HEADER PROTON TRANSPORT 20-MAR-13 4JQ6 TITLE CRYSTAL STRUCTURE OF BLUE LIGHT-ABSORBING PROTEORHODOPSIN FROM MED12 TITLE 2 AT 2.3 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEORHODOPSIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED BACTERIUM; SOURCE 3 ORGANISM_TAXID: 77133; SOURCE 4 GENE: PROTEORHODOPSIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: C43(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A KEYWDS RETINYLIDENE PROTEIN, ION TRANSPORT, PROTON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR G.OZOROWSKI,H.LUECKE REVDAT 5 30-OCT-24 4JQ6 1 REMARK REVDAT 4 03-APR-24 4JQ6 1 REMARK LINK REVDAT 3 23-OCT-13 4JQ6 1 JRNL REVDAT 2 19-JUN-13 4JQ6 1 ATOM REVDAT 1 08-MAY-13 4JQ6 0 JRNL AUTH T.RAN,G.OZOROWSKI,Y.GAO,O.A.SINESHCHEKOV,W.WANG,J.L.SPUDICH, JRNL AUTH 2 H.LUECKE JRNL TITL CROSS-PROTOMER INTERACTION WITH THE PHOTOACTIVE SITE IN JRNL TITL 2 OLIGOMERIC PROTEORHODOPSIN COMPLEXES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 1965 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 24100316 JRNL DOI 10.1107/S0907444913017575 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 27109 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1454 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) : 2.31 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1605 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.4060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4816 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.404 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.269 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.197 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.384 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5057 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6913 ; 1.482 ; 1.931 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 590 ; 4.904 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;40.057 ;22.969 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 735 ;16.249 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;13.303 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 770 ; 0.172 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3785 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4JQ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078364. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28615 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.71700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: PROTEORHODOPSIN MUTANT D97N FROM HOT75 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN USING THE BICELLE REMARK 280 METHOD. THE CRYSTALLIZATION BUFFER WAS 32% V/V (+/-)-2-METHYL-2, REMARK 280 4-PENTANEDIOL, 100 MM SODIUM ACETATE PH 4.5 AND 20 MM CALCIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 22.11191 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.97600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.00832 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.11191 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.97600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 38.00832 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -122.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLU A 3 REMARK 465 ILE A 4 REMARK 465 LEU A 5 REMARK 465 ALA A 6 REMARK 465 VAL A 7 REMARK 465 ASP A 8 REMARK 465 ALA A 97 REMARK 465 VAL A 98 REMARK 465 THR A 99 REMARK 465 ALA A 100 REMARK 465 ILE A 101 REMARK 465 SER A 102 REMARK 465 SER A 103 REMARK 465 ALA A 104 REMARK 465 GLY A 151 REMARK 465 GLU A 152 REMARK 465 THR A 153 REMARK 465 ALA A 154 REMARK 465 LYS A 155 REMARK 465 ALA A 156 REMARK 465 ASN A 157 REMARK 465 ALA A 158 REMARK 465 GLY A 159 REMARK 465 SER A 160 REMARK 465 GLY A 161 REMARK 465 ASN A 162 REMARK 465 ALA A 163 REMARK 465 ALA A 164 REMARK 465 SER A 165 REMARK 465 GLN A 166 REMARK 465 GLN A 167 REMARK 465 ALA A 168 REMARK 465 THR A 232 REMARK 465 SER A 233 REMARK 465 HIS A 234 REMARK 465 ALA A 235 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 GLU B 3 REMARK 465 ILE B 4 REMARK 465 LEU B 5 REMARK 465 ALA B 6 REMARK 465 VAL B 7 REMARK 465 ASP B 8 REMARK 465 VAL B 98 REMARK 465 THR B 99 REMARK 465 ALA B 100 REMARK 465 ILE B 101 REMARK 465 SER B 102 REMARK 465 SER B 103 REMARK 465 GLU B 152 REMARK 465 THR B 153 REMARK 465 ALA B 154 REMARK 465 LYS B 155 REMARK 465 ALA B 156 REMARK 465 ASN B 157 REMARK 465 ALA B 158 REMARK 465 GLY B 159 REMARK 465 SER B 160 REMARK 465 GLY B 161 REMARK 465 ASN B 162 REMARK 465 GLU B 229 REMARK 465 THR B 230 REMARK 465 SER B 231 REMARK 465 THR B 232 REMARK 465 SER B 233 REMARK 465 HIS B 234 REMARK 465 ALA B 235 REMARK 465 MET C 1 REMARK 465 GLY C 2 REMARK 465 GLU C 3 REMARK 465 ILE C 4 REMARK 465 LEU C 5 REMARK 465 ALA C 6 REMARK 465 VAL C 7 REMARK 465 ASP C 8 REMARK 465 ALA C 97 REMARK 465 VAL C 98 REMARK 465 THR C 99 REMARK 465 ALA C 100 REMARK 465 ILE C 101 REMARK 465 SER C 102 REMARK 465 SER C 103 REMARK 465 ALA C 104 REMARK 465 LEU C 150 REMARK 465 GLY C 151 REMARK 465 GLU C 152 REMARK 465 THR C 153 REMARK 465 ALA C 154 REMARK 465 LYS C 155 REMARK 465 ALA C 156 REMARK 465 ASN C 157 REMARK 465 ALA C 158 REMARK 465 GLY C 159 REMARK 465 SER C 160 REMARK 465 GLY C 161 REMARK 465 ASN C 162 REMARK 465 ALA C 163 REMARK 465 ALA C 164 REMARK 465 SER C 231 REMARK 465 THR C 232 REMARK 465 SER C 233 REMARK 465 HIS C 234 REMARK 465 ALA C 235 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 DISTANCE REMARK 500 O HOH B 1001 O HOH B 1005 1.99 REMARK 500 O HOH C 1001 O HOH C 1007 2.09 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 THR A 177 -81.12 -93.69 REMARK 500 ASP A 194 -71.21 -86.92 REMARK 500 THR B 177 -73.20 -112.60 REMARK 500 ASP B 194 45.99 -91.17 REMARK 500 ASN B 197 78.69 -111.05 REMARK 500 ILE C 148 -31.64 -131.97 REMARK 500 THR C 177 -71.09 -96.46 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 LI1 B 302 REMARK 610 LI1 B 303 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI1 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET C 301 DBREF 4JQ6 A 1 235 UNP Q4PP54 Q4PP54_9BACT 1 235 DBREF 4JQ6 B 1 235 UNP Q4PP54 Q4PP54_9BACT 1 235 DBREF 4JQ6 C 1 235 UNP Q4PP54 Q4PP54_9BACT 1 235 SEQRES 1 A 235 MET GLY GLU ILE LEU ALA VAL ASP ASP TYR VAL GLY ILE SEQRES 2 A 235 SER PHE TRP LEU ALA ALA ALA ILE MET LEU ALA SER THR SEQRES 3 A 235 VAL PHE PHE PHE VAL GLU ARG SER ASP VAL PRO VAL LYS SEQRES 4 A 235 TRP LYS THR SER LEU THR VAL ALA GLY LEU VAL THR GLY SEQRES 5 A 235 VAL ALA PHE TRP HIS TYR LEU TYR MET ARG GLY VAL TRP SEQRES 6 A 235 ILE TYR ALA GLY GLU THR PRO THR VAL PHE ARG TYR ILE SEQRES 7 A 235 ASP TRP LEU ILE THR VAL PRO LEU GLN ILE ILE GLU PHE SEQRES 8 A 235 TYR LEU ILE ILE ALA ALA VAL THR ALA ILE SER SER ALA SEQRES 9 A 235 VAL PHE TRP LYS LEU LEU ILE ALA SER LEU VAL MET LEU SEQRES 10 A 235 ILE GLY GLY PHE ILE GLY GLU ALA GLY LEU GLY ASP VAL SEQRES 11 A 235 VAL VAL TRP TRP ILE VAL GLY MET ILE ALA TRP LEU TYR SEQRES 12 A 235 ILE ILE TYR GLU ILE PHE LEU GLY GLU THR ALA LYS ALA SEQRES 13 A 235 ASN ALA GLY SER GLY ASN ALA ALA SER GLN GLN ALA PHE SEQRES 14 A 235 ASN THR ILE LYS TRP ILE VAL THR VAL GLY TRP ALA ILE SEQRES 15 A 235 TYR PRO ILE GLY TYR ALA TRP GLY TYR PHE GLY ASP GLY SEQRES 16 A 235 LEU ASN GLU ASP ALA LEU ASN ILE VAL TYR ASN LEU ALA SEQRES 17 A 235 ASP LEU ILE ASN LYS ALA ALA PHE GLY LEU ALA ILE TRP SEQRES 18 A 235 ALA ALA ALA MET LYS ASP LYS GLU THR SER THR SER HIS SEQRES 19 A 235 ALA SEQRES 1 B 235 MET GLY GLU ILE LEU ALA VAL ASP ASP TYR VAL GLY ILE SEQRES 2 B 235 SER PHE TRP LEU ALA ALA ALA ILE MET LEU ALA SER THR SEQRES 3 B 235 VAL PHE PHE PHE VAL GLU ARG SER ASP VAL PRO VAL LYS SEQRES 4 B 235 TRP LYS THR SER LEU THR VAL ALA GLY LEU VAL THR GLY SEQRES 5 B 235 VAL ALA PHE TRP HIS TYR LEU TYR MET ARG GLY VAL TRP SEQRES 6 B 235 ILE TYR ALA GLY GLU THR PRO THR VAL PHE ARG TYR ILE SEQRES 7 B 235 ASP TRP LEU ILE THR VAL PRO LEU GLN ILE ILE GLU PHE SEQRES 8 B 235 TYR LEU ILE ILE ALA ALA VAL THR ALA ILE SER SER ALA SEQRES 9 B 235 VAL PHE TRP LYS LEU LEU ILE ALA SER LEU VAL MET LEU SEQRES 10 B 235 ILE GLY GLY PHE ILE GLY GLU ALA GLY LEU GLY ASP VAL SEQRES 11 B 235 VAL VAL TRP TRP ILE VAL GLY MET ILE ALA TRP LEU TYR SEQRES 12 B 235 ILE ILE TYR GLU ILE PHE LEU GLY GLU THR ALA LYS ALA SEQRES 13 B 235 ASN ALA GLY SER GLY ASN ALA ALA SER GLN GLN ALA PHE SEQRES 14 B 235 ASN THR ILE LYS TRP ILE VAL THR VAL GLY TRP ALA ILE SEQRES 15 B 235 TYR PRO ILE GLY TYR ALA TRP GLY TYR PHE GLY ASP GLY SEQRES 16 B 235 LEU ASN GLU ASP ALA LEU ASN ILE VAL TYR ASN LEU ALA SEQRES 17 B 235 ASP LEU ILE ASN LYS ALA ALA PHE GLY LEU ALA ILE TRP SEQRES 18 B 235 ALA ALA ALA MET LYS ASP LYS GLU THR SER THR SER HIS SEQRES 19 B 235 ALA SEQRES 1 C 235 MET GLY GLU ILE LEU ALA VAL ASP ASP TYR VAL GLY ILE SEQRES 2 C 235 SER PHE TRP LEU ALA ALA ALA ILE MET LEU ALA SER THR SEQRES 3 C 235 VAL PHE PHE PHE VAL GLU ARG SER ASP VAL PRO VAL LYS SEQRES 4 C 235 TRP LYS THR SER LEU THR VAL ALA GLY LEU VAL THR GLY SEQRES 5 C 235 VAL ALA PHE TRP HIS TYR LEU TYR MET ARG GLY VAL TRP SEQRES 6 C 235 ILE TYR ALA GLY GLU THR PRO THR VAL PHE ARG TYR ILE SEQRES 7 C 235 ASP TRP LEU ILE THR VAL PRO LEU GLN ILE ILE GLU PHE SEQRES 8 C 235 TYR LEU ILE ILE ALA ALA VAL THR ALA ILE SER SER ALA SEQRES 9 C 235 VAL PHE TRP LYS LEU LEU ILE ALA SER LEU VAL MET LEU SEQRES 10 C 235 ILE GLY GLY PHE ILE GLY GLU ALA GLY LEU GLY ASP VAL SEQRES 11 C 235 VAL VAL TRP TRP ILE VAL GLY MET ILE ALA TRP LEU TYR SEQRES 12 C 235 ILE ILE TYR GLU ILE PHE LEU GLY GLU THR ALA LYS ALA SEQRES 13 C 235 ASN ALA GLY SER GLY ASN ALA ALA SER GLN GLN ALA PHE SEQRES 14 C 235 ASN THR ILE LYS TRP ILE VAL THR VAL GLY TRP ALA ILE SEQRES 15 C 235 TYR PRO ILE GLY TYR ALA TRP GLY TYR PHE GLY ASP GLY SEQRES 16 C 235 LEU ASN GLU ASP ALA LEU ASN ILE VAL TYR ASN LEU ALA SEQRES 17 C 235 ASP LEU ILE ASN LYS ALA ALA PHE GLY LEU ALA ILE TRP SEQRES 18 C 235 ALA ALA ALA MET LYS ASP LYS GLU THR SER THR SER HIS SEQRES 19 C 235 ALA HET RET A 301 20 HET RET B 301 20 HET LI1 B 302 13 HET LI1 B 303 8 HET RET C 301 20 HETNAM RET RETINAL HETNAM LI1 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14- HETNAM 2 LI1 TRIMETHYLHEXADECAN-16-YL]GLYCEROL HETSYN LI1 LIPID FRAGMENT FORMUL 4 RET 3(C20 H28 O) FORMUL 6 LI1 2(C42 H86 O3) FORMUL 9 HOH *42(H2 O) HELIX 1 1 ASP A 9 ARG A 33 1 25 HELIX 2 2 PRO A 37 LYS A 39 5 3 HELIX 3 3 TRP A 40 GLY A 69 1 30 HELIX 4 4 PRO A 72 ALA A 96 1 25 HELIX 5 5 PHE A 106 ALA A 125 1 20 HELIX 6 6 ASP A 129 LEU A 150 1 22 HELIX 7 7 THR A 171 PHE A 192 1 22 HELIX 8 8 ASN A 197 GLU A 229 1 33 HELIX 9 9 TYR B 10 ARG B 33 1 24 HELIX 10 10 PRO B 37 LYS B 39 5 3 HELIX 11 11 TRP B 40 GLY B 69 1 30 HELIX 12 12 PRO B 72 ALA B 97 1 26 HELIX 13 13 VAL B 105 ALA B 125 1 21 HELIX 14 14 ASP B 129 LEU B 150 1 22 HELIX 15 15 ALA B 164 VAL B 176 1 13 HELIX 16 16 THR B 177 PHE B 192 1 16 HELIX 17 17 ASN B 197 LYS B 228 1 32 HELIX 18 18 TYR C 10 ARG C 33 1 24 HELIX 19 19 SER C 34 VAL C 36 5 3 HELIX 20 20 PRO C 37 GLY C 69 1 33 HELIX 21 21 PRO C 72 ALA C 96 1 25 HELIX 22 22 PHE C 106 ALA C 125 1 20 HELIX 23 23 ASP C 129 GLU C 147 1 19 HELIX 24 24 GLN C 166 PHE C 192 1 27 HELIX 25 25 ASN C 197 THR C 230 1 34 LINK NZ LYS A 213 C15 RET A 301 1555 1555 1.35 LINK NZ LYS B 213 C15 RET B 301 1555 1555 1.35 LINK NZ LYS C 213 C15 RET C 301 1555 1555 1.35 CISPEP 1 PHE A 169 ASN A 170 0 4.31 SITE 1 AC1 13 TRP A 80 THR A 83 VAL A 84 GLN A 87 SITE 2 AC1 13 MET A 116 GLY A 120 TRP A 134 GLY A 137 SITE 3 AC1 13 TRP A 180 TYR A 183 TYR A 187 ASP A 209 SITE 4 AC1 13 LYS A 213 SITE 1 AC2 14 TYR B 77 TRP B 80 THR B 83 VAL B 84 SITE 2 AC2 14 GLN B 87 MET B 116 GLY B 120 TRP B 134 SITE 3 AC2 14 GLY B 137 TRP B 141 TRP B 180 TYR B 183 SITE 4 AC2 14 ASP B 209 LYS B 213 SITE 1 AC3 2 PHE B 30 ARG B 33 SITE 1 AC4 11 TRP C 80 THR C 83 VAL C 84 GLN C 87 SITE 2 AC4 11 MET C 116 GLY C 120 TRP C 141 TRP C 180 SITE 3 AC4 11 TYR C 183 ASP C 209 LYS C 213 CRYST1 87.267 101.952 87.357 90.00 119.52 90.00 I 1 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 0.011459 0.000000 0.006489 0.00000 SCALE2 0.000000 0.009809 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013155 0.00000