HEADER SIGNALING PROTEIN 14-AUG-09 2WQ9 TITLE CRYSTAL STRUCTURE OF RBP4 BOUND TO OLEIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 19-192; COMPND 5 SYNONYM: PLASMA RETINOL-BINDING PROTEIN, PRBP, RBP, RBP4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS DISEASE MUTATION, SENSORY TRANSDUCTION, SIGNALING PROTEIN, RETINOL- KEYWDS 2 BINDING, VISION, VITAMIN A EXPDTA X-RAY DIFFRACTION AUTHOR M.NANAO,D.MERCER,L.NGUYEN,D.BUCKLEY,T.J.STOUT REVDAT 4 20-DEC-23 2WQ9 1 REMARK REVDAT 3 03-APR-19 2WQ9 1 SOURCE REVDAT 2 28-JUN-17 2WQ9 1 REMARK REVDAT 1 01-SEP-10 2WQ9 0 JRNL AUTH M.NANAO,T.J.STOUT JRNL TITL CRYSTAL STRUCTURE OF RBP4 BOUND TO OLEIC ACID JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 32522 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) : 0.188 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1727 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2415 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1399 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.19000 REMARK 3 B12 (A**2) : 0.06000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.082 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.035 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 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): 1504 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2028 ; 1.116 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 181 ; 6.074 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;31.697 ;23.580 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 251 ;12.372 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.494 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 207 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1156 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 726 ; 0.199 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1029 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 197 ; 0.115 ; 0.200 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): 39 ; 0.189 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.150 ; 0.200 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): 888 ; 0.501 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1407 ; 0.806 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 693 ; 1.507 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 616 ; 2.374 ; 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 : 10 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 21 REMARK 3 ORIGIN FOR THE GROUP (A): -30.6879 13.2124 15.9501 REMARK 3 T TENSOR REMARK 3 T11: -0.0464 T22: -0.0412 REMARK 3 T33: -0.0899 T12: 0.0184 REMARK 3 T13: 0.0418 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 3.0140 L22: 8.9002 REMARK 3 L33: 2.2452 L12: 2.5499 REMARK 3 L13: 1.4619 L23: 2.7585 REMARK 3 S TENSOR REMARK 3 S11: 0.1280 S12: 0.1950 S13: 0.3605 REMARK 3 S21: -0.2909 S22: -0.2486 S23: 0.5140 REMARK 3 S31: -0.2482 S32: -0.1032 S33: 0.1206 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 22 A 46 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1787 10.3815 28.8855 REMARK 3 T TENSOR REMARK 3 T11: -0.0632 T22: -0.0523 REMARK 3 T33: -0.1103 T12: -0.0444 REMARK 3 T13: 0.0068 T23: -0.0422 REMARK 3 L TENSOR REMARK 3 L11: 2.8403 L22: 3.5336 REMARK 3 L33: 1.6773 L12: 0.1503 REMARK 3 L13: -0.4289 L23: 0.0062 REMARK 3 S TENSOR REMARK 3 S11: 0.0925 S12: -0.0691 S13: 0.1564 REMARK 3 S21: 0.3759 S22: -0.0552 S23: -0.2141 REMARK 3 S31: -0.1215 S32: 0.2737 S33: -0.0373 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 47 A 51 REMARK 3 ORIGIN FOR THE GROUP (A): -13.2025 26.6564 12.8032 REMARK 3 T TENSOR REMARK 3 T11: 0.3620 T22: 0.0875 REMARK 3 T33: 0.2379 T12: -0.0735 REMARK 3 T13: 0.2467 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 32.1372 L22: 95.9174 REMARK 3 L33: 25.7439 L12: 31.1507 REMARK 3 L13: 7.4945 L23: 45.1441 REMARK 3 S TENSOR REMARK 3 S11: -0.5370 S12: 1.9127 S13: 0.0301 REMARK 3 S21: -6.7634 S22: 2.8597 S23: -1.4416 REMARK 3 S31: -3.2590 S32: 1.1552 S33: -2.3227 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 52 A 60 REMARK 3 ORIGIN FOR THE GROUP (A): -12.5655 15.1821 24.7232 REMARK 3 T TENSOR REMARK 3 T11: -0.0485 T22: 0.0429 REMARK 3 T33: 0.0482 T12: -0.0643 REMARK 3 T13: 0.0480 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 2.5457 L22: 9.3942 REMARK 3 L33: 18.8027 L12: -3.9622 REMARK 3 L13: 4.9083 L23: -10.2693 REMARK 3 S TENSOR REMARK 3 S11: -0.1241 S12: -0.0639 S13: 0.1898 REMARK 3 S21: 0.1472 S22: 0.1599 S23: -0.5122 REMARK 3 S31: -0.0891 S32: 0.3343 S33: -0.0357 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 61 A 67 REMARK 3 ORIGIN FOR THE GROUP (A): -8.2804 -1.0288 33.5673 REMARK 3 T TENSOR REMARK 3 T11: 0.4055 T22: 0.3118 REMARK 3 T33: 0.3548 T12: 0.1224 REMARK 3 T13: -0.1122 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 31.9878 L22: 69.8613 REMARK 3 L33: 41.6675 L12: -17.2826 REMARK 3 L13: 10.6797 L23: -32.9603 REMARK 3 S TENSOR REMARK 3 S11: -0.1817 S12: -1.7443 S13: -2.1738 REMARK 3 S21: 0.4406 S22: 0.1668 S23: -1.4334 REMARK 3 S31: 2.8820 S32: 0.6106 S33: 0.0149 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 68 A 84 REMARK 3 ORIGIN FOR THE GROUP (A): -14.8657 12.9823 18.5912 REMARK 3 T TENSOR REMARK 3 T11: -0.0565 T22: -0.0160 REMARK 3 T33: -0.0273 T12: -0.0787 REMARK 3 T13: 0.0874 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 8.8447 L22: 2.0367 REMARK 3 L33: 7.2568 L12: -1.8474 REMARK 3 L13: 5.9599 L23: -0.9764 REMARK 3 S TENSOR REMARK 3 S11: 0.1062 S12: 0.3021 S13: 0.1710 REMARK 3 S21: -0.1608 S22: -0.0418 S23: -0.2907 REMARK 3 S31: -0.1192 S32: 0.3739 S33: -0.0644 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 85 A 113 REMARK 3 ORIGIN FOR THE GROUP (A): -16.6638 11.4860 19.3530 REMARK 3 T TENSOR REMARK 3 T11: -0.0804 T22: -0.0343 REMARK 3 T33: -0.0764 T12: -0.0440 REMARK 3 T13: 0.0573 T23: -0.0199 REMARK 3 L TENSOR REMARK 3 L11: 2.7353 L22: 2.8905 REMARK 3 L33: 1.9097 L12: -0.4207 REMARK 3 L13: 0.2668 L23: -0.0863 REMARK 3 S TENSOR REMARK 3 S11: 0.0792 S12: 0.3350 S13: 0.0738 REMARK 3 S21: -0.0339 S22: -0.0656 S23: -0.3025 REMARK 3 S31: -0.0738 S32: 0.3260 S33: -0.0136 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 114 A 131 REMARK 3 ORIGIN FOR THE GROUP (A): -25.9859 2.5330 17.4424 REMARK 3 T TENSOR REMARK 3 T11: -0.0911 T22: -0.0761 REMARK 3 T33: -0.1046 T12: -0.0009 REMARK 3 T13: 0.0092 T23: -0.0636 REMARK 3 L TENSOR REMARK 3 L11: 0.4201 L22: 1.2990 REMARK 3 L33: 1.9158 L12: 0.6904 REMARK 3 L13: 0.6112 L23: 0.5939 REMARK 3 S TENSOR REMARK 3 S11: 0.1424 S12: 0.1913 S13: 0.0008 REMARK 3 S21: -0.0936 S22: 0.0430 S23: -0.0446 REMARK 3 S31: -0.0105 S32: 0.1567 S33: -0.1855 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 132 A 145 REMARK 3 ORIGIN FOR THE GROUP (A): -24.6026 14.5049 30.1878 REMARK 3 T TENSOR REMARK 3 T11: -0.0375 T22: -0.1137 REMARK 3 T33: -0.1125 T12: -0.0462 REMARK 3 T13: 0.0488 T23: -0.0534 REMARK 3 L TENSOR REMARK 3 L11: 1.8097 L22: 3.3975 REMARK 3 L33: 1.2788 L12: -0.7995 REMARK 3 L13: -0.3812 L23: 0.2840 REMARK 3 S TENSOR REMARK 3 S11: 0.0919 S12: -0.1559 S13: 0.1951 REMARK 3 S21: 0.3215 S22: 0.0249 S23: -0.1509 REMARK 3 S31: -0.1898 S32: 0.1219 S33: -0.1169 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 146 A 174 REMARK 3 ORIGIN FOR THE GROUP (A): -29.3291 9.1051 30.6579 REMARK 3 T TENSOR REMARK 3 T11: -0.0475 T22: -0.1047 REMARK 3 T33: -0.1345 T12: -0.0305 REMARK 3 T13: 0.0761 T23: -0.0251 REMARK 3 L TENSOR REMARK 3 L11: 2.2486 L22: 3.6629 REMARK 3 L33: 3.7131 L12: 0.4308 REMARK 3 L13: -0.8123 L23: 1.4873 REMARK 3 S TENSOR REMARK 3 S11: 0.0647 S12: -0.0643 S13: 0.0348 REMARK 3 S21: 0.2677 S22: 0.0481 S23: 0.1588 REMARK 3 S31: -0.1018 S32: 0.1205 S33: -0.1128 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2WQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1290040745. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34250 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1QAB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 TO 4.2 M NACL, 1M HEPES PH 7.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.53000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.75086 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.23667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 51.53000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 29.75086 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.23667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 51.53000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 29.75086 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.23667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.50172 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 48.47333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 59.50172 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 48.47333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 59.50172 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 48.47333 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2143 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 65 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 GLN A 38 -62.37 -95.17 REMARK 500 TYR A 111 -34.78 68.02 REMARK 500 THR A 113 -57.48 -138.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2092 DISTANCE = 6.50 ANGSTROMS REMARK 700 REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1175 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1174 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1176 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1177 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1178 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 1179 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1180 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1181 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1182 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RBP RELATED DB: PDB REMARK 900 RELATED ID: 1JYJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DOUBLE VARIANT (W67L /W91H) OFRECOMBINANT REMARK 900 HUMAN SERUM RETINOL- BINDING PROTEIN AT 2.0 ARESOLUTION REMARK 900 RELATED ID: 1JYD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RECOMBINANT HUMAN SERUM RETINOL-BINDING REMARK 900 PROTEIN AT 1.7 A RESOLUTION REMARK 900 RELATED ID: 1QAB RELATED DB: PDB REMARK 900 THE STRUCTURE OF HUMAN RETINOL BINDING PROTEIN WITH ITSCARRIER REMARK 900 PROTEIN TRANSTHYRETIN REVEALS INTERACTION WITH THECARBOXY TERMINUS REMARK 900 OF RBP REMARK 900 RELATED ID: 2WQA RELATED DB: PDB REMARK 900 COMPLEX OF TTR AND RBP4 AND LINOLEIC ACID DBREF 2WQ9 A 1 174 UNP P02753 RET4_HUMAN 19 192 SEQRES 1 A 174 GLU ARG ASP CYS ARG VAL SER SER PHE ARG VAL LYS GLU SEQRES 2 A 174 ASN PHE ASP LYS ALA ARG PHE SER GLY THR TRP TYR ALA SEQRES 3 A 174 MET ALA LYS LYS ASP PRO GLU GLY LEU PHE LEU GLN ASP SEQRES 4 A 174 ASN ILE VAL ALA GLU PHE SER VAL ASP GLU THR GLY GLN SEQRES 5 A 174 MET SER ALA THR ALA LYS GLY ARG VAL ARG LEU LEU ASN SEQRES 6 A 174 ASN TRP ASP VAL CYS ALA ASP MET VAL GLY THR PHE THR SEQRES 7 A 174 ASP THR GLU ASP PRO ALA LYS PHE LYS MET LYS TYR TRP SEQRES 8 A 174 GLY VAL ALA SER PHE LEU GLN LYS GLY ASN ASP ASP HIS SEQRES 9 A 174 TRP ILE VAL ASP THR ASP TYR ASP THR TYR ALA VAL GLN SEQRES 10 A 174 TYR SER CYS ARG LEU LEU ASN LEU ASP GLY THR CYS ALA SEQRES 11 A 174 ASP SER TYR SER PHE VAL PHE SER ARG ASP PRO ASN GLY SEQRES 12 A 174 LEU PRO PRO GLU ALA GLN LYS ILE VAL ARG GLN ARG GLN SEQRES 13 A 174 GLU GLU LEU CYS LEU ALA ARG GLN TYR ARG LEU ILE VAL SEQRES 14 A 174 HIS ASN GLY TYR CYS HET CL A1175 1 HET CL A1176 1 HET CL A1177 1 HET CL A1178 1 HET OLA A1179 20 HET GOL A1180 6 HET GOL A1181 6 HET GOL A1182 6 HET CL A1174 1 HETNAM CL CHLORIDE ION HETNAM OLA OLEIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CL 5(CL 1-) FORMUL 6 OLA C18 H34 O2 FORMUL 7 GOL 3(C3 H8 O3) FORMUL 11 HOH *233(H2 O) HELIX 1 1 ARG A 5 PHE A 9 5 5 HELIX 2 2 ASP A 16 SER A 21 1 6 HELIX 3 3 PRO A 145 LEU A 159 1 15 SHEET 1 AA 9 ASP A 68 VAL A 69 0 SHEET 2 AA 9 MET A 53 ARG A 62 -1 O VAL A 61 N VAL A 69 SHEET 3 AA 9 LEU A 37 VAL A 47 -1 N GLN A 38 O ARG A 60 SHEET 4 AA 9 TRP A 24 LYS A 30 -1 O TRP A 24 N ALA A 43 SHEET 5 AA 9 CYS A 129 SER A 138 -1 O SER A 134 N LYS A 30 SHEET 6 AA 9 TYR A 114 LEU A 123 -1 O ALA A 115 N PHE A 137 SHEET 7 AA 9 ASP A 102 THR A 109 -1 O TRP A 105 N TYR A 118 SHEET 8 AA 9 LYS A 85 TRP A 91 -1 O PHE A 86 N HIS A 104 SHEET 9 AA 9 VAL A 74 ASP A 79 -1 O VAL A 74 N TRP A 91 SHEET 1 AB 4 ASP A 68 VAL A 69 0 SHEET 2 AB 4 MET A 53 ARG A 62 -1 O VAL A 61 N VAL A 69 SHEET 3 AB 4 LEU A 37 VAL A 47 -1 N GLN A 38 O ARG A 60 SHEET 4 AB 4 TRP A 24 LYS A 30 -1 O TRP A 24 N ALA A 43 SSBOND 1 CYS A 4 CYS A 160 1555 1555 2.04 SSBOND 2 CYS A 70 CYS A 174 1555 1555 2.04 SSBOND 3 CYS A 120 CYS A 129 1555 1555 2.05 SITE 1 AC1 5 SER A 7 ARG A 153 ALA A 162 ARG A 163 SITE 2 AC1 5 HOH A2182 SITE 1 AC2 2 LEU A 123 HOH A2204 SITE 1 AC3 1 ASP A 79 SITE 1 AC4 2 SER A 46 VAL A 47 SITE 1 AC5 4 LYS A 150 ARG A 153 HOH A2204 HOH A2205 SITE 1 AC6 15 LYS A 29 PRO A 32 LEU A 35 PHE A 36 SITE 2 AC6 15 LEU A 37 PHE A 45 ALA A 55 VAL A 74 SITE 3 AC6 15 GLY A 75 TYR A 90 HIS A 104 GLN A 117 SITE 4 AC6 15 PHE A 135 PHE A 137 HOH A2226 SITE 1 AC7 10 ARG A 10 VAL A 11 LYS A 12 VAL A 107 SITE 2 AC7 10 ASP A 108 ARG A 155 GLU A 158 HOH A2206 SITE 3 AC7 10 HOH A2208 HOH A2227 SITE 1 AC8 7 GLY A 22 THR A 23 GLU A 44 ARG A 139 SITE 2 AC8 7 HOH A2228 HOH A2229 HOH A2230 SITE 1 AC9 10 LYS A 29 LYS A 30 ASP A 31 GLN A 164 SITE 2 AC9 10 ARG A 166 HOH A2073 HOH A2216 HOH A2231 SITE 3 AC9 10 HOH A2232 HOH A2233 CRYST1 103.060 103.060 72.710 90.00 90.00 120.00 H 3 9 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 0.009703 0.005602 0.000000 0.00000 SCALE2 0.000000 0.011204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013753 0.00000