HEADER MEMBRANE PROTEIN 01-DEC-22 8FCZ TITLE CRYSTAL STRUCTURE OF GROUND-STATE RHODOPSIN IN COMPLEX WITH A NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A, B; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: NANOBODY NB2; COMPND 6 CHAIN: C, D; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 7 ORGANISM_COMMON: LLAMA; SOURCE 8 ORGANISM_TAXID: 9844; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSMEMBRANE PROTEIN, GPCR, NANOBODY, RETINAL, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.SALOM,K.PALCZEWSKI,P.D.KISER REVDAT 2 28-FEB-24 8FCZ 1 JRNL REVDAT 1 30-AUG-23 8FCZ 0 JRNL AUTH A.WU,D.SALOM,J.D.HONG,A.TWORAK,K.WATANABE,E.PARDON, JRNL AUTH 2 J.STEYAERT,H.KANDORI,K.KATAYAMA,P.D.KISER,K.PALCZEWSKI JRNL TITL STRUCTURAL BASIS FOR THE ALLOSTERIC MODULATION OF RHODOPSIN JRNL TITL 2 BY NANOBODY BINDING TO ITS EXTRACELLULAR DOMAIN. JRNL REF NAT COMMUN V. 14 5209 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37626045 JRNL DOI 10.1038/S41467-023-40911-9 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 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) : 3.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19540 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) : 0.283 REMARK 3 R VALUE (WORKING SET) : 0.281 REMARK 3 FREE R VALUE : 0.332 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1029 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) : 3.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1398 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3780 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6627 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 243 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 211.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.71000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 2.31000 REMARK 3 B12 (A**2) : -0.36000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.741 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.718 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 55.867 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.874 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7085 ; 0.002 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 6415 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9673 ; 0.718 ; 1.654 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14896 ; 0.262 ; 1.542 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 837 ; 5.493 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 39 ; 8.621 ; 7.949 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1053 ;13.064 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1120 ; 0.040 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7772 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1508 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.30 REMARK 3 ION PROBE RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 8FCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270382. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20570 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.92 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.83100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.710 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 600 0.1 M TRICINE PH 8 1.2 MM REMARK 280 F3215-0002 2% IPTG 50 MM PHENOL 5 MM EDTA 5 MM BETA REMARK 280 MERCAPTOETHANOL 50 MM CYGLU-4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 75.70500 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 151.41000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 151.41000 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 75.70500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PHE A 148 REMARK 465 GLY A 149 REMARK 465 GLU A 150 REMARK 465 LYS A 231 REMARK 465 GLU A 232 REMARK 465 ALA A 233 REMARK 465 ALA A 234 REMARK 465 ALA A 235 REMARK 465 GLN A 236 REMARK 465 GLN A 237 REMARK 465 GLN A 238 REMARK 465 GLU A 239 REMARK 465 SER A 240 REMARK 465 GLY A 324 REMARK 465 LYS A 325 REMARK 465 ASN A 326 REMARK 465 PRO A 327 REMARK 465 LEU A 328 REMARK 465 GLY A 329 REMARK 465 ASP A 330 REMARK 465 ASP A 331 REMARK 465 GLU A 332 REMARK 465 ALA A 333 REMARK 465 SER A 334 REMARK 465 THR A 335 REMARK 465 THR A 336 REMARK 465 VAL A 337 REMARK 465 SER A 338 REMARK 465 LYS A 339 REMARK 465 THR A 340 REMARK 465 GLU A 341 REMARK 465 THR A 342 REMARK 465 SER A 343 REMARK 465 GLN A 344 REMARK 465 VAL A 345 REMARK 465 ALA A 346 REMARK 465 PRO A 347 REMARK 465 ALA A 348 REMARK 465 ASN B 145 REMARK 465 PHE B 146 REMARK 465 ARG B 147 REMARK 465 PHE B 148 REMARK 465 THR B 229 REMARK 465 VAL B 230 REMARK 465 LYS B 231 REMARK 465 GLU B 232 REMARK 465 ALA B 233 REMARK 465 ALA B 234 REMARK 465 ALA B 235 REMARK 465 GLN B 236 REMARK 465 GLN B 237 REMARK 465 GLN B 238 REMARK 465 GLU B 239 REMARK 465 SER B 240 REMARK 465 GLY B 324 REMARK 465 LYS B 325 REMARK 465 ASN B 326 REMARK 465 PRO B 327 REMARK 465 LEU B 328 REMARK 465 GLY B 329 REMARK 465 ASP B 330 REMARK 465 ASP B 331 REMARK 465 GLU B 332 REMARK 465 ALA B 333 REMARK 465 SER B 334 REMARK 465 THR B 335 REMARK 465 THR B 336 REMARK 465 VAL B 337 REMARK 465 SER B 338 REMARK 465 LYS B 339 REMARK 465 THR B 340 REMARK 465 GLU B 341 REMARK 465 THR B 342 REMARK 465 SER B 343 REMARK 465 GLN B 344 REMARK 465 VAL B 345 REMARK 465 ALA B 346 REMARK 465 PRO B 347 REMARK 465 ALA B 348 REMARK 465 SER C 115 REMARK 465 SER C 116 REMARK 465 HIS C 117 REMARK 465 HIS C 118 REMARK 465 HIS C 119 REMARK 465 HIS C 120 REMARK 465 HIS C 121 REMARK 465 HIS C 122 REMARK 465 GLU C 123 REMARK 465 PRO C 124 REMARK 465 GLU C 125 REMARK 465 ALA C 126 REMARK 465 SER D 115 REMARK 465 SER D 116 REMARK 465 HIS D 117 REMARK 465 HIS D 118 REMARK 465 HIS D 119 REMARK 465 HIS D 120 REMARK 465 HIS D 121 REMARK 465 HIS D 122 REMARK 465 GLU D 123 REMARK 465 PRO D 124 REMARK 465 GLU D 125 REMARK 465 ALA D 126 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 197 CG CD OE1 OE2 REMARK 470 ARG A 314 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 52 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 106 CG CD OE1 OE2 REMARK 470 GLU D 106 CG CD OE1 OE2 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 ASN A 15 43.53 -108.88 REMARK 500 PHE A 103 83.48 -69.90 REMARK 500 LYS A 141 68.25 60.68 REMARK 500 SER A 176 177.90 71.74 REMARK 500 GLN A 184 38.71 70.33 REMARK 500 TYR A 192 -91.48 -89.94 REMARK 500 ASN A 199 47.27 70.24 REMARK 500 PHE A 212 -66.68 -138.61 REMARK 500 LEU A 321 -75.18 -68.03 REMARK 500 ASN B 15 43.37 -109.37 REMARK 500 PHE B 103 83.51 -69.93 REMARK 500 LYS B 141 69.00 63.58 REMARK 500 SER B 176 176.77 73.52 REMARK 500 GLN B 184 38.84 70.71 REMARK 500 ASN B 199 47.45 71.67 REMARK 500 PHE B 212 -54.95 -120.52 REMARK 500 HIS B 278 59.28 -98.01 REMARK 500 LEU B 321 -75.60 -68.23 REMARK 500 LYS C 77 70.87 54.25 REMARK 500 GLU C 106 -133.78 61.65 REMARK 500 GLN C 108 -62.25 72.65 REMARK 500 LYS D 77 71.06 54.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FCZ A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 8FCZ B 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 8FCZ C 1 126 PDB 8FCZ 8FCZ 1 126 DBREF 8FCZ D 1 126 PDB 8FCZ 8FCZ 1 126 SEQRES 1 A 348 MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO PHE SEQRES 2 A 348 SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU ALA SEQRES 3 A 348 PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER MET SEQRES 4 A 348 LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY PHE SEQRES 5 A 348 PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN HIS SEQRES 6 A 348 LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU ASN SEQRES 7 A 348 LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY PHE SEQRES 8 A 348 THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE VAL SEQRES 9 A 348 PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE ALA SEQRES 10 A 348 THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL VAL SEQRES 11 A 348 LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO MET SEQRES 12 A 348 SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET GLY SEQRES 13 A 348 VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA ALA SEQRES 14 A 348 PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU GLY SEQRES 15 A 348 MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO HIS SEQRES 16 A 348 GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET PHE SEQRES 17 A 348 VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE PHE SEQRES 18 A 348 CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA ALA SEQRES 19 A 348 ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA GLU SEQRES 20 A 348 LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE ALA SEQRES 21 A 348 PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA PHE SEQRES 22 A 348 TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO ILE SEQRES 23 A 348 PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER ALA SEQRES 24 A 348 VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS GLN SEQRES 25 A 348 PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY LYS SEQRES 26 A 348 ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SER SEQRES 27 A 348 LYS THR GLU THR SER GLN VAL ALA PRO ALA SEQRES 1 B 348 MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO PHE SEQRES 2 B 348 SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU ALA SEQRES 3 B 348 PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER MET SEQRES 4 B 348 LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY PHE SEQRES 5 B 348 PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN HIS SEQRES 6 B 348 LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU ASN SEQRES 7 B 348 LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY PHE SEQRES 8 B 348 THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE VAL SEQRES 9 B 348 PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE ALA SEQRES 10 B 348 THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL VAL SEQRES 11 B 348 LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO MET SEQRES 12 B 348 SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET GLY SEQRES 13 B 348 VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA ALA SEQRES 14 B 348 PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU GLY SEQRES 15 B 348 MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO HIS SEQRES 16 B 348 GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET PHE SEQRES 17 B 348 VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE PHE SEQRES 18 B 348 CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA ALA SEQRES 19 B 348 ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA GLU SEQRES 20 B 348 LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE ALA SEQRES 21 B 348 PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA PHE SEQRES 22 B 348 TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO ILE SEQRES 23 B 348 PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER ALA SEQRES 24 B 348 VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS GLN SEQRES 25 B 348 PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY LYS SEQRES 26 B 348 ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SER SEQRES 27 B 348 LYS THR GLU THR SER GLN VAL ALA PRO ALA SEQRES 1 C 126 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 126 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 126 PHE THR PHE SER LYS TYR ALA MET ASN TRP VAL ARG GLN SEQRES 4 C 126 PRO PRO GLY LYS GLY LEU GLU TRP VAL SER GLY ILE ARG SEQRES 5 C 126 PRO SER GLY ASP ASN PRO THR TYR ALA ASP SER VAL GLU SEQRES 6 C 126 GLY ARG PHE THR ILE ILE ARG ASP ASN ASP LYS LYS MET SEQRES 7 C 126 VAL TYR LEU GLN MET THR SER LEU LYS THR GLU ASP THR SEQRES 8 C 126 ALA VAL TYR TYR CYS THR ARG GLY TYR GLY THR MET THR SEQRES 9 C 126 ILE GLU GLY GLN GLY THR GLN VAL THR VAL SER SER HIS SEQRES 10 C 126 HIS HIS HIS HIS HIS GLU PRO GLU ALA SEQRES 1 D 126 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 126 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 126 PHE THR PHE SER LYS TYR ALA MET ASN TRP VAL ARG GLN SEQRES 4 D 126 PRO PRO GLY LYS GLY LEU GLU TRP VAL SER GLY ILE ARG SEQRES 5 D 126 PRO SER GLY ASP ASN PRO THR TYR ALA ASP SER VAL GLU SEQRES 6 D 126 GLY ARG PHE THR ILE ILE ARG ASP ASN ASP LYS LYS MET SEQRES 7 D 126 VAL TYR LEU GLN MET THR SER LEU LYS THR GLU ASP THR SEQRES 8 D 126 ALA VAL TYR TYR CYS THR ARG GLY TYR GLY THR MET THR SEQRES 9 D 126 ILE GLU GLY GLN GLY THR GLN VAL THR VAL SER SER HIS SEQRES 10 D 126 HIS HIS HIS HIS HIS GLU PRO GLU ALA HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET NAG E 5 14 HET MAN E 6 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET NAG G 1 14 HET NAG G 2 14 HET BMA G 3 11 HET MAN G 4 11 HET MAN G 5 11 HET NAG H 1 14 HET NAG H 2 14 HET RET A 401 20 HET RET B 401 20 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM RET RETINAL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 5 NAG 9(C8 H15 N O6) FORMUL 5 BMA 3(C6 H12 O6) FORMUL 5 MAN 4(C6 H12 O6) FORMUL 9 RET 2(C20 H28 O) HELIX 1 AA1 GLU A 33 HIS A 65 1 33 HELIX 2 AA2 THR A 70 GLY A 90 1 21 HELIX 3 AA3 GLY A 90 GLY A 101 1 12 HELIX 4 AA4 GLY A 106 CYS A 140 1 35 HELIX 5 AA5 HIS A 152 GLY A 174 1 23 HELIX 6 AA6 ASN A 199 PHE A 212 1 14 HELIX 7 AA7 PHE A 212 LEU A 226 1 15 HELIX 8 AA8 THR A 242 GLU A 247 1 6 HELIX 9 AA9 GLU A 247 HIS A 278 1 32 HELIX 10 AB1 PRO A 285 ALA A 295 1 11 HELIX 11 AB2 LYS A 296 VAL A 300 5 5 HELIX 12 AB3 TYR A 301 MET A 309 1 9 HELIX 13 AB4 ASN A 310 CYS A 322 1 13 HELIX 14 AB5 GLU B 33 HIS B 65 1 33 HELIX 15 AB6 THR B 70 GLY B 90 1 21 HELIX 16 AB7 GLY B 90 GLY B 101 1 12 HELIX 17 AB8 GLY B 106 CYS B 140 1 35 HELIX 18 AB9 ASN B 151 GLY B 174 1 24 HELIX 19 AC1 ASN B 199 PHE B 212 1 14 HELIX 20 AC2 PHE B 212 LEU B 226 1 15 HELIX 21 AC3 THR B 242 GLU B 247 1 6 HELIX 22 AC4 GLU B 247 HIS B 278 1 32 HELIX 23 AC5 PRO B 285 ALA B 295 1 11 HELIX 24 AC6 LYS B 296 VAL B 300 5 5 HELIX 25 AC7 TYR B 301 MET B 309 1 9 HELIX 26 AC8 ASN B 310 CYS B 322 1 13 HELIX 27 AC9 LYS C 87 THR C 91 5 5 HELIX 28 AD1 LYS D 87 THR D 91 5 5 SHEET 1 AA1 2 THR A 4 GLU A 5 0 SHEET 2 AA1 2 TYR A 10 VAL A 11 -1 O VAL A 11 N THR A 4 SHEET 1 AA2 2 TYR A 178 PRO A 180 0 SHEET 2 AA2 2 CYS A 187 ILE A 189 -1 O GLY A 188 N ILE A 179 SHEET 1 AA3 2 THR B 4 GLU B 5 0 SHEET 2 AA3 2 TYR B 10 VAL B 11 -1 O VAL B 11 N THR B 4 SHEET 1 AA4 2 TYR B 178 PRO B 180 0 SHEET 2 AA4 2 CYS B 187 ILE B 189 -1 O GLY B 188 N ILE B 179 SHEET 1 AA5 4 GLN C 3 LEU C 4 0 SHEET 2 AA5 4 SER C 17 SER C 25 -1 O SER C 25 N GLN C 3 SHEET 3 AA5 4 MET C 78 THR C 84 -1 O MET C 83 N LEU C 18 SHEET 4 AA5 4 PHE C 68 ASP C 73 -1 N ILE C 71 O TYR C 80 SHEET 1 AA6 5 PRO C 58 TYR C 60 0 SHEET 2 AA6 5 GLU C 46 ILE C 51 -1 N GLY C 50 O THR C 59 SHEET 3 AA6 5 MET C 34 GLN C 39 -1 N TRP C 36 O SER C 49 SHEET 4 AA6 5 ALA C 92 ARG C 98 -1 O TYR C 95 N VAL C 37 SHEET 5 AA6 5 GLN C 111 VAL C 112 -1 O VAL C 112 N ALA C 92 SHEET 1 AA7 4 GLN D 3 LEU D 4 0 SHEET 2 AA7 4 SER D 17 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AA7 4 MET D 78 THR D 84 -1 O MET D 83 N LEU D 18 SHEET 4 AA7 4 PHE D 68 ASP D 73 -1 N ILE D 71 O TYR D 80 SHEET 1 AA8 5 PRO D 58 TYR D 60 0 SHEET 2 AA8 5 GLU D 46 ILE D 51 -1 N GLY D 50 O THR D 59 SHEET 3 AA8 5 MET D 34 GLN D 39 -1 N TRP D 36 O SER D 49 SHEET 4 AA8 5 ALA D 92 ARG D 98 -1 O TYR D 95 N VAL D 37 SHEET 5 AA8 5 GLN D 111 VAL D 112 -1 O VAL D 112 N ALA D 92 SSBOND 1 CYS A 110 CYS A 187 1555 1555 2.03 SSBOND 2 CYS B 110 CYS B 187 1555 1555 2.04 SSBOND 3 CYS C 22 CYS C 96 1555 1555 2.03 SSBOND 4 CYS D 22 CYS D 96 1555 1555 2.04 LINK ND2 ASN A 2 C1 NAG F 1 1555 1555 1.44 LINK ND2 ASN A 15 C1 NAG E 1 1555 1555 1.44 LINK NZ LYS A 296 C15 RET A 401 1555 1555 1.27 LINK ND2 ASN B 2 C1 NAG H 1 1555 1555 1.45 LINK ND2 ASN B 15 C1 NAG G 1 1555 1555 1.44 LINK NZ LYS B 296 C15 RET B 401 1555 1555 1.27 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.44 LINK O3 BMA E 3 C1 MAN E 4 1555 1555 1.44 LINK O6 BMA E 3 C1 MAN E 6 1555 1555 1.44 LINK O2 MAN E 4 C1 NAG E 5 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.44 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.44 LINK O4 NAG G 2 C1 BMA G 3 1555 1555 1.44 LINK O3 BMA G 3 C1 MAN G 4 1555 1555 1.44 LINK O6 BMA G 3 C1 MAN G 5 1555 1555 1.44 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.44 CRYST1 119.277 119.277 227.115 90.00 90.00 120.00 P 31 2 1 12 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 0.008384 0.004840 0.000000 0.00000 SCALE2 0.000000 0.009681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004403 0.00000