HEADER TRANSPORT PROTEIN 28-MAR-12 4EEJ TITLE CRYSTAL STRUCTURE OF THE Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:Q4R TITLE 2 MUTANT OF CELLULAR RETINOL BINDING PROTEIN TYPE II IN COMPLEX WITH TITLE 3 ALL-TRANS-RETINAL AT 1.5 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CELLULAR RETINOL-BINDING PROTEIN II, CRBP-II; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RBP2, CRBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17 KEYWDS RETINAL COMPLEX, BETA BARREL, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.NOSSONI,J.H.GEIGER REVDAT 2 13-SEP-23 4EEJ 1 REMARK SEQADV LINK REVDAT 1 26-DEC-12 4EEJ 0 JRNL AUTH W.WANG,Z.NOSSONI,T.BERBASOVA,C.T.WATSON,I.YAPICI,K.S.LEE, JRNL AUTH 2 C.VASILEIOU,J.H.GEIGER,B.BORHAN JRNL TITL TUNING THE ELECTRONIC ABSORPTION OF PROTEIN-EMBEDDED JRNL TITL 2 ALL-TRANS-RETINAL. JRNL REF SCIENCE V. 338 1340 2012 JRNL REFN ISSN 0036-8075 JRNL PMID 23224553 JRNL DOI 10.1126/SCIENCE.1226135 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 34239 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1917 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2480 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2156 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 301 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.207 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2263 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3058 ; 2.389 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 7.412 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;32.880 ;24.464 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 394 ;13.175 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.306 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 327 ; 0.153 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1720 ; 0.016 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1328 ; 1.678 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2129 ; 2.810 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 935 ; 3.986 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 929 ; 6.115 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4EEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1272 REMARK 200 MONOCHROMATOR : KOHZU SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39769 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.501 REMARK 200 RESOLUTION RANGE LOW (A) : 32.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2RCQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG4000, 0.1 M SODIUM ACETATE REMARK 280 TRIHYDRATE, PH 4.6, 0.1 M AMMONIUM ACETATE, EVAPORATION, REMARK 280 RECRYSTALLIZATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 102 CG CD OE1 OE2 REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 ASP A 113 CG OD1 OD2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 GLU B 9 CG CD OE1 OE2 REMARK 470 GLU B 11 CG CD OE1 OE2 REMARK 470 GLU B 14 CG CD OE1 OE2 REMARK 470 GLU B 17 CG CD OE1 OE2 REMARK 470 ASP B 26 CG OD1 OD2 REMARK 470 GLU B 102 CG CD OE1 OE2 REMARK 470 LYS B 133 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 12 N CA C O CB OG REMARK 480 VAL A 96 N CA C O CB CG1 CG2 REMARK 480 ASN A 103 N CA C O CB CG OD1 REMARK 480 ASN A 103 ND2 REMARK 480 SER B 12 N CA C O CB OG REMARK 480 VAL B 34 N CA C O CB CG1 CG2 REMARK 480 VAL B 96 N CA C O CB CG1 CG2 REMARK 480 LEU B 115 N CA C O CB CG CD1 REMARK 480 LEU B 115 CD2 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 C LYS A 133 O HOH A 437 1.46 REMARK 500 O HOH A 324 O HOH A 411 1.72 REMARK 500 OH TYR B 60 O ACT B 202 1.79 REMARK 500 OE2 GLU B 72 O ACT B 202 1.95 REMARK 500 O HOH B 422 O HOH B 451 2.08 REMARK 500 NZ LYS B 21 O HOH B 463 2.12 REMARK 500 OE2 GLU A 72 OXT ACT A 202 2.13 REMARK 500 O HOH A 431 O HOH B 402 2.14 REMARK 500 OH TYR A 60 OXT ACT A 202 2.18 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 368 O HOH A 405 1645 2.02 REMARK 500 OD1 ASP B 45 O HOH B 449 1545 2.09 REMARK 500 O HOH B 431 O HOH B 452 1565 2.13 REMARK 500 O HOH B 349 O HOH B 452 1565 2.14 REMARK 500 O HOH B 354 O HOH B 447 1545 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 12 CB SER A 12 OG -0.091 REMARK 500 GLU A 72 CB GLU A 72 CG -0.140 REMARK 500 VAL B 96 CB VAL B 96 CG2 -0.148 REMARK 500 LYS B 132 N LYS B 132 CA -0.130 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 47 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 123 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 47 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 LYS B 75 CD - CE - NZ ANGL. DEV. = -15.7 DEGREES REMARK 500 TRP B 109 O - C - N ANGL. DEV. = -9.6 DEGREES REMARK 500 ARG B 127 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES 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 TRP A 58 108.23 -163.33 REMARK 500 LEU A 77 -113.10 -107.92 REMARK 500 LEU B 77 -109.75 -111.80 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 PHE A 57 TRP A 58 -142.67 REMARK 500 PHE B 57 TRP B 58 -147.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TRP B 109 -13.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EDE RELATED DB: PDB REMARK 900 RELATED ID: 4EFG RELATED DB: PDB DBREF 4EEJ A 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 4EEJ B 1 133 UNP P50120 RET2_HUMAN 2 134 SEQADV 4EEJ ARG A 4 UNP P50120 GLN 5 ENGINEERED MUTATION SEQADV 4EEJ TRP A 19 UNP P50120 TYR 20 ENGINEERED MUTATION SEQADV 4EEJ LEU A 29 UNP P50120 THR 30 ENGINEERED MUTATION SEQADV 4EEJ LEU A 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQADV 4EEJ VAL A 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 4EEJ CYS A 53 UNP P50120 THR 54 ENGINEERED MUTATION SEQADV 4EEJ TRP A 58 UNP P50120 ARG 59 ENGINEERED MUTATION SEQADV 4EEJ LYS A 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQADV 4EEJ ARG B 4 UNP P50120 GLN 5 ENGINEERED MUTATION SEQADV 4EEJ TRP B 19 UNP P50120 TYR 20 ENGINEERED MUTATION SEQADV 4EEJ LEU B 29 UNP P50120 THR 30 ENGINEERED MUTATION SEQADV 4EEJ LEU B 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQADV 4EEJ VAL B 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 4EEJ CYS B 53 UNP P50120 THR 54 ENGINEERED MUTATION SEQADV 4EEJ TRP B 58 UNP P50120 ARG 59 ENGINEERED MUTATION SEQADV 4EEJ LYS B 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQRES 1 A 133 THR ARG ASP ARG ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 A 133 GLU ASN PHE GLU GLY TRP MET LYS ALA LEU ASP ILE ASP SEQRES 3 A 133 PHE ALA LEU ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 A 133 LEU VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS VAL LYS SEQRES 5 A 133 CYS THR SER THR PHE TRP ASN TYR ASP VAL ASP PHE THR SEQRES 6 A 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 A 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 A 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 A 133 GLY TRP LYS LYS TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 A 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 A 133 LYS LYS LYS SEQRES 1 B 133 THR ARG ASP ARG ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 B 133 GLU ASN PHE GLU GLY TRP MET LYS ALA LEU ASP ILE ASP SEQRES 3 B 133 PHE ALA LEU ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 B 133 LEU VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS VAL LYS SEQRES 5 B 133 CYS THR SER THR PHE TRP ASN TYR ASP VAL ASP PHE THR SEQRES 6 B 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 B 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 B 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 B 133 GLY TRP LYS LYS TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 B 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 B 133 LYS LYS LYS HET RET A 201 20 HET ACT A 202 4 HET RET B 201 20 HET ACT B 202 4 HETNAM RET RETINAL HETNAM ACT ACETATE ION FORMUL 3 RET 2(C20 H28 O) FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 7 HOH *301(H2 O) HELIX 1 1 ASN A 15 LEU A 23 1 9 HELIX 2 2 ASP A 26 VAL A 34 1 9 HELIX 3 3 ASN B 15 LEU B 23 1 9 HELIX 4 4 ASP B 26 VAL B 34 1 9 SHEET 1 A10 TYR A 60 THR A 65 0 SHEET 2 A10 ASN A 48 THR A 54 -1 N VAL A 51 O VAL A 62 SHEET 3 A10 THR A 39 ASP A 45 -1 N VAL A 41 O LYS A 52 SHEET 4 A10 GLY A 6 GLU A 14 -1 N TRP A 8 O LEU A 40 SHEET 5 A10 GLN A 124 LYS A 132 -1 O VAL A 129 N GLU A 11 SHEET 6 A10 LYS A 114 CYS A 121 -1 N LEU A 117 O GLN A 128 SHEET 7 A10 GLY A 105 GLU A 111 -1 N TRP A 109 O TYR A 116 SHEET 8 A10 VAL A 92 LYS A 98 -1 N CYS A 95 O TRP A 106 SHEET 9 A10 HIS A 81 GLU A 89 -1 N THR A 87 O VAL A 94 SHEET 10 A10 PHE A 70 TYR A 73 -1 N PHE A 70 O ALA A 84 SHEET 1 B10 TYR B 60 THR B 65 0 SHEET 2 B10 ASN B 48 THR B 54 -1 N CYS B 53 O TYR B 60 SHEET 3 B10 THR B 39 ASP B 45 -1 N VAL B 41 O LYS B 52 SHEET 4 B10 GLY B 6 GLU B 14 -1 N TRP B 8 O LEU B 40 SHEET 5 B10 GLN B 124 LYS B 132 -1 O VAL B 129 N GLU B 11 SHEET 6 B10 LYS B 114 CYS B 121 -1 N LEU B 117 O GLN B 128 SHEET 7 B10 GLY B 105 GLU B 111 -1 N GLY B 105 O THR B 120 SHEET 8 B10 VAL B 92 LYS B 98 -1 N CYS B 95 O TRP B 106 SHEET 9 B10 HIS B 81 GLU B 89 -1 N LYS B 83 O LYS B 98 SHEET 10 B10 PHE B 70 TYR B 73 -1 N PHE B 70 O ALA B 84 LINK NZ LYS A 108 C15 RET A 201 1555 1555 1.25 LINK NZ LYS B 108 C15 RET B 201 1555 1555 1.25 SITE 1 AC1 9 PHE A 16 TRP A 19 ALA A 33 GLN A 38 SITE 2 AC1 9 TRP A 58 TRP A 106 LYS A 108 ACT A 202 SITE 3 AC1 9 HOH A 395 SITE 1 AC2 7 TYR A 60 VAL A 62 GLU A 72 GLN A 97 SITE 2 AC2 7 TRP A 106 RET A 201 HOH A 360 SITE 1 AC3 8 TRP B 19 ALA B 33 GLN B 38 TRP B 58 SITE 2 AC3 8 LEU B 77 TRP B 106 LYS B 108 ACT B 202 SITE 1 AC4 8 TYR B 60 VAL B 62 GLU B 72 CYS B 95 SITE 2 AC4 8 GLN B 97 TRP B 106 RET B 201 HOH B 319 CRYST1 30.918 35.756 64.376 86.40 86.44 64.94 P 1 2 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 0.032344 -0.015125 -0.001400 0.00000 SCALE2 0.000000 0.030874 -0.001249 0.00000 SCALE3 0.000000 0.000000 0.015576 0.00000