HEADER ISOMERASE, HYDROLASE 09-MAY-12 4F3D TITLE STRUCTURE OF RPE65: P65 CRYSTAL FORM GROWN IN FOS-CHOLINE-10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOID ISOMEROHYDROLASE; COMPND 3 CHAIN: A, B; 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 3 13-SEP-23 4F3D 1 REMARK SEQADV LINK REVDAT 2 02-JUL-14 4F3D 1 JRNL REVDAT 1 03-OCT-12 4F3D 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 49415 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : FROM PDB ENTRY 3FSN REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2662 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3635 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 193 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8261 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.86000 REMARK 3 B22 (A**2) : 7.86000 REMARK 3 B33 (A**2) : -15.71000 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): 0.076 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.116 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8541 ; 0.006 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 7975 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11622 ; 1.091 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18399 ; 0.710 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1028 ; 6.171 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 409 ;32.093 ;24.279 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1379 ;12.298 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;12.469 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1261 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9636 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 2012 ; 0.002 ; 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 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 3 533 B 3 533 32589 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 4F3D 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_1000072403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : KOHZU HLD8-24 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52159 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.75 REMARK 200 R MERGE FOR SHELL (I) : 0.88200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.530 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3FSN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% 2-ETHOXYETHANOL, 22 MM FOS-CHOLINE REMARK 280 -10, PH 6.5, 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 57.63267 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 28.81633 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 43.22450 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 14.40817 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 72.04083 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: 4440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 MET A 1 REMARK 465 SER A 2 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 TRP A 268 REMARK 465 SER A 269 REMARK 465 LEU A 270 REMARK 465 TRP A 271 REMARK 465 MET B 1 REMARK 465 SER B 2 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 TRP B 268 REMARK 465 SER B 269 REMARK 465 LEU B 270 REMARK 465 TRP B 271 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 ARG A 124 CB CG CD NE CZ NH1 NH2 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 92.42 -65.89 REMARK 500 THR A 147 -132.33 -120.10 REMARK 500 LYS A 198 -169.25 -105.38 REMARK 500 HIS A 321 -124.66 48.93 REMARK 500 PHE A 442 -2.68 77.56 REMARK 500 ASP A 445 10.03 -140.74 REMARK 500 PHE A 526 -72.08 -94.44 REMARK 500 ASN B 131 92.60 -65.62 REMARK 500 THR B 147 -131.69 -119.34 REMARK 500 LYS B 198 -168.85 -105.76 REMARK 500 HIS B 321 -125.14 49.13 REMARK 500 PHE B 442 -2.58 78.27 REMARK 500 PHE B 526 -72.10 -94.16 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 95.1 REMARK 620 3 HIS A 313 NE2 95.4 95.4 REMARK 620 4 HIS A 527 NE2 87.6 172.6 91.3 REMARK 620 N 1 2 3 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 95.1 REMARK 620 3 HIS B 313 NE2 97.1 97.4 REMARK 620 4 HIS B 527 NE2 86.9 169.8 92.3 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 FE2 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ETX A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ETX 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 ETX B 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: 4F3A RELATED DB: PDB DBREF 4F3D A 1 533 UNP Q28175 RPE65_BOVIN 1 533 DBREF 4F3D B 1 533 UNP Q28175 RPE65_BOVIN 1 533 SEQADV 4F3D LEU A 341 UNP Q28175 SER 341 CONFLICT SEQADV 4F3D LEU B 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 SEQRES 1 B 533 MET 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 FE2 A 601 1 HET ETX A 602 6 HET ETX A 603 6 HET FE2 B 601 1 HET ETX B 602 6 HETNAM FE2 FE (II) ION HETNAM ETX 2-ETHOXYETHANOL FORMUL 3 FE2 2(FE 2+) FORMUL 4 ETX 3(C4 H10 O2) FORMUL 8 HOH *115(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 SER A 267 1 8 HELIX 6 6 TYR A 275 ASP A 277 5 3 HELIX 7 7 PHE A 336 LEU A 341 5 6 HELIX 8 8 TYR A 342 GLU A 348 1 7 HELIX 9 9 ASN A 349 ALA A 357 1 9 HELIX 10 10 ASP A 375 THR A 379 5 5 HELIX 11 11 ASN A 422 GLY A 427 1 6 HELIX 12 12 GLY B 10 GLU B 17 5 8 HELIX 13 13 THR B 86 LYS B 96 1 11 HELIX 14 14 CYS B 169 TYR B 171 5 3 HELIX 15 15 ASP B 218 SER B 223 5 6 HELIX 16 16 ASN B 260 SER B 267 1 8 HELIX 17 17 TYR B 275 ASP B 277 5 3 HELIX 18 18 PHE B 336 LEU B 341 5 6 HELIX 19 19 TYR B 342 GLU B 348 1 7 HELIX 20 20 ASN B 349 ALA B 357 1 9 HELIX 21 21 ASP B 375 THR B 379 5 5 HELIX 22 22 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 73 O HIS A 76 SHEET 4 A 5 GLY A 40 LEU A 49 -1 N GLY A 46 O LEU A 66 SHEET 5 A 5 GLY A 528 LYS A 532 -1 O LEU A 529 N LEU A 43 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 LEU A 502 O ALA A 516 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 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 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 226 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 ARG A 305 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 GLN A 362 N LYS A 332 SHEET 4 H 4 GLU A 406 PHE A 409 -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 LEU A 437 N GLU A 417 SHEET 3 I 4 VAL A 443 ASN A 451 -1 O LEU A 450 N ALA A 434 SHEET 4 I 4 THR A 457 TRP A 460 -1 O TRP A 460 N LEU A 447 SHEET 1 J 5 LEU B 26 THR B 27 0 SHEET 2 J 5 HIS B 76 PHE B 83 -1 O TYR B 79 N LEU B 26 SHEET 3 J 5 GLN B 64 LYS B 73 -1 N LYS B 73 O HIS B 76 SHEET 4 J 5 GLY B 40 LEU B 49 -1 N GLY B 46 O LEU B 66 SHEET 5 J 5 GLY B 528 LYS B 532 -1 O LEU B 529 N LEU B 43 SHEET 1 K 5 HIS B 29 GLY B 32 0 SHEET 2 K 5 GLU B 512 VAL B 518 -1 O GLU B 517 N HIS B 29 SHEET 3 K 5 ALA B 500 ASN B 506 -1 N LEU B 502 O ALA B 516 SHEET 4 K 5 GLY B 484 VAL B 491 -1 N SER B 488 O LEU B 503 SHEET 5 K 5 ILE B 471 SER B 474 -1 N VAL B 473 O VAL B 485 SHEET 1 L 2 GLU B 51 VAL B 52 0 SHEET 2 L 2 GLU B 55 PRO B 56 -1 O GLU B 55 N VAL B 52 SHEET 1 M 4 ASN B 135 VAL B 139 0 SHEET 2 M 4 ASP B 142 CYS B 146 -1 O TYR B 144 N TYR B 137 SHEET 3 M 4 PHE B 151 VAL B 155 -1 O THR B 153 N ALA B 145 SHEET 4 M 4 THR B 162 ASP B 167 -1 O VAL B 166 N ILE B 152 SHEET 1 N 4 HIS B 182 ILE B 183 0 SHEET 2 N 4 VAL B 189 CYS B 195 -1 O TYR B 190 N HIS B 182 SHEET 3 N 4 ALA B 203 ILE B 209 -1 O ILE B 209 N VAL B 189 SHEET 4 N 4 GLU B 224 PRO B 230 -1 O VAL B 226 N ILE B 206 SHEET 1 O 6 GLY B 244 LEU B 245 0 SHEET 2 O 6 TYR B 249 GLU B 254 -1 O VAL B 251 N GLY B 244 SHEET 3 O 6 VAL B 287 ASP B 293 -1 O TRP B 288 N GLU B 254 SHEET 4 O 6 LYS B 298 THR B 306 -1 O LYS B 298 N ASP B 293 SHEET 5 O 6 THR B 400 GLU B 404 1 O ILE B 401 N ARG B 305 SHEET 6 O 6 THR B 392 LEU B 395 -1 N ILE B 394 O TRP B 402 SHEET 1 P 2 VAL B 257 ILE B 259 0 SHEET 2 P 2 PHE B 279 SER B 281 -1 O GLU B 280 N LYS B 258 SHEET 1 Q 4 PHE B 309 ASP B 320 0 SHEET 2 Q 4 PHE B 323 LYS B 332 -1 O ILE B 325 N TYR B 318 SHEET 3 Q 4 GLN B 362 PRO B 371 -1 O GLN B 362 N LYS B 332 SHEET 4 Q 4 GLU B 406 PHE B 409 -1 O GLU B 406 N ARG B 367 SHEET 1 R 4 GLN B 414 GLN B 420 0 SHEET 2 R 4 TYR B 433 ASN B 440 -1 O LEU B 437 N GLU B 417 SHEET 3 R 4 VAL B 443 ASN B 451 -1 O LEU B 450 N ALA B 434 SHEET 4 R 4 THR B 457 TRP B 460 -1 O TRP B 460 N LEU B 447 LINK NE2 HIS A 180 FE FE2 A 601 1555 1555 2.33 LINK NE2 HIS A 241 FE FE2 A 601 1555 1555 2.21 LINK NE2 HIS A 313 FE FE2 A 601 1555 1555 2.39 LINK NE2 HIS A 527 FE FE2 A 601 1555 1555 2.27 LINK NE2 HIS B 180 FE FE2 B 601 1555 1555 2.33 LINK NE2 HIS B 241 FE FE2 B 601 1555 1555 2.20 LINK NE2 HIS B 313 FE FE2 B 601 1555 1555 2.32 LINK NE2 HIS B 527 FE FE2 B 601 1555 1555 2.29 CISPEP 1 ARG A 124 GLY A 125 0 0.68 SITE 1 AC1 4 HIS A 180 HIS A 241 HIS A 313 HIS A 527 SITE 1 AC2 4 TYR A 137 ALA A 177 ASN A 191 VAL A 207 SITE 1 AC3 6 ILE A 183 GLU A 184 ASN A 185 LEU A 245 SITE 2 AC3 6 TYR A 423 GLY A 427 SITE 1 AC4 4 HIS B 180 HIS B 241 HIS B 313 HIS B 527 SITE 1 AC5 6 TYR B 137 VAL B 174 GLY B 176 ALA B 177 SITE 2 AC5 6 ASN B 191 VAL B 207 CRYST1 175.258 175.258 86.449 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 0.005706 0.003294 0.000000 0.00000 SCALE2 0.000000 0.006589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011568 0.00000