HEADER MEMBRANE PROTEIN 12-APR-19 6RFC TITLE CRYSTAL STRUCTURE OF THE POTASSIUM-PUMPING G263F MUTANT OF THE LIGHT- TITLE 2 DRIVEN SODIUM PUMP KR2 IN THE MONOMERIC FORM, PH 4.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SODIUM PUMPING RHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DOKDONIA EIKASTA; SOURCE 3 ORGANISM_TAXID: 308116; SOURCE 4 GENE: NAR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGHT-DRIVEN SODIUM PUMP, ION TRANSLOCATION, RETINAL, RHODOPSIN, KEYWDS 2 MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.KOVALEV,V.POLOVINKIN,I.GUSHCHIN,V.BORSHCHEVSKIY,V.GORDELIY REVDAT 3 20-NOV-24 6RFC 1 REMARK REVDAT 2 24-JAN-24 6RFC 1 REMARK LINK REVDAT 1 24-APR-19 6RFC 0 JRNL AUTH K.KOVALEV,V.POLOVINKIN,I.GUSHCHIN,A.ALEKSEEV,V.SHEVCHENKO, JRNL AUTH 2 V.BORSHCHEVSKIY,R.ASTASHKIN,T.BALANDIN,D.BRATANOV, JRNL AUTH 3 S.VAGANOVA,A.POPOV,V.CHUPIN,G.BULDT,E.BAMBERG,V.GORDELIY JRNL TITL STRUCTURE AND MECHANISMS OF SODIUM-PUMPING KR2 RHODOPSIN. JRNL REF SCI ADV V. 5 V2671 2019 JRNL REFN ESSN 2375-2548 JRNL PMID 30989112 JRNL DOI 10.1126/SCIADV.AAV2671 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 25525 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1305 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1882 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2142 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 358 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.01000 REMARK 3 B22 (A**2) : 2.61000 REMARK 3 B33 (A**2) : -4.62000 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): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.801 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2547 ; 0.004 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 2654 ; 0.000 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3333 ; 0.769 ; 1.750 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6140 ; 0.809 ; 1.957 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 6.795 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;35.925 ;23.125 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 344 ;15.002 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;19.863 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 295 ; 0.047 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2518 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 523 ; 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 : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6RFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26858 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 4XTL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M SODIUM MALONATE, PH 4.3, LIPIDIC REMARK 280 CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.38450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.98200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 116.46500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.38450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.98200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 116.46500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.38450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.98200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 116.46500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.38450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.98200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 116.46500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 126.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 444 LIES ON A SPECIAL POSITION. 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 LYS A 273 REMARK 465 GLU A 274 REMARK 465 LEU A 275 REMARK 465 VAL A 276 REMARK 465 GLU A 277 REMARK 465 ALA A 278 REMARK 465 ASN A 279 REMARK 465 SER A 280 REMARK 465 LEU A 281 REMARK 465 GLU A 282 REMARK 465 HIS A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 HIS A 288 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 THR A 2 OG1 CG2 REMARK 470 GLU A 4 CD OE1 OE2 REMARK 470 ASN A 7 CA CB CG OD1 ND2 REMARK 470 LYS A 56 CE NZ REMARK 470 GLU A 90 OE1 OE2 REMARK 470 LYS A 134 NZ REMARK 470 LYS A 186 NZ REMARK 470 LYS A 187 CE NZ REMARK 470 GLU A 194 OE1 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 ASP A 231 CG OD1 OD2 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 ND2 ASN A 61 O HOH A 401 1.82 REMARK 500 O ALA A 16 O2 GOL A 333 1.87 REMARK 500 NE2 GLN A 244 O HOH A 402 2.09 REMARK 500 CE3 TRP A 183 C13 LFA A 335 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O1 GOL A 333 O1 GOL A 333 3555 1.60 REMARK 500 O2 GOL A 333 O2 GOL A 333 3555 1.87 REMARK 500 C2 GOL A 333 O2 GOL A 333 3555 2.08 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 ALA A 8 -63.14 -26.39 REMARK 500 THR A 17 -75.88 -108.56 REMARK 500 LEU A 103 149.75 77.72 REMARK 500 THR A 131 -78.17 -111.05 REMARK 500 ASN A 163 83.99 -163.80 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 ARG A 109 0.11 SIDE CHAIN 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 LFA A 302 REMARK 610 LFA A 303 REMARK 610 LFA A 304 REMARK 610 LFA A 305 REMARK 610 LFA A 306 REMARK 610 LFA A 307 REMARK 610 LFA A 308 REMARK 610 LFA A 309 REMARK 610 LFA A 310 REMARK 610 LFA A 311 REMARK 610 LFA A 312 REMARK 610 LFA A 313 REMARK 610 LFA A 314 REMARK 610 LFA A 315 REMARK 610 LFA A 316 REMARK 610 LFA A 317 REMARK 610 LFA A 318 REMARK 610 LFA A 319 REMARK 610 LFA A 320 REMARK 610 LFA A 321 REMARK 610 LFA A 322 REMARK 610 LFA A 323 REMARK 610 LFA A 324 REMARK 610 LFA A 325 REMARK 610 LFA A 326 REMARK 610 LFA A 327 REMARK 610 OLC A 330 REMARK 610 LFA A 334 REMARK 610 LFA A 335 REMARK 610 LFA A 336 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 NA A 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 25 OH REMARK 620 2 THR A 83 O 89.8 REMARK 620 3 PHE A 86 O 105.9 93.1 REMARK 620 4 HOH A 438 O 168.7 84.3 84.1 REMARK 620 5 HOH A 448 O 88.4 81.0 164.6 81.2 REMARK 620 6 HOH A 449 O 89.7 158.2 108.0 92.2 77.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 323 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 324 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 326 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 327 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 328 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 329 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLC A 330 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 331 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 333 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 335 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RET A 337 DBREF 6RFC A 1 280 UNP N0DKS8 N0DKS8_9FLAO 1 280 SEQADV 6RFC PHE A 263 UNP N0DKS8 GLY 263 ENGINEERED MUTATION SEQADV 6RFC LEU A 281 UNP N0DKS8 EXPRESSION TAG SEQADV 6RFC GLU A 282 UNP N0DKS8 EXPRESSION TAG SEQADV 6RFC HIS A 283 UNP N0DKS8 EXPRESSION TAG SEQADV 6RFC HIS A 284 UNP N0DKS8 EXPRESSION TAG SEQADV 6RFC HIS A 285 UNP N0DKS8 EXPRESSION TAG SEQADV 6RFC HIS A 286 UNP N0DKS8 EXPRESSION TAG SEQADV 6RFC HIS A 287 UNP N0DKS8 EXPRESSION TAG SEQADV 6RFC HIS A 288 UNP N0DKS8 EXPRESSION TAG SEQRES 1 A 288 MET THR GLN GLU LEU GLY ASN ALA ASN PHE GLU ASN PHE SEQRES 2 A 288 ILE GLY ALA THR GLU GLY PHE SER GLU ILE ALA TYR GLN SEQRES 3 A 288 PHE THR SER HIS ILE LEU THR LEU GLY TYR ALA VAL MET SEQRES 4 A 288 LEU ALA GLY LEU LEU TYR PHE ILE LEU THR ILE LYS ASN SEQRES 5 A 288 VAL ASP LYS LYS PHE GLN MET SER ASN ILE LEU SER ALA SEQRES 6 A 288 VAL VAL MET VAL SER ALA PHE LEU LEU LEU TYR ALA GLN SEQRES 7 A 288 ALA GLN ASN TRP THR SER SER PHE THR PHE ASN GLU GLU SEQRES 8 A 288 VAL GLY ARG TYR PHE LEU ASP PRO SER GLY ASP LEU PHE SEQRES 9 A 288 ASN ASN GLY TYR ARG TYR LEU ASN TRP LEU ILE ASP VAL SEQRES 10 A 288 PRO MET LEU LEU PHE GLN ILE LEU PHE VAL VAL SER LEU SEQRES 11 A 288 THR THR SER LYS PHE SER SER VAL ARG ASN GLN PHE TRP SEQRES 12 A 288 PHE SER GLY ALA MET MET ILE ILE THR GLY TYR ILE GLY SEQRES 13 A 288 GLN PHE TYR GLU VAL SER ASN LEU THR ALA PHE LEU VAL SEQRES 14 A 288 TRP GLY ALA ILE SER SER ALA PHE PHE PHE HIS ILE LEU SEQRES 15 A 288 TRP VAL MET LYS LYS VAL ILE ASN GLU GLY LYS GLU GLY SEQRES 16 A 288 ILE SER PRO ALA GLY GLN LYS ILE LEU SER ASN ILE TRP SEQRES 17 A 288 ILE LEU PHE LEU ILE SER TRP THR LEU TYR PRO GLY ALA SEQRES 18 A 288 TYR LEU MET PRO TYR LEU THR GLY VAL ASP GLY PHE LEU SEQRES 19 A 288 TYR SER GLU ASP GLY VAL MET ALA ARG GLN LEU VAL TYR SEQRES 20 A 288 THR ILE ALA ASP VAL SER SER LYS VAL ILE TYR GLY VAL SEQRES 21 A 288 LEU LEU PHE ASN LEU ALA ILE THR LEU SER LYS ASN LYS SEQRES 22 A 288 GLU LEU VAL GLU ALA ASN SER LEU GLU HIS HIS HIS HIS SEQRES 23 A 288 HIS HIS HET NA A 301 1 HET LFA A 302 16 HET LFA A 303 9 HET LFA A 304 6 HET LFA A 305 5 HET LFA A 306 13 HET LFA A 307 8 HET LFA A 308 8 HET LFA A 309 12 HET LFA A 310 10 HET LFA A 311 5 HET LFA A 312 5 HET LFA A 313 11 HET LFA A 314 12 HET LFA A 315 10 HET LFA A 316 6 HET LFA A 317 5 HET LFA A 318 6 HET LFA A 319 6 HET LFA A 320 10 HET LFA A 321 7 HET LFA A 322 5 HET LFA A 323 11 HET LFA A 324 4 HET LFA A 325 5 HET LFA A 326 10 HET LFA A 327 12 HET OLC A 328 25 HET OLC A 329 25 HET OLC A 330 12 HET GOL A 331 6 HET GOL A 332 6 HET GOL A 333 6 HET LFA A 334 14 HET LFA A 335 18 HET LFA A 336 8 HET RET A 337 20 HETNAM NA SODIUM ION HETNAM LFA EICOSANE HETNAM OLC (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETNAM GOL GLYCEROL HETNAM RET RETINAL HETSYN LFA LIPID FRAGMENT HETSYN OLC 1-OLEOYL-R-GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NA NA 1+ FORMUL 3 LFA 29(C20 H42) FORMUL 29 OLC 3(C21 H40 O4) FORMUL 32 GOL 3(C3 H8 O3) FORMUL 38 RET C20 H28 O FORMUL 39 HOH *54(H2 O) HELIX 1 AA1 ASN A 9 THR A 17 1 9 HELIX 2 AA2 SER A 21 THR A 49 1 29 HELIX 3 AA3 ILE A 50 VAL A 53 5 4 HELIX 4 AA4 ASP A 54 LYS A 56 5 3 HELIX 5 AA5 PHE A 57 SER A 85 1 29 HELIX 6 AA6 ASN A 106 ILE A 124 1 19 HELIX 7 AA7 LEU A 125 VAL A 127 5 3 HELIX 8 AA8 LYS A 134 TYR A 159 1 26 HELIX 9 AA9 ASN A 163 GLU A 194 1 32 HELIX 10 AB1 SER A 197 MET A 224 1 28 HELIX 11 AB2 PRO A 225 LEU A 227 5 3 HELIX 12 AB3 SER A 236 LYS A 271 1 36 SHEET 1 AA1 2 PHE A 86 ASN A 89 0 SHEET 2 AA1 2 ARG A 94 LEU A 97 -1 O ARG A 94 N ASN A 89 LINK NZ LYS A 255 C15 RET A 337 1555 1555 1.44 LINK OH TYR A 25 NA NA A 301 1555 1555 2.54 LINK O THR A 83 NA NA A 301 1555 1555 2.29 LINK O PHE A 86 NA NA A 301 1555 1555 2.29 LINK NA NA A 301 O HOH A 438 1555 1555 2.17 LINK NA NA A 301 O HOH A 448 1555 1555 2.68 LINK NA NA A 301 O HOH A 449 1555 1555 2.32 SITE 1 AC1 6 TYR A 25 THR A 83 PHE A 86 HOH A 438 SITE 2 AC1 6 HOH A 448 HOH A 449 SITE 1 AC2 2 ASN A 264 LFA A 313 SITE 1 AC3 3 ASN A 163 VAL A 169 TRP A 170 SITE 1 AC4 3 ILE A 257 LFA A 320 LFA A 324 SITE 1 AC5 2 ASN A 105 TYR A 108 SITE 1 AC6 1 VAL A 230 SITE 1 AC7 1 ASN A 140 SITE 1 AC8 3 ASN A 206 ILE A 213 SER A 253 SITE 1 AC9 1 LFA A 323 SITE 1 AD1 2 LFA A 312 GOL A 332 SITE 1 AD2 2 ALA A 37 LFA A 311 SITE 1 AD3 1 LFA A 302 SITE 1 AD4 1 LFA A 316 SITE 1 AD5 2 LYS A 51 LFA A 319 SITE 1 AD6 2 LFA A 314 HOH A 408 SITE 1 AD7 2 MET A 59 LFA A 326 SITE 1 AD8 1 HIS A 30 SITE 1 AD9 4 PHE A 122 PHE A 135 ARG A 139 LFA A 315 SITE 1 AE1 1 LFA A 304 SITE 1 AE2 1 GLY A 229 SITE 1 AE3 2 GLY A 220 LFA A 310 SITE 1 AE4 1 LFA A 304 SITE 1 AE5 2 TRP A 143 LFA A 317 SITE 1 AE6 1 LFA A 334 SITE 1 AE7 3 ASN A 264 THR A 268 HOH A 412 SITE 1 AE8 6 ASN A 163 LEU A 164 THR A 165 LEU A 168 SITE 2 AE8 6 GLY A 171 SER A 175 SITE 1 AE9 3 PHE A 233 GLU A 237 ASP A 238 SITE 1 AF1 4 PHE A 13 THR A 17 GLU A 18 TYR A 235 SITE 1 AF2 5 TYR A 36 TYR A 76 GLN A 80 LFA A 311 SITE 2 AF2 5 HOH A 405 SITE 1 AF3 5 GLN A 3 LEU A 5 ALA A 16 PHE A 96 SITE 2 AF3 5 LEU A 97 SITE 1 AF4 3 PHE A 72 TYR A 76 LFA A 327 SITE 1 AF5 4 PHE A 179 HIS A 180 TRP A 183 LYS A 186 SITE 1 AF6 10 TRP A 113 LEU A 120 MET A 149 SER A 174 SITE 2 AF6 10 PHE A 178 TRP A 215 TYR A 218 TYR A 222 SITE 3 AF6 10 SER A 254 LYS A 255 CRYST1 40.769 81.964 232.930 90.00 90.00 90.00 I 2 2 2 8 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 0.024528 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012200 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004293 0.00000