PDB Short entry for 4GKC HEADER TRANSPORT PROTEIN 10-AUG-12 4GKC TITLE CRYSTAL STRUCTURE OF Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A MUTANT OF TITLE 2 CELLULAR RETINOL BINDING PROTEIN II COMPLEX WITH ALL-TRANS-RETINAL AT TITLE 3 1.33 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 3 13-SEP-23 4GKC 1 REMARK SEQADV LINK REVDAT 2 24-JAN-18 4GKC 1 AUTHOR REMARK REVDAT 1 26-DEC-12 4GKC 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 3 NUMBER OF REFLECTIONS : 50433 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2670 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2926 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2187 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.61 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): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.831 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2331 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3157 ; 2.491 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 6.950 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;37.828 ;25.126 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 422 ;13.281 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.299 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 336 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1790 ; 0.014 ; 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): 1352 ; 1.581 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2191 ; 2.682 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 979 ; 3.817 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 966 ; 5.880 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4GKC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074291. 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 : NULL 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50433 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 28.122 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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: 2RCQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 4000, 0.1M CH3COONA.3H2O, 0.1 REMARK 280 M CH3COONH4, EVAPORATION, TEMPERATURE 298K, PH 4.6 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 ASP A 113 CG OD1 OD2 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 B 12 N CA C O CB OG 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 O HOH A 367 O HOH A 461 1.62 REMARK 500 O GLY A 112 O HOH A 401 1.63 REMARK 500 O HOH A 412 O HOH A 460 1.75 REMARK 500 O HOH B 340 O HOH B 423 1.82 REMARK 500 O HOH B 404 O HOH B 459 1.85 REMARK 500 O HOH B 357 O HOH B 463 1.97 REMARK 500 O ASP A 26 O HOH A 455 2.03 REMARK 500 OH TYR A 60 O HOH A 461 2.04 REMARK 500 OE1 GLU A 17 O HOH A 417 2.10 REMARK 500 O HOH B 369 O HOH B 473 2.10 REMARK 500 O HOH A 432 O HOH A 454 2.10 REMARK 500 O HOH B 421 O HOH B 427 2.12 REMARK 500 OH TYR B 60 O HOH B 459 2.13 REMARK 500 O HOH A 306 O HOH A 424 2.14 REMARK 500 CD GLU B 111 O HOH B 477 2.14 REMARK 500 O HOH A 405 O HOH A 424 2.15 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 C LYS A 133 O HOH A 437 1545 1.35 REMARK 500 C LYS B 133 O HOH B 368 1645 1.53 REMARK 500 NZ LYS A 21 O HOH A 469 1565 1.75 REMARK 500 O HOH A 462 O HOH B 381 1556 1.93 REMARK 500 O HOH A 442 O HOH B 430 1556 2.01 REMARK 500 CE LYS A 132 O HOH A 389 1545 2.05 REMARK 500 O HOH B 441 O HOH B 444 1455 2.15 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 ARG A 2 CZ ARG A 2 NH2 0.080 REMARK 500 GLU B 11 CB GLU B 11 CG -0.155 REMARK 500 TRP B 88 CE3 TRP B 88 CZ3 0.102 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 PHE A 16 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG A 30 NE - CZ - NH2 ANGL. DEV. = -12.9 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 30 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ASP B 47 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 GLU B 69 OE1 - CD - OE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP B 71 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 TYR B 73 CZ - CE2 - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP B 123 CB - CG - OD1 ANGL. DEV. = 6.6 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 LEU A 77 -107.61 -113.65 REMARK 500 TRP B 58 113.37 -168.38 REMARK 500 LEU B 77 -110.16 -108.50 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 B 57 TRP B 58 -139.59 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 RET B 201 DBREF 4GKC A 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 4GKC B 1 133 UNP P50120 RET2_HUMAN 2 134 SEQADV 4GKC ALA A 4 UNP P50120 GLN 5 ENGINEERED MUTATION SEQADV 4GKC TRP A 19 UNP P50120 TYR 20 ENGINEERED MUTATION SEQADV 4GKC LEU A 29 UNP P50120 THR 30 ENGINEERED MUTATION SEQADV 4GKC LEU A 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQADV 4GKC VAL A 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 4GKC CYS A 53 UNP P50120 THR 54 ENGINEERED MUTATION SEQADV 4GKC TRP A 58 UNP P50120 ARG 59 ENGINEERED MUTATION SEQADV 4GKC LYS A 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQADV 4GKC ALA B 4 UNP P50120 GLN 5 ENGINEERED MUTATION SEQADV 4GKC TRP B 19 UNP P50120 TYR 20 ENGINEERED MUTATION SEQADV 4GKC LEU B 29 UNP P50120 THR 30 ENGINEERED MUTATION SEQADV 4GKC LEU B 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQADV 4GKC VAL B 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 4GKC CYS B 53 UNP P50120 THR 54 ENGINEERED MUTATION SEQADV 4GKC TRP B 58 UNP P50120 ARG 59 ENGINEERED MUTATION SEQADV 4GKC LYS B 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQRES 1 A 133 THR ARG ASP ALA 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 ALA 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 RET B 201 20 HETNAM RET RETINAL FORMUL 3 RET 2(C20 H28 O) FORMUL 5 HOH *354(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 CYS A 53 O TYR A 60 SHEET 3 A10 THR A 39 ASP A 45 -1 N ASP A 45 O ASN A 48 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 GLU A 111 O LYS A 114 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 PHE B 49 O PHE B 64 SHEET 3 B10 THR B 39 ASP B 45 -1 N THR B 39 O THR B 54 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 GLU B 111 O LYS B 114 SHEET 8 B10 VAL B 92 LYS B 98 -1 N LEU B 93 O LYS B 108 SHEET 9 B10 HIS B 81 GLU B 89 -1 N THR B 87 O VAL B 94 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 1.24 LINK NZ LYS B 108 C15 RET B 201 1555 1555 1.24 SITE 1 AC1 9 TRP A 19 ALA A 33 GLN A 38 TRP A 58 SITE 2 AC1 9 ASN A 59 TYR A 60 LEU A 77 TRP A 106 SITE 3 AC1 9 LYS A 108 SITE 1 AC2 8 ALA B 33 GLN B 38 TRP B 58 LEU B 77 SITE 2 AC2 8 TRP B 106 LYS B 108 HOH B 341 HOH B 391 CRYST1 30.970 36.002 64.016 86.10 86.46 65.32 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 0.032289 -0.014838 -0.001308 0.00000 SCALE2 0.000000 0.030569 -0.001425 0.00000 SCALE3 0.000000 0.000000 0.015668 0.00000