HEADER MEMBRANE PROTEIN 18-MAR-20 6YBY TITLE CRYSTAL STRUCTURE OF THE D116N MUTANT OF THE LIGHT-DRIVEN SODIUM PUMP TITLE 2 KR2 IN THE MONOMERIC FORM, PH 4.6 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 RHODOPSIN, ION PUMPING, RETINAL, SODIUM PUMP, INTERMEDIATE STATE, KEYWDS 2 MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.KOVALEV,I.GUSHCHIN,V.GORDELIY REVDAT 3 24-JAN-24 6YBY 1 LINK REVDAT 2 13-MAY-20 6YBY 1 JRNL REVDAT 1 08-APR-20 6YBY 0 JRNL AUTH K.KOVALEV,R.ASTASHKIN,I.GUSHCHIN,P.OREKHOV,D.VOLKOV, JRNL AUTH 2 E.ZINOVEV,E.MARIN,M.RULEV,A.ALEKSEEV,A.ROYANT,P.CARPENTIER, JRNL AUTH 3 S.VAGANOVA,D.ZABELSKII,C.BAEKEN,I.SERGEEV,T.BALANDIN, JRNL AUTH 4 G.BOURENKOV,X.CARPENA,R.BOER,N.MALIAR,V.BORSHCHEVSKIY, JRNL AUTH 5 G.BULDT,E.BAMBERG,V.GORDELIY JRNL TITL MOLECULAR MECHANISM OF LIGHT-DRIVEN SODIUM PUMPING. JRNL REF NAT COMMUN V. 11 2137 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32358514 JRNL DOI 10.1038/S41467-020-16032-Y REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0257 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 35822 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1921 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2597 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.4340 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.4530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2127 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 289 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : -0.66000 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): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.571 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2585 ; 0.003 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2709 ; 0.000 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3418 ; 1.068 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6246 ; 1.097 ; 1.542 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 304 ; 4.729 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 111 ;29.118 ;21.261 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 368 ;12.954 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;27.804 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 307 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2655 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 552 ; 0.000 ; 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 6YBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37771 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 (%): 61.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M NAMAL PH 4.6, LIPIDIC CUBIC PHASE, REMARK 280 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 20.44350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.80050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 116.91500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.44350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.80050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 116.91500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.44350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.80050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 116.91500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.44350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.80050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 116.91500 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: 11720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 164.0 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 429 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 444 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 508 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 LYS A 271 REMARK 465 GLU A 274 REMARK 465 LEU A 275 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 GLU A 91 CG CD 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 470 LYS A 273 CG CD CE NZ 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 OE1 GLN A 58 O HOH A 401 1.86 REMARK 500 O HOH A 505 O HOH A 512 2.11 REMARK 500 O HOH A 468 O HOH A 541 2.12 REMARK 500 O HOH A 430 O HOH A 502 2.14 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 O HOH A 546 O HOH A 549 8555 2.14 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 17 -83.08 -107.97 REMARK 500 LEU A 103 155.73 75.98 REMARK 500 THR A 131 -78.31 -116.02 REMARK 500 ASN A 163 88.83 -151.82 REMARK 500 SER A 236 -177.96 179.71 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 LFA A 328 REMARK 610 LFA A 329 REMARK 610 LFA A 330 REMARK 610 LFA A 331 REMARK 610 LFA A 332 REMARK 610 LFA A 333 REMARK 610 LFA A 334 REMARK 610 LFA A 335 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 85.6 REMARK 620 3 PHE A 86 O 100.8 92.6 REMARK 620 4 HOH A 490 O 90.5 80.6 166.4 REMARK 620 5 HOH A 502 O 167.1 87.8 90.5 77.5 REMARK 620 6 HOH A 518 O 80.8 148.6 117.7 71.4 99.4 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 305 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 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 322 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 325 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 328 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 330 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 331 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 333 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LFA A 335 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RET A 336 DBREF 6YBY A 2 275 UNP N0DKS8 N0DKS8_9FLAO 2 275 SEQADV 6YBY ASN A 116 UNP N0DKS8 ASP 116 ENGINEERED MUTATION SEQRES 1 A 274 THR GLN GLU LEU GLY ASN ALA ASN PHE GLU ASN PHE ILE SEQRES 2 A 274 GLY ALA THR GLU GLY PHE SER GLU ILE ALA TYR GLN PHE SEQRES 3 A 274 THR SER HIS ILE LEU THR LEU GLY TYR ALA VAL MET LEU SEQRES 4 A 274 ALA GLY LEU LEU TYR PHE ILE LEU THR ILE LYS ASN VAL SEQRES 5 A 274 ASP LYS LYS PHE GLN MET SER ASN ILE LEU SER ALA VAL SEQRES 6 A 274 VAL MET VAL SER ALA PHE LEU LEU LEU TYR ALA GLN ALA SEQRES 7 A 274 GLN ASN TRP THR SER SER PHE THR PHE ASN GLU GLU VAL SEQRES 8 A 274 GLY ARG TYR PHE LEU ASP PRO SER GLY ASP LEU PHE ASN SEQRES 9 A 274 ASN GLY TYR ARG TYR LEU ASN TRP LEU ILE ASN VAL PRO SEQRES 10 A 274 MET LEU LEU PHE GLN ILE LEU PHE VAL VAL SER LEU THR SEQRES 11 A 274 THR SER LYS PHE SER SER VAL ARG ASN GLN PHE TRP PHE SEQRES 12 A 274 SER GLY ALA MET MET ILE ILE THR GLY TYR ILE GLY GLN SEQRES 13 A 274 PHE TYR GLU VAL SER ASN LEU THR ALA PHE LEU VAL TRP SEQRES 14 A 274 GLY ALA ILE SER SER ALA PHE PHE PHE HIS ILE LEU TRP SEQRES 15 A 274 VAL MET LYS LYS VAL ILE ASN GLU GLY LYS GLU GLY ILE SEQRES 16 A 274 SER PRO ALA GLY GLN LYS ILE LEU SER ASN ILE TRP ILE SEQRES 17 A 274 LEU PHE LEU ILE SER TRP THR LEU TYR PRO GLY ALA TYR SEQRES 18 A 274 LEU MET PRO TYR LEU THR GLY VAL ASP GLY PHE LEU TYR SEQRES 19 A 274 SER GLU ASP GLY VAL MET ALA ARG GLN LEU VAL TYR THR SEQRES 20 A 274 ILE ALA ASP VAL SER SER LYS VAL ILE TYR GLY VAL LEU SEQRES 21 A 274 LEU GLY ASN LEU ALA ILE THR LEU SER LYS ASN LYS GLU SEQRES 22 A 274 LEU HET NA A 301 1 HET LFA A 302 16 HET LFA A 303 8 HET LFA A 304 9 HET LFA A 305 6 HET LFA A 306 5 HET LFA A 307 13 HET LFA A 308 10 HET LFA A 309 5 HET LFA A 310 8 HET LFA A 311 10 HET LFA A 312 16 HET LFA A 313 5 HET LFA A 314 10 HET LFA A 315 4 HET LFA A 316 5 HET LFA A 317 11 HET LFA A 318 12 HET LFA A 319 10 HET LFA A 320 6 HET LFA A 321 5 HET LFA A 322 6 HET LFA A 323 4 HET LFA A 324 6 HET LFA A 325 6 HET LFA A 326 10 HET LFA A 327 7 HET LFA A 328 3 HET LFA A 329 5 HET LFA A 330 11 HET LFA A 331 4 HET LFA A 332 5 HET LFA A 333 10 HET LFA A 334 7 HET LFA A 335 10 HET RET A 336 40 HETNAM NA SODIUM ION HETNAM LFA EICOSANE HETNAM RET RETINAL HETSYN LFA LIPID FRAGMENT FORMUL 2 NA NA 1+ FORMUL 3 LFA 34(C20 H42) FORMUL 37 RET C20 H28 O FORMUL 38 HOH *151(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 GLY A 195 1 33 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 SER A 270 1 35 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 ALYS A 255 C15ARET A 336 1555 1555 1.45 LINK NZ BLYS A 255 C15BRET A 336 1555 1555 1.46 LINK OH TYR A 25 NA NA A 301 1555 1555 2.65 LINK O THR A 83 NA NA A 301 1555 1555 2.23 LINK O PHE A 86 NA NA A 301 1555 1555 2.33 LINK NA NA A 301 O HOH A 490 1555 1555 2.43 LINK NA NA A 301 O HOH A 502 1555 1555 2.26 LINK NA NA A 301 O HOH A 518 1555 1555 2.45 SITE 1 AC1 6 TYR A 25 THR A 83 PHE A 86 HOH A 490 SITE 2 AC1 6 HOH A 502 HOH A 518 SITE 1 AC2 3 ALA A 41 TYR A 45 LFA A 317 SITE 1 AC3 1 TYR A 76 SITE 1 AC4 3 ASN A 163 VAL A 169 TRP A 170 SITE 1 AC5 2 ILE A 257 LFA A 326 SITE 1 AC6 3 ASN A 105 TYR A 108 TYR A 154 SITE 1 AC7 3 ALA A 41 LFA A 317 LFA A 328 SITE 1 AC8 1 TYR A 226 SITE 1 AC9 1 ASN A 140 SITE 1 AD1 4 ASN A 206 ILE A 213 SER A 253 LFA A 326 SITE 1 AD2 3 LEU A 168 GLY A 171 SER A 175 SITE 1 AD3 3 SER A 175 PHE A 179 LFA A 330 SITE 1 AD4 3 ALA A 37 LFA A 316 LFA A 322 SITE 1 AD5 2 ALA A 37 LFA A 315 SITE 1 AD6 2 LFA A 302 LFA A 308 SITE 1 AD7 1 LFA A 320 SITE 1 AD8 4 MET A 59 PHE A 122 LFA A 325 HOH A 451 SITE 1 AD9 4 GLN A 141 PHE A 177 LFA A 318 HOH A 421 SITE 1 AE1 1 MET A 59 SITE 1 AE2 2 HIS A 30 LFA A 315 SITE 1 AE3 2 GLN A 80 HOH A 538 SITE 1 AE4 4 PHE A 122 PHE A 135 ARG A 139 LFA A 319 SITE 1 AE5 2 LFA A 305 LFA A 311 SITE 1 AE6 3 LEU A 48 MET A 59 LFA A 308 SITE 1 AE7 3 THR A 216 GLY A 220 LFA A 314 SITE 1 AE8 1 LFA A 332 SITE 1 AE9 1 LFA A 331 SITE 1 AF1 2 MET A 119 TRP A 143 SITE 1 AF2 1 LEU A 74 SITE 1 AF3 1 THR A 165 SITE 1 AF4 11 TRP A 113 LEU A 120 MET A 149 GLY A 171 SITE 2 AF4 11 SER A 174 SER A 175 PHE A 178 TYR A 218 SITE 3 AF4 11 TYR A 222 SER A 254 LYS A 255 CRYST1 40.887 83.601 233.830 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 0.024458 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004277 0.00000