HEADER ISOMERASE 07-NOV-14 4RSE TITLE CRYSTAL STRUCTURE OF RPE65 IN COMPLEX WITH MB-001 AND PALMITATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOID ISOMEROHYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALL-TRANS-RETINYL-PALMITATE HYDROLASE, RETINAL PIGMENT COMPND 5 EPITHELIUM-SPECIFIC 65 KDA PROTEIN, RETINOL ISOMERASE; COMPND 6 EC: 3.1.1.64 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS 7-BLADED BETA PROPELLER, MONOTOPIC MEMBRANE PROTEIN, NON-HEME IRON KEYWDS 2 ENZYME, SMOOTH ENDOPLASMIC RETICULUM, RETINOID ISOMERASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.D.KISER,W.SHI,K.PALCZEWSKI REVDAT 3 20-SEP-23 4RSE 1 REMARK SEQADV LINK REVDAT 2 03-JUN-15 4RSE 1 JRNL REVDAT 1 15-APR-15 4RSE 0 JRNL AUTH P.D.KISER,J.ZHANG,M.BADIEE,Q.LI,W.SHI,X.SUI,M.GOLCZAK, JRNL AUTH 2 G.P.TOCHTROP,K.PALCZEWSKI JRNL TITL CATALYTIC MECHANISM OF A RETINOID ISOMERASE ESSENTIAL FOR JRNL TITL 2 VERTEBRATE VISION. JRNL REF NAT.CHEM.BIOL. V. 11 409 2015 JRNL REFN ISSN 1552-4450 JRNL PMID 25894083 JRNL DOI 10.1038/NCHEMBIO.1799 REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 56801 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3079 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) : 2.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3741 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE SET COUNT : 215 REMARK 3 BIN FREE R VALUE : 0.4160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 401 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -1.75000 REMARK 3 B12 (A**2) : 0.27000 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): 0.304 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.226 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.221 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.598 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8625 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 8050 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11744 ; 1.398 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18576 ; 0.979 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1024 ; 6.939 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 410 ;34.122 ;24.098 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1374 ;13.885 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;17.243 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1265 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9786 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 2032 ; 0.003 ; 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): 4103 ; 2.430 ; 4.560 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4102 ; 2.429 ; 4.560 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5126 ; 3.975 ; 6.831 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 5127 ; 3.975 ; 6.831 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4522 ; 2.555 ; 4.864 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4523 ; 2.555 ; 4.864 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 6619 ; 4.197 ; 7.175 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9482 ; 6.600 ;84.769 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9371 ; 6.558 ;85.265 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): 2 ;18.333 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 533 B 2 533 61796 0.04 0.05 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 : 1.10 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 REMARK 4 REMARK 4 4RSE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 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) : 1.0750 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: REFMAC REMARK 200 STARTING MODEL: 3FSN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 300 200 MM NACL 100 MM CHES REMARK 280 -NAOH, PH 9.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 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 57.74067 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 28.87033 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 43.30550 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 14.43517 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 72.17583 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: 5330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 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 465 GLY A 125 REMARK 465 VAL A 126 REMARK 465 GLY A 197 REMARK 465 LYS A 198 REMARK 465 ASN A 199 REMARK 465 PHE A 200 REMARK 465 SER A 201 REMARK 465 ASP B 110 REMARK 465 PRO B 111 REMARK 465 CYS B 112 REMARK 465 LYS B 113 REMARK 465 ASN B 114 REMARK 465 ILE B 115 REMARK 465 PHE B 116 REMARK 465 SER B 117 REMARK 465 ARG B 118 REMARK 465 PHE B 119 REMARK 465 PHE B 120 REMARK 465 SER B 121 REMARK 465 TYR B 122 REMARK 465 PHE B 123 REMARK 465 ARG B 124 REMARK 465 GLY B 125 REMARK 465 VAL B 126 REMARK 465 GLY B 197 REMARK 465 LYS B 198 REMARK 465 ASN B 199 REMARK 465 PHE B 200 REMARK 465 SER B 201 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 131 94.46 -65.57 REMARK 500 THR A 147 -131.81 -108.82 REMARK 500 HIS A 321 -131.95 49.07 REMARK 500 GLU A 322 42.68 -95.88 REMARK 500 THR A 432 -31.49 -131.86 REMARK 500 PHE A 442 -12.95 76.18 REMARK 500 PHE A 526 -73.32 -100.27 REMARK 500 ASN B 131 93.62 -66.46 REMARK 500 THR B 147 -134.22 -111.30 REMARK 500 HIS B 321 -130.68 49.86 REMARK 500 GLU B 322 46.98 -98.04 REMARK 500 THR B 432 -31.99 -132.19 REMARK 500 PHE B 442 -15.51 78.30 REMARK 500 PHE B 526 -68.42 -100.18 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 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 180 NE2 REMARK 620 2 HIS A 241 NE2 96.8 REMARK 620 3 HIS A 313 NE2 100.5 91.5 REMARK 620 4 HIS A 527 NE2 89.7 171.1 93.3 REMARK 620 5 PLM A 602 O2 130.8 86.2 128.6 84.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 180 NE2 REMARK 620 2 HIS B 241 NE2 95.6 REMARK 620 3 HIS B 313 NE2 99.1 94.7 REMARK 620 4 HIS B 527 NE2 85.8 171.2 93.7 REMARK 620 5 PLM B 602 O1 119.1 85.1 141.7 86.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A6V A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A6V B 603 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: 4RSC RELATED DB: PDB DBREF 4RSE A 2 533 UNP Q28175 RPE65_BOVIN 2 533 DBREF 4RSE B 2 533 UNP Q28175 RPE65_BOVIN 2 533 SEQADV 4RSE ACE A 1 UNP Q28175 EXPRESSION TAG SEQADV 4RSE LEU A 341 UNP Q28175 SER 341 CONFLICT SEQADV 4RSE ACE B 1 UNP Q28175 EXPRESSION TAG SEQADV 4RSE LEU B 341 UNP Q28175 SER 341 CONFLICT SEQRES 1 A 533 ACE 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 SEQRES 1 B 533 ACE SER SER GLN VAL GLU HIS PRO ALA GLY GLY TYR LYS SEQRES 2 B 533 LYS LEU PHE GLU THR VAL GLU GLU LEU SER SER PRO LEU SEQRES 3 B 533 THR ALA HIS VAL THR GLY ARG ILE PRO LEU TRP LEU THR SEQRES 4 B 533 GLY SER LEU LEU ARG CYS GLY PRO GLY LEU PHE GLU VAL SEQRES 5 B 533 GLY SER GLU PRO PHE TYR HIS LEU PHE ASP GLY GLN ALA SEQRES 6 B 533 LEU LEU HIS LYS PHE ASP PHE LYS GLU GLY HIS VAL THR SEQRES 7 B 533 TYR HIS ARG ARG PHE ILE ARG THR ASP ALA TYR VAL ARG SEQRES 8 B 533 ALA MET THR GLU LYS ARG ILE VAL ILE THR GLU PHE GLY SEQRES 9 B 533 THR CYS ALA PHE PRO ASP PRO CYS LYS ASN ILE PHE SER SEQRES 10 B 533 ARG PHE PHE SER TYR PHE ARG GLY VAL GLU VAL THR ASP SEQRES 11 B 533 ASN ALA LEU VAL ASN ILE TYR PRO VAL GLY GLU ASP TYR SEQRES 12 B 533 TYR ALA CYS THR GLU THR ASN PHE ILE THR LYS VAL ASN SEQRES 13 B 533 PRO GLU THR LEU GLU THR ILE LYS GLN VAL ASP LEU CYS SEQRES 14 B 533 ASN TYR VAL SER VAL ASN GLY ALA THR ALA HIS PRO HIS SEQRES 15 B 533 ILE GLU ASN ASP GLY THR VAL TYR ASN ILE GLY ASN CYS SEQRES 16 B 533 PHE GLY LYS ASN PHE SER ILE ALA TYR ASN ILE VAL LYS SEQRES 17 B 533 ILE PRO PRO LEU GLN ALA ASP LYS GLU ASP PRO ILE SER SEQRES 18 B 533 LYS SER GLU ILE VAL VAL GLN PHE PRO CYS SER ASP ARG SEQRES 19 B 533 PHE LYS PRO SER TYR VAL HIS SER PHE GLY LEU THR PRO SEQRES 20 B 533 ASN TYR ILE VAL PHE VAL GLU THR PRO VAL LYS ILE ASN SEQRES 21 B 533 LEU PHE LYS PHE LEU SER SER TRP SER LEU TRP GLY ALA SEQRES 22 B 533 ASN TYR MET ASP CYS PHE GLU SER ASN GLU THR MET GLY SEQRES 23 B 533 VAL TRP LEU HIS ILE ALA ASP LYS LYS ARG LYS LYS TYR SEQRES 24 B 533 ILE ASN ASN LYS TYR ARG THR SER PRO PHE ASN LEU PHE SEQRES 25 B 533 HIS HIS ILE ASN THR TYR GLU ASP HIS GLU PHE LEU ILE SEQRES 26 B 533 VAL ASP LEU CYS CYS TRP LYS GLY PHE GLU PHE VAL TYR SEQRES 27 B 533 ASN TYR LEU TYR LEU ALA ASN LEU ARG GLU ASN TRP GLU SEQRES 28 B 533 GLU VAL LYS LYS ASN ALA ARG LYS ALA PRO GLN PRO GLU SEQRES 29 B 533 VAL ARG ARG TYR VAL LEU PRO LEU ASN ILE ASP LYS ALA SEQRES 30 B 533 ASP THR GLY LYS ASN LEU VAL THR LEU PRO ASN THR THR SEQRES 31 B 533 ALA THR ALA ILE LEU CYS SER ASP GLU THR ILE TRP LEU SEQRES 32 B 533 GLU PRO GLU VAL LEU PHE SER GLY PRO ARG GLN ALA PHE SEQRES 33 B 533 GLU PHE PRO GLN ILE ASN TYR GLN LYS TYR GLY GLY LYS SEQRES 34 B 533 PRO TYR THR TYR ALA TYR GLY LEU GLY LEU ASN HIS PHE SEQRES 35 B 533 VAL PRO ASP ARG LEU CYS LYS LEU ASN VAL LYS THR LYS SEQRES 36 B 533 GLU THR TRP VAL TRP GLN GLU PRO ASP SER TYR PRO SER SEQRES 37 B 533 GLU PRO ILE PHE VAL SER HIS PRO ASP ALA LEU GLU GLU SEQRES 38 B 533 ASP ASP GLY VAL VAL LEU SER VAL VAL VAL SER PRO GLY SEQRES 39 B 533 ALA GLY GLN LYS PRO ALA TYR LEU LEU ILE LEU ASN ALA SEQRES 40 B 533 LYS ASP LEU SER GLU VAL ALA ARG ALA GLU VAL GLU ILE SEQRES 41 B 533 ASN ILE PRO VAL THR PHE HIS GLY LEU PHE LYS LYS SER HET ACE A 1 3 HET ACE B 1 3 HET FE2 A 601 1 HET PLM A 602 18 HET A6V A 603 22 HET FE2 B 601 1 HET PLM B 602 18 HET A6V B 603 22 HETNAM ACE ACETYL GROUP HETNAM FE2 FE (II) ION HETNAM PLM PALMITIC ACID HETNAM A6V (1R)-3-AMINO-1-{3-[(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL) HETNAM 2 A6V METHOXY]PHENYL}PROPAN-1-OL FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 FE2 2(FE 2+) FORMUL 4 PLM 2(C16 H32 O2) FORMUL 5 A6V 2(C19 H29 N O2) FORMUL 9 HOH *401(H2 O) HELIX 1 1 GLY A 10 GLU A 17 5 8 HELIX 2 2 THR A 86 LYS A 96 1 11 HELIX 3 3 CYS A 169 TYR A 171 5 3 HELIX 4 4 ASP A 218 SER A 223 5 6 HELIX 5 5 ASN A 260 LEU A 265 1 6 HELIX 6 6 SER A 267 GLY A 272 1 6 HELIX 7 7 TYR A 275 ASP A 277 5 3 HELIX 8 8 PHE A 336 LEU A 341 5 6 HELIX 9 9 TYR A 342 ARG A 347 1 6 HELIX 10 10 ASN A 349 ALA A 357 1 9 HELIX 11 11 ASP A 375 THR A 379 5 5 HELIX 12 12 ASN A 422 GLY A 427 1 6 HELIX 13 13 GLY B 10 GLU B 17 5 8 HELIX 14 14 THR B 86 LYS B 96 1 11 HELIX 15 15 CYS B 169 TYR B 171 5 3 HELIX 16 16 ASP B 218 SER B 223 5 6 HELIX 17 17 ASN B 260 SER B 266 1 7 HELIX 18 18 TYR B 275 ASP B 277 5 3 HELIX 19 19 PHE B 336 LEU B 341 5 6 HELIX 20 20 TYR B 342 ARG B 347 1 6 HELIX 21 21 ASN B 349 ARG B 358 1 10 HELIX 22 22 ASP B 375 THR B 379 5 5 HELIX 23 23 ASN B 422 GLY B 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 GLY A 528 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 ARG A 515 N THR A 31 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 VAL A 473 O VAL A 485 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 ASP A 142 N VAL A 139 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 CYS A 195 -1 O TYR A 190 N HIS A 182 SHEET 3 E 4 ALA A 203 ILE A 209 -1 O ILE A 209 N VAL A 189 SHEET 4 E 4 GLU A 224 PRO A 230 -1 O VAL A 227 N ILE A 206 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 TRP A 288 N GLU A 254 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 GLU A 364 N CYS A 330 SHEET 4 H 4 GLU A 406 SER A 410 -1 O GLU A 406 N ARG A 367 SHEET 1 I 4 GLN A 414 GLN A 420 0 SHEET 2 I 4 TYR A 433 ASN A 440 -1 O TYR A 435 N GLN A 420 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 SHEET 1 J 9 ILE B 471 SER B 474 0 SHEET 2 J 9 GLY B 484 VAL B 491 -1 O VAL B 485 N VAL B 473 SHEET 3 J 9 ALA B 500 ASN B 506 -1 O LEU B 503 N SER B 488 SHEET 4 J 9 GLU B 512 VAL B 518 -1 O VAL B 513 N ILE B 504 SHEET 5 J 9 LEU B 26 GLY B 32 -1 N THR B 31 O ARG B 515 SHEET 6 J 9 HIS B 76 PHE B 83 -1 O TYR B 79 N LEU B 26 SHEET 7 J 9 GLN B 64 LYS B 73 -1 N LYS B 69 O HIS B 80 SHEET 8 J 9 GLY B 40 LEU B 49 -1 N ARG B 44 O HIS B 68 SHEET 9 J 9 HIS B 527 LYS B 532 -1 O LEU B 529 N LEU B 43 SHEET 1 K 2 GLU B 51 VAL B 52 0 SHEET 2 K 2 GLU B 55 PRO B 56 -1 O GLU B 55 N VAL B 52 SHEET 1 L 4 ASN B 135 VAL B 139 0 SHEET 2 L 4 ASP B 142 CYS B 146 -1 O ASP B 142 N VAL B 139 SHEET 3 L 4 PHE B 151 VAL B 155 -1 O THR B 153 N ALA B 145 SHEET 4 L 4 THR B 162 ASP B 167 -1 O VAL B 166 N ILE B 152 SHEET 1 M 4 HIS B 182 ILE B 183 0 SHEET 2 M 4 VAL B 189 CYS B 195 -1 O TYR B 190 N HIS B 182 SHEET 3 M 4 ALA B 203 ILE B 209 -1 O ILE B 209 N VAL B 189 SHEET 4 M 4 GLU B 224 PRO B 230 -1 O VAL B 227 N ILE B 206 SHEET 1 N 6 GLY B 244 LEU B 245 0 SHEET 2 N 6 TYR B 249 GLU B 254 -1 O VAL B 251 N GLY B 244 SHEET 3 N 6 VAL B 287 ASP B 293 -1 O TRP B 288 N GLU B 254 SHEET 4 N 6 LYS B 298 THR B 306 -1 O LYS B 298 N ASP B 293 SHEET 5 N 6 THR B 400 GLU B 404 1 O LEU B 403 N ARG B 305 SHEET 6 N 6 THR B 392 LEU B 395 -1 N ILE B 394 O TRP B 402 SHEET 1 O 2 VAL B 257 ILE B 259 0 SHEET 2 O 2 PHE B 279 SER B 281 -1 O GLU B 280 N LYS B 258 SHEET 1 P 4 PHE B 309 ASP B 320 0 SHEET 2 P 4 PHE B 323 LYS B 332 -1 O ILE B 325 N TYR B 318 SHEET 3 P 4 GLN B 362 PRO B 371 -1 O TYR B 368 N VAL B 326 SHEET 4 P 4 GLU B 406 SER B 410 -1 O GLU B 406 N ARG B 367 SHEET 1 Q 4 GLN B 414 GLN B 420 0 SHEET 2 Q 4 TYR B 433 ASN B 440 -1 O LEU B 437 N GLU B 417 SHEET 3 Q 4 VAL B 443 ASN B 451 -1 O LEU B 450 N ALA B 434 SHEET 4 Q 4 THR B 457 TRP B 460 -1 O TRP B 460 N LEU B 447 LINK C ACE A 1 N SER A 2 1555 1555 1.33 LINK C ACE B 1 N SER B 2 1555 1555 1.31 LINK NE2 HIS A 180 FE FE2 A 601 1555 1555 2.22 LINK NE2 HIS A 241 FE FE2 A 601 1555 1555 2.39 LINK NE2 HIS A 313 FE FE2 A 601 1555 1555 2.35 LINK NE2 HIS A 527 FE FE2 A 601 1555 1555 2.27 LINK FE FE2 A 601 O2 PLM A 602 1555 1555 1.90 LINK NE2 HIS B 180 FE FE2 B 601 1555 1555 2.33 LINK NE2 HIS B 241 FE FE2 B 601 1555 1555 2.33 LINK NE2 HIS B 313 FE FE2 B 601 1555 1555 2.29 LINK NE2 HIS B 527 FE FE2 B 601 1555 1555 2.32 LINK FE FE2 B 601 O1 PLM B 602 1555 1555 1.90 SITE 1 AC1 5 HIS A 180 HIS A 241 HIS A 313 HIS A 527 SITE 2 AC1 5 PLM A 602 SITE 1 AC2 13 LEU A 60 VAL A 134 HIS A 241 PHE A 312 SITE 2 AC2 13 TYR A 338 GLU A 417 PHE A 418 LEU A 439 SITE 3 AC2 13 PHE A 442 VAL A 524 HIS A 527 FE2 A 601 SITE 4 AC2 13 A6V A 603 SITE 1 AC3 12 PHE A 61 PHE A 103 VAL A 134 THR A 147 SITE 2 AC3 12 GLU A 148 ASN A 194 HIS A 241 ILE A 259 SITE 3 AC3 12 TYR A 275 TYR A 338 PLM A 602 HOH A 795 SITE 1 AC4 5 HIS B 180 HIS B 241 HIS B 313 HIS B 527 SITE 2 AC4 5 PLM B 602 SITE 1 AC5 13 LEU B 60 VAL B 134 HIS B 180 HIS B 241 SITE 2 AC5 13 TYR B 338 GLU B 417 PHE B 418 LEU B 439 SITE 3 AC5 13 PRO B 444 VAL B 524 HIS B 527 FE2 B 601 SITE 4 AC5 13 A6V B 603 SITE 1 AC6 11 PHE B 61 PHE B 103 VAL B 134 THR B 147 SITE 2 AC6 11 GLU B 148 ASN B 175 ASN B 194 ILE B 259 SITE 3 AC6 11 TYR B 275 PLM B 602 HOH B 723 CRYST1 175.639 175.639 86.611 90.00 90.00 120.00 P 65 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 0.005693 0.003287 0.000000 0.00000 SCALE2 0.000000 0.006574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011546 0.00000 HETATM 1 C ACE A 1 -27.166 113.184 -4.905 1.00 69.86 C HETATM 2 O ACE A 1 -27.486 113.936 -3.991 1.00 68.70 O HETATM 3 CH3 ACE A 1 -26.143 113.613 -5.940 1.00 70.90 C