HEADER ISOMERASE, HYDROLASE 09-MAY-12 4F3A TITLE STRUCTURE OF RPE65: P6522 CRYSTAL FORM, IRIDIUM DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOID ISOMEROHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RPE65, RETINOID ISOMERASE, ALL-TRANS-RETINYL-PALMITATE COMPND 5 HYDROLASE, RETINAL PIGMENT EPITHELIUM-SPECIFIC 65 KDA PROTEIN, COMPND 6 RETINOL ISOMERASE; COMPND 7 EC: 3.1.1.64 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 TISSUE: RETINA KEYWDS MONOTOPIC MEMBRANE PROTEIN, METALLOPROTEIN, NON-HEME IRON PROTEIN, KEYWDS 2 BETA-PROPELLER, SMOOTH ER MEMBRANE, ISOMERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.D.KISER,K.PALCZEWSKI REVDAT 4 28-FEB-24 4F3A 1 REMARK SEQADV LINK REVDAT 3 15-NOV-17 4F3A 1 REMARK REVDAT 2 02-JUL-14 4F3A 1 JRNL REVDAT 1 03-OCT-12 4F3A 0 JRNL AUTH P.D.KISER,E.R.FARQUHAR,W.SHI,X.SUI,M.R.CHANCE,K.PALCZEWSKI JRNL TITL STRUCTURE OF RPE65 ISOMERASE IN A LIPIDIC MATRIX REVEALS JRNL TITL 2 ROLES FOR PHOSPHOLIPIDS AND IRON IN CATALYSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 E2747 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23012475 JRNL DOI 10.1073/PNAS.1212025109 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0025 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 23925 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1261 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1518 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4159 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.17000 REMARK 3 B12 (A**2) : 0.06000 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): 0.398 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.258 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.024 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4282 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3981 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5833 ; 1.354 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9184 ; 0.732 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 513 ; 6.977 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;34.236 ;24.265 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 688 ;13.961 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.883 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 632 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4832 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1013 ; 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): 1 ;25.189 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1 ;11.236 ; 5.000 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4F3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-08 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 : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0952 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL REMARK 200 SAGITTAL FOCUSING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25186 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.89800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11% PEG3350, PH 8, CRYSTAL SOAKED IN 1 REMARK 280 MM IRIDIUM HEXACHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 57.64600 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 28.82300 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 43.23450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.41150 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 72.05750 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.64600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 28.82300 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 14.41150 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 43.23450 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 72.05750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -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 43.23450 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 IR IR3 A 601 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 841 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 SER A 2 REMARK 465 SER A 3 REMARK 465 ASP A 110 REMARK 465 PRO A 111 REMARK 465 CYS A 112 REMARK 465 LYS A 113 REMARK 465 ASN A 114 REMARK 465 ILE A 115 REMARK 465 PHE A 116 REMARK 465 SER A 117 REMARK 465 ARG A 118 REMARK 465 PHE A 119 REMARK 465 PHE A 120 REMARK 465 SER A 121 REMARK 465 TYR A 122 REMARK 465 PHE A 123 REMARK 465 ARG A 124 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 GLU A 74 62.05 36.39 REMARK 500 LYS A 96 18.88 58.04 REMARK 500 ASN A 131 91.82 -67.31 REMARK 500 THR A 147 -130.15 -121.57 REMARK 500 ASP A 215 -24.87 -37.76 REMARK 500 LEU A 270 -82.51 -82.16 REMARK 500 TRP A 271 -99.57 -83.73 REMARK 500 HIS A 321 -131.40 53.02 REMARK 500 GLU A 322 40.91 -94.77 REMARK 500 ASN A 373 77.15 -103.55 REMARK 500 ASP A 398 -34.99 -9.25 REMARK 500 GLU A 399 -1.82 81.82 REMARK 500 THR A 432 -34.21 -130.25 REMARK 500 PHE A 442 -7.30 73.90 REMARK 500 LYS A 455 7.74 83.24 REMARK 500 PHE A 526 -63.59 -101.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 397 ASP A 398 143.34 REMARK 500 REMARK 500 REMARK: NULL 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 FE2 A 602 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 180 NE2 REMARK 620 2 HIS A 241 NE2 99.2 REMARK 620 3 HIS A 313 NE2 102.8 95.0 REMARK 620 4 HIS A 527 NE2 86.0 162.1 100.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IR3 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FSN RELATED DB: PDB REMARK 900 RELATED ID: 4F2Z RELATED DB: PDB REMARK 900 RELATED ID: 4F30 RELATED DB: PDB REMARK 900 RELATED ID: 4F3D RELATED DB: PDB DBREF 4F3A A 1 533 UNP Q28175 RPE65_BOVIN 1 533 SEQADV 4F3A LEU A 341 UNP Q28175 SER 341 CONFLICT SEQRES 1 A 533 MET SER SER GLN VAL GLU HIS PRO ALA GLY GLY TYR LYS SEQRES 2 A 533 LYS LEU PHE GLU THR VAL GLU GLU LEU SER SER PRO LEU SEQRES 3 A 533 THR ALA HIS VAL THR GLY ARG ILE PRO LEU TRP LEU THR SEQRES 4 A 533 GLY SER LEU LEU ARG CYS GLY PRO GLY LEU PHE GLU VAL SEQRES 5 A 533 GLY SER GLU PRO PHE TYR HIS LEU PHE ASP GLY GLN ALA SEQRES 6 A 533 LEU LEU HIS LYS PHE ASP PHE LYS GLU GLY HIS VAL THR SEQRES 7 A 533 TYR HIS ARG ARG PHE ILE ARG THR ASP ALA TYR VAL ARG SEQRES 8 A 533 ALA MET THR GLU LYS ARG ILE VAL ILE THR GLU PHE GLY SEQRES 9 A 533 THR CYS ALA PHE PRO ASP PRO CYS LYS ASN ILE PHE SER SEQRES 10 A 533 ARG PHE PHE SER TYR PHE ARG GLY VAL GLU VAL THR ASP SEQRES 11 A 533 ASN ALA LEU VAL ASN ILE TYR PRO VAL GLY GLU ASP TYR SEQRES 12 A 533 TYR ALA CYS THR GLU THR ASN PHE ILE THR LYS VAL ASN SEQRES 13 A 533 PRO GLU THR LEU GLU THR ILE LYS GLN VAL ASP LEU CYS SEQRES 14 A 533 ASN TYR VAL SER VAL ASN GLY ALA THR ALA HIS PRO HIS SEQRES 15 A 533 ILE GLU ASN ASP GLY THR VAL TYR ASN ILE GLY ASN CYS SEQRES 16 A 533 PHE GLY LYS ASN PHE SER ILE ALA TYR ASN ILE VAL LYS SEQRES 17 A 533 ILE PRO PRO LEU GLN ALA ASP LYS GLU ASP PRO ILE SER SEQRES 18 A 533 LYS SER GLU ILE VAL VAL GLN PHE PRO CYS SER ASP ARG SEQRES 19 A 533 PHE LYS PRO SER TYR VAL HIS SER PHE GLY LEU THR PRO SEQRES 20 A 533 ASN TYR ILE VAL PHE VAL GLU THR PRO VAL LYS ILE ASN SEQRES 21 A 533 LEU PHE LYS PHE LEU SER SER TRP SER LEU TRP GLY ALA SEQRES 22 A 533 ASN TYR MET ASP CYS PHE GLU SER ASN GLU THR MET GLY SEQRES 23 A 533 VAL TRP LEU HIS ILE ALA ASP LYS LYS ARG LYS LYS TYR SEQRES 24 A 533 ILE ASN ASN LYS TYR ARG THR SER PRO PHE ASN LEU PHE SEQRES 25 A 533 HIS HIS ILE ASN THR TYR GLU ASP HIS GLU PHE LEU ILE SEQRES 26 A 533 VAL ASP LEU CYS CYS TRP LYS GLY PHE GLU PHE VAL TYR SEQRES 27 A 533 ASN TYR LEU TYR LEU ALA ASN LEU ARG GLU ASN TRP GLU SEQRES 28 A 533 GLU VAL LYS LYS ASN ALA ARG LYS ALA PRO GLN PRO GLU SEQRES 29 A 533 VAL ARG ARG TYR VAL LEU PRO LEU ASN ILE ASP LYS ALA SEQRES 30 A 533 ASP THR GLY LYS ASN LEU VAL THR LEU PRO ASN THR THR SEQRES 31 A 533 ALA THR ALA ILE LEU CYS SER ASP GLU THR ILE TRP LEU SEQRES 32 A 533 GLU PRO GLU VAL LEU PHE SER GLY PRO ARG GLN ALA PHE SEQRES 33 A 533 GLU PHE PRO GLN ILE ASN TYR GLN LYS TYR GLY GLY LYS SEQRES 34 A 533 PRO TYR THR TYR ALA TYR GLY LEU GLY LEU ASN HIS PHE SEQRES 35 A 533 VAL PRO ASP ARG LEU CYS LYS LEU ASN VAL LYS THR LYS SEQRES 36 A 533 GLU THR TRP VAL TRP GLN GLU PRO ASP SER TYR PRO SER SEQRES 37 A 533 GLU PRO ILE PHE VAL SER HIS PRO ASP ALA LEU GLU GLU SEQRES 38 A 533 ASP ASP GLY VAL VAL LEU SER VAL VAL VAL SER PRO GLY SEQRES 39 A 533 ALA GLY GLN LYS PRO ALA TYR LEU LEU ILE LEU ASN ALA SEQRES 40 A 533 LYS ASP LEU SER GLU VAL ALA ARG ALA GLU VAL GLU ILE SEQRES 41 A 533 ASN ILE PRO VAL THR PHE HIS GLY LEU PHE LYS LYS SER HET IR3 A 601 1 HET FE2 A 602 1 HETNAM IR3 IRIDIUM (III) ION HETNAM FE2 FE (II) ION FORMUL 2 IR3 IR 3+ FORMUL 3 FE2 FE 2+ FORMUL 4 HOH *165(H2 O) HELIX 1 1 GLY A 10 GLU A 17 5 8 HELIX 2 2 THR A 86 GLU A 95 1 10 HELIX 3 3 ASP A 218 SER A 223 5 6 HELIX 4 4 ASN A 260 TRP A 268 1 9 HELIX 5 5 TYR A 275 ASP A 277 5 3 HELIX 6 6 PHE A 336 LEU A 341 5 6 HELIX 7 7 TYR A 342 GLU A 348 1 7 HELIX 8 8 ASN A 349 ARG A 358 1 10 HELIX 9 9 ASP A 375 THR A 379 5 5 HELIX 10 10 ASN A 422 GLY A 427 1 6 SHEET 1 A 5 LEU A 26 THR A 27 0 SHEET 2 A 5 HIS A 76 PHE A 83 -1 O TYR A 79 N LEU A 26 SHEET 3 A 5 GLN A 64 LYS A 73 -1 N LYS A 69 O HIS A 80 SHEET 4 A 5 GLY A 40 LEU A 49 -1 N ARG A 44 O HIS A 68 SHEET 5 A 5 HIS A 527 LYS A 532 -1 O LYS A 531 N SER A 41 SHEET 1 B 5 HIS A 29 GLY A 32 0 SHEET 2 B 5 GLU A 512 VAL A 518 -1 O GLU A 517 N HIS A 29 SHEET 3 B 5 ALA A 500 ASN A 506 -1 N ILE A 504 O VAL A 513 SHEET 4 B 5 GLY A 484 VAL A 491 -1 N SER A 488 O LEU A 503 SHEET 5 B 5 ILE A 471 SER A 474 -1 N ILE A 471 O LEU A 487 SHEET 1 C 2 GLU A 51 VAL A 52 0 SHEET 2 C 2 GLU A 55 PRO A 56 -1 O GLU A 55 N VAL A 52 SHEET 1 D 4 ASN A 135 VAL A 139 0 SHEET 2 D 4 ASP A 142 CYS A 146 -1 O TYR A 144 N TYR A 137 SHEET 3 D 4 PHE A 151 VAL A 155 -1 O THR A 153 N ALA A 145 SHEET 4 D 4 THR A 162 ASP A 167 -1 O VAL A 166 N ILE A 152 SHEET 1 E 4 HIS A 182 ILE A 183 0 SHEET 2 E 4 VAL A 189 PHE A 196 -1 O TYR A 190 N HIS A 182 SHEET 3 E 4 ILE A 202 ILE A 209 -1 O ILE A 209 N VAL A 189 SHEET 4 E 4 GLU A 224 PRO A 230 -1 O PHE A 229 N TYR A 204 SHEET 1 F 6 GLY A 244 LEU A 245 0 SHEET 2 F 6 TYR A 249 GLU A 254 -1 O VAL A 251 N GLY A 244 SHEET 3 F 6 VAL A 287 ASP A 293 -1 O HIS A 290 N PHE A 252 SHEET 4 F 6 LYS A 298 THR A 306 -1 O LYS A 298 N ASP A 293 SHEET 5 F 6 THR A 400 GLU A 404 1 O ILE A 401 N LYS A 303 SHEET 6 F 6 THR A 392 LEU A 395 -1 N ILE A 394 O TRP A 402 SHEET 1 G 2 VAL A 257 ILE A 259 0 SHEET 2 G 2 PHE A 279 SER A 281 -1 O GLU A 280 N LYS A 258 SHEET 1 H 4 PHE A 309 ASP A 320 0 SHEET 2 H 4 PHE A 323 LYS A 332 -1 O ILE A 325 N TYR A 318 SHEET 3 H 4 GLN A 362 PRO A 371 -1 O TYR A 368 N VAL A 326 SHEET 4 H 4 GLU A 406 SER A 410 -1 O LEU A 408 N VAL A 365 SHEET 1 I 4 GLN A 414 GLN A 420 0 SHEET 2 I 4 TYR A 433 ASN A 440 -1 O LEU A 437 N GLU A 417 SHEET 3 I 4 VAL A 443 ASN A 451 -1 O VAL A 443 N ASN A 440 SHEET 4 I 4 THR A 457 TRP A 460 -1 O TRP A 460 N LEU A 447 LINK NE2 HIS A 180 FE FE2 A 602 1555 1555 2.19 LINK NE2 HIS A 241 FE FE2 A 602 1555 1555 2.23 LINK NE2 HIS A 313 FE FE2 A 602 1555 1555 2.25 LINK NE2 HIS A 527 FE FE2 A 602 1555 1555 2.15 SITE 1 AC1 1 HOH A 861 SITE 1 AC2 4 HIS A 180 HIS A 241 HIS A 313 HIS A 527 CRYST1 178.639 178.639 86.469 90.00 90.00 120.00 P 65 2 2 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 0.005598 0.003232 0.000000 0.00000 SCALE2 0.000000 0.006464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011565 0.00000