007051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 15 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57755 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 47.421 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.551 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.51 REMARK 200 R MERGE FOR SHELL (I) : 0.94400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1C3W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MO, 2.0-2.5 M PHOSPHATE, PH 5.6, REMARK 280 LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.37000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 55.37000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.37000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -204.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 121.18000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -104.94496 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 151.47500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 52.47248 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 232 CG CD OE1 OE2 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 ASP A 36 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 82 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 LEU A 94 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG A 164 CD - NE - CZ ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 175 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 L2P A 290 DBREF 5ZIL A 5 233 UNP P02945 BACR_HALSA 18 246 SEQRES 1 A 229 THR GLY ARG PRO GLU TRP ILE TRP LEU ALA LEU GLY THR SEQRES 2 A 229 ALA LEU MET GLY LEU GLY THR LEU TYR PHE LEU VAL LYS SEQRES 3 A 229 GLY MET GLY VAL SER ASP PRO ASP ALA LYS LYS PHE TYR SEQRES 4 A 229 ALA ILE THR THR LEU VAL PRO ALA ILE ALA PHE THR MET SEQRES 5 A 229 TYR LEU SER MET LEU LEU GLY TYR GLY LEU THR MET VAL SEQRES 6 A 229 PRO PHE GLY GLY GLU GLN ASN PRO ILE TYR TRP ALA ARG SEQRES 7 A 229 TYR ALA ASP TRP LEU PHE THR THR PRO LEU LEU LEU LEU SEQRES 8 A 229 ASP LEU ALA LEU LEU VAL ASP ALA ASP GLN GLY THR ILE SEQRES 9 A 229 LEU ALA LEU VAL GLY ALA ASP GLY ILE MET ILE GLY THR SEQRES 10 A 229 GLY LEU VAL GLY ALA LEU THR LYS VAL TYR SER TYR ARG SEQRES 11 A 229 PHE VAL TRP TRP ALA ILE SER THR ALA ALA MET LEU TYR SEQRES 12 A 229 ILE LEU TYR VAL LEU PHE PHE GLY PHE THR SER LYS ALA SEQRES 13 A 229 GLU SER MET ARG PRO GLU VAL ALA SER THR PHE LYS VAL SEQRES 14 A 229 LEU ARG ASN VAL THR VAL VAL LEU TRP SER ALA TYR PRO SEQRES 15 A 229 VAL VAL TRP LEU ILE GLY SER GLU GLY ALA GLY ILE VAL SEQRES 16 A 229 PRO LEU ASN ILE GLU THR LEU LEU PHE MET VAL LEU ASP SEQRES 17 A 229 VAL SER ALA LYS VAL GLY PHE GLY LEU ILE LEU LEU ARG SEQRES 18 A 229 SER ARG ALA ILE PHE GLY GLU ALA HET RET A 250 20 HET L2P A 270 46 HET L2P A 290 28 HET L2P A 300 46 HET L2P A 310 46 HETNAM RET RETINAL HETNAM L2P 2,3-DI-PHYTANYL-GLYCEROL HETSYN L2P 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL FORMUL 2 RET C20 H28 O FORMUL 3 L2P 4(C43 H88 O3) FORMUL 7 HOH *30(H2 O) HELIX 1 AA1 GLU A 9 GLY A 31 1 23 HELIX 2 AA2 ASP A 36 LEU A 62 1 27 HELIX 3 AA3 TRP A 80 VAL A 101 1 22 HELIX 4 AA4 ASP A 104 THR A 128 1 25 HELIX 5 AA5 VAL A 130 GLY A 155 1 26 HELIX 6 AA6 LYS A 159 MET A 163 5 5 HELIX 7 AA7 ARG A 164 GLY A 192 1 29 HELIX 8 AA8 PRO A 200 SER A 226 1 27 HELIX 9 AA9 ARG A 227 PHE A 230 5 4 SHEET 1 AA1 2 LEU A 66 PHE A 71 0 SHEET 2 AA1 2 GLU A 74 TYR A 79 -1 O ILE A 78 N THR A 67 LINK NZ LYS A 216 C15 RET A 250 1555 1555 1.34 CRYST1 60.590 60.590 110.740 90.00 90.00 120.00 P 63 6 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 0.016504 0.009529 0.000000 0.00000 SCALE2 0.000000 0.019058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009030 0.00000