HEADER BIOTIN BINDING PROTEIN 14-MAR-16 5IRU TITLE CRYSTAL STRUCTURE OF AVIDIN IN COMPLEX WITH 1-BIOTINYLPYRENE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AVIDIN; COMPND 3 CHAIN: A, B, C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS COMPLEX, BIOTIN BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.STRZELCZYK,G.BUJACZ REVDAT 5 16-OCT-24 5IRU 1 REMARK REVDAT 4 10-JAN-24 5IRU 1 HETSYN REVDAT 3 29-JUL-20 5IRU 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 07-MAR-18 5IRU 1 REMARK REVDAT 1 12-OCT-16 5IRU 0 JRNL AUTH P.STRZELCZYK,D.PLAZUK,J.ZAKRZEWSKI,G.BUJACZ JRNL TITL STRUCTURAL CHARACTERIZATION OF THE AVIDIN INTERACTIONS WITH JRNL TITL 2 FLUORESCENT PYRENE-CONJUGATES: 1-BIOTINYLPYRENE AND JRNL TITL 3 1-DESTHIOBIOTINYLPYRENE. JRNL REF MOLECULES V. 21 2016 JRNL REFN ESSN 1420-3049 JRNL PMID 27689976 JRNL DOI 10.3390/MOLECULES21101270 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 33028 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1739 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2402 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3828 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 180 REMARK 3 SOLVENT ATOMS : 227 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.33000 REMARK 3 B22 (A**2) : -5.42000 REMARK 3 B33 (A**2) : -0.90000 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): 0.232 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.221 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.654 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4108 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3804 ; 0.011 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5584 ; 1.979 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8732 ; 1.822 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 484 ; 7.241 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;34.629 ;23.721 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 676 ;12.763 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.802 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.164 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4584 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1020 ; 0.009 ; 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): 1948 ; 1.817 ; 2.044 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1947 ; 1.808 ; 2.042 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2428 ; 3.127 ; 3.041 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2429 ; 3.128 ; 3.044 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2160 ; 2.151 ; 2.551 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2160 ; 2.151 ; 2.551 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3157 ; 3.381 ; 3.735 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4867 ; 8.530 ;21.539 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4868 ; 8.529 ;21.547 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 : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 3 122 B 3 122 12788 0.09 0.05 REMARK 3 2 A 3 122 C 3 122 12968 0.08 0.05 REMARK 3 3 A 3 122 D 3 122 12768 0.10 0.05 REMARK 3 4 B 2 123 C 2 123 13154 0.09 0.05 REMARK 3 5 B 2 122 D 2 122 13074 0.08 0.05 REMARK 3 6 C 2 122 D 2 122 12918 0.10 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 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 3 A 46 REMARK 3 ORIGIN FOR THE GROUP (A): 31.2740 -5.1310 0.8960 REMARK 3 T TENSOR REMARK 3 T11: 0.1200 T22: 0.3154 REMARK 3 T33: 0.1084 T12: 0.0344 REMARK 3 T13: 0.0072 T23: -0.1283 REMARK 3 L TENSOR REMARK 3 L11: 3.2180 L22: 6.0614 REMARK 3 L33: 12.5926 L12: -1.9416 REMARK 3 L13: 4.0571 L23: 0.1314 REMARK 3 S TENSOR REMARK 3 S11: 0.1770 S12: 0.4084 S13: -0.1432 REMARK 3 S21: -0.3247 S22: -0.1698 S23: -0.0200 REMARK 3 S31: 0.8777 S32: 0.5137 S33: -0.0072 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 47 A 95 REMARK 3 ORIGIN FOR THE GROUP (A): 28.5980 2.9230 1.0890 REMARK 3 T TENSOR REMARK 3 T11: 0.2800 T22: 0.2950 REMARK 3 T33: 0.1892 T12: 0.0202 REMARK 3 T13: 0.0930 T23: -0.0437 REMARK 3 L TENSOR REMARK 3 L11: 5.5787 L22: 10.8658 REMARK 3 L33: 8.2342 L12: 1.1390 REMARK 3 L13: 1.0248 L23: -0.3226 REMARK 3 S TENSOR REMARK 3 S11: -0.0776 S12: 0.3364 S13: 0.7663 REMARK 3 S21: -1.6789 S22: 0.2879 S23: -0.5501 REMARK 3 S31: -0.1241 S32: 0.1553 S33: -0.2102 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 96 A 121 REMARK 3 ORIGIN FOR THE GROUP (A): 20.8680 -3.6870 15.2030 REMARK 3 T TENSOR REMARK 3 T11: 0.0592 T22: 0.1769 REMARK 3 T33: 0.0473 T12: -0.0004 REMARK 3 T13: -0.0252 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 11.7227 L22: 2.0599 REMARK 3 L33: 8.5393 L12: 0.5141 REMARK 3 L13: -6.1376 L23: -1.2517 REMARK 3 S TENSOR REMARK 3 S11: -0.0426 S12: -0.3497 S13: -0.3080 REMARK 3 S21: 0.0451 S22: 0.0975 S23: 0.1612 REMARK 3 S31: 0.3315 S32: 0.0920 S33: -0.0550 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 : B 3 B 46 REMARK 3 ORIGIN FOR THE GROUP (A): 8.3540 1.7120 -0.0270 REMARK 3 T TENSOR REMARK 3 T11: 0.4740 T22: 0.5812 REMARK 3 T33: 0.1338 T12: -0.1178 REMARK 3 T13: -0.2371 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 3.3273 L22: 11.1318 REMARK 3 L33: 17.0019 L12: -1.7867 REMARK 3 L13: -2.8197 L23: 6.4482 REMARK 3 S TENSOR REMARK 3 S11: -0.3611 S12: 0.7266 S13: 0.2484 REMARK 3 S21: -1.8397 S22: 0.0376 S23: 0.8194 REMARK 3 S31: -0.3300 S32: -1.4542 S33: 0.3235 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 : B 47 B 95 REMARK 3 ORIGIN FOR THE GROUP (A): 11.6390 -4.3650 5.4110 REMARK 3 T TENSOR REMARK 3 T11: 0.0728 T22: 0.3849 REMARK 3 T33: 0.1201 T12: -0.0319 REMARK 3 T13: -0.0563 T23: -0.0618 REMARK 3 L TENSOR REMARK 3 L11: 3.9597 L22: 8.9132 REMARK 3 L33: 8.3591 L12: 0.6851 REMARK 3 L13: -0.4940 L23: 2.3399 REMARK 3 S TENSOR REMARK 3 S11: -0.1230 S12: 0.3813 S13: -0.3435 REMARK 3 S21: -0.1365 S22: 0.2194 S23: 0.4342 REMARK 3 S31: 0.4507 S32: -1.0152 S33: -0.0964 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 : B 96 B 121 REMARK 3 ORIGIN FOR THE GROUP (A): 20.8620 10.2830 9.1010 REMARK 3 T TENSOR REMARK 3 T11: 0.1217 T22: 0.2532 REMARK 3 T33: 0.1105 T12: 0.0799 REMARK 3 T13: 0.0763 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 8.6117 L22: 2.1751 REMARK 3 L33: 4.6375 L12: 2.0812 REMARK 3 L13: 2.1796 L23: 1.1371 REMARK 3 S TENSOR REMARK 3 S11: 0.2178 S12: 0.0977 S13: 0.7649 REMARK 3 S21: -0.1400 S22: -0.0232 S23: 0.1788 REMARK 3 S31: -0.6096 S32: -0.3096 S33: -0.1947 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 : C 3 C 46 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8750 7.6120 34.8230 REMARK 3 T TENSOR REMARK 3 T11: 0.4589 T22: 0.3454 REMARK 3 T33: 0.1238 T12: -0.0131 REMARK 3 T13: 0.2346 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 3.4099 L22: 8.5443 REMARK 3 L33: 9.3002 L12: 1.0349 REMARK 3 L13: 0.9294 L23: 3.5215 REMARK 3 S TENSOR REMARK 3 S11: 0.1869 S12: 0.0750 S13: 0.2069 REMARK 3 S21: 1.8370 S22: -0.2448 S23: 0.9493 REMARK 3 S31: 0.0498 S32: -0.4573 S33: 0.0578 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 : C 47 C 95 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1670 13.8820 28.8390 REMARK 3 T TENSOR REMARK 3 T11: 0.2255 T22: 0.3105 REMARK 3 T33: 0.2146 T12: 0.0709 REMARK 3 T13: 0.2039 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 3.4494 L22: 9.5636 REMARK 3 L33: 6.0817 L12: -1.0646 REMARK 3 L13: 1.6136 L23: -2.7385 REMARK 3 S TENSOR REMARK 3 S11: 0.2852 S12: 0.0218 S13: 0.5427 REMARK 3 S21: 1.1075 S22: -0.0298 S23: 0.8629 REMARK 3 S31: -0.6320 S32: -0.6866 S33: -0.2554 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 : C 96 C 121 REMARK 3 ORIGIN FOR THE GROUP (A): 22.7690 -0.0460 23.2160 REMARK 3 T TENSOR REMARK 3 T11: 0.1722 T22: 0.1663 REMARK 3 T33: 0.0189 T12: -0.0724 REMARK 3 T13: 0.0225 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 9.0518 L22: 2.9839 REMARK 3 L33: 2.9447 L12: -1.9526 REMARK 3 L13: -0.7473 L23: 0.5051 REMARK 3 S TENSOR REMARK 3 S11: -0.0476 S12: 0.4234 S13: -0.1351 REMARK 3 S21: 0.1702 S22: -0.0798 S23: -0.0996 REMARK 3 S31: 0.7016 S32: -0.2876 S33: 0.1274 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 : D 3 D 46 REMARK 3 ORIGIN FOR THE GROUP (A): 33.3780 16.5450 28.9920 REMARK 3 T TENSOR REMARK 3 T11: 0.4623 T22: 0.2159 REMARK 3 T33: 0.0458 T12: -0.1349 REMARK 3 T13: -0.0413 T23: -0.0537 REMARK 3 L TENSOR REMARK 3 L11: 1.0612 L22: 9.8392 REMARK 3 L33: 4.6267 L12: 1.7517 REMARK 3 L13: -0.8358 L23: 1.4709 REMARK 3 S TENSOR REMARK 3 S11: 0.1733 S12: -0.1171 S13: -0.1211 REMARK 3 S21: 0.7906 S22: -0.2286 S23: -0.2257 REMARK 3 S31: -0.9572 S32: 0.5434 S33: 0.0554 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 47 D 95 REMARK 3 ORIGIN FOR THE GROUP (A): 31.4280 7.9630 29.8720 REMARK 3 T TENSOR REMARK 3 T11: 0.0976 T22: 0.1949 REMARK 3 T33: 0.0574 T12: -0.0212 REMARK 3 T13: -0.0640 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 0.6704 L22: 9.8021 REMARK 3 L33: 6.8632 L12: -1.3346 REMARK 3 L13: 0.5615 L23: -2.8724 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: 0.0149 S13: 0.0733 REMARK 3 S21: 0.7820 S22: -0.0648 S23: -0.6625 REMARK 3 S31: -0.0238 S32: 0.3241 S33: 0.0660 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 96 D 121 REMARK 3 ORIGIN FOR THE GROUP (A): 20.1940 13.8050 17.3040 REMARK 3 T TENSOR REMARK 3 T11: 0.1749 T22: 0.1647 REMARK 3 T33: 0.0791 T12: -0.0063 REMARK 3 T13: -0.0437 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 12.1112 L22: 1.1138 REMARK 3 L33: 4.2050 L12: 0.9289 REMARK 3 L13: 3.4118 L23: 0.8500 REMARK 3 S TENSOR REMARK 3 S11: -0.0393 S12: 0.0090 S13: 0.2738 REMARK 3 S21: -0.3932 S22: 0.1470 S23: 0.1868 REMARK 3 S31: -0.4156 S32: -0.1729 S33: -0.1077 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5IRU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219335. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-15 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99999 REMARK 200 MONOCHROMATOR : NULL 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 : 34767 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.410 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4800 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.62 REMARK 200 R MERGE FOR SHELL (I) : 0.50800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.610 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: 3VGW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% W/V POLYETHYLENE GLYCOL MONOMETHYL REMARK 280 ETHER 2000, 0.1 M BIS-TRIS, 0.1 M TRIMETHYLAMINE HYDROCHLORIDE, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 28.58000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.94500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.97500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.94500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.58000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.97500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 ALA A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 124 REMARK 465 THR A 125 REMARK 465 GLN A 126 REMARK 465 LYS A 127 REMARK 465 GLU A 128 REMARK 465 ALA B 1 REMARK 465 ARG B 124 REMARK 465 THR B 125 REMARK 465 GLN B 126 REMARK 465 LYS B 127 REMARK 465 GLU B 128 REMARK 465 ALA C 1 REMARK 465 ARG C 124 REMARK 465 THR C 125 REMARK 465 GLN C 126 REMARK 465 LYS C 127 REMARK 465 GLU C 128 REMARK 465 ALA D 1 REMARK 465 THR D 125 REMARK 465 GLN D 126 REMARK 465 LYS D 127 REMARK 465 GLU D 128 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 OE1 GLU D 91 NH1 ARG D 122 1.91 REMARK 500 O THR D 7 NH2 ARG D 122 2.19 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 26 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 26 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 LEU C 14 CB - CG - CD2 ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG C 26 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG C 26 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG D 59 NE - CZ - NH1 ANGL. DEV. = 4.9 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 LYS A 58 60.43 33.01 REMARK 500 ASN B 57 17.19 59.85 REMARK 500 LYS B 58 62.26 31.81 REMARK 500 LYS C 58 60.43 32.65 REMARK 500 LYS D 58 59.26 34.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VGW RELATED DB: PDB REMARK 900 MONOAC-BIOTIN - AVIDIN COMPLEX REMARK 900 RELATED ID: 1VYO RELATED DB: PDB REMARK 900 AVIDIN, FREE-LIGAND STRUCTURE REMARK 900 RELATED ID: 4I60 RELATED DB: PDB REMARK 900 AVIDIN - BIOTINYLRUTHENOCENE COMPLEX DBREF 5IRU A 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5IRU B 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5IRU C 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5IRU D 1 128 UNP P02701 AVID_CHICK 25 152 SEQADV 5IRU THR A 34 UNP P02701 ILE 58 CONFLICT SEQADV 5IRU THR B 34 UNP P02701 ILE 58 CONFLICT SEQADV 5IRU THR C 34 UNP P02701 ILE 58 CONFLICT SEQADV 5IRU THR D 34 UNP P02701 ILE 58 CONFLICT SEQRES 1 A 128 ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP SEQRES 2 A 128 LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG SEQRES 3 A 128 GLY GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA SEQRES 4 A 128 THR SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR SEQRES 5 A 128 GLN ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY SEQRES 6 A 128 PHE THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL SEQRES 7 A 128 PHE THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU SEQRES 8 A 128 VAL LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN SEQRES 9 A 128 ASP ILE GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE SEQRES 10 A 128 ASN ILE PHE THR ARG LEU ARG THR GLN LYS GLU SEQRES 1 B 128 ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP SEQRES 2 B 128 LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG SEQRES 3 B 128 GLY GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA SEQRES 4 B 128 THR SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR SEQRES 5 B 128 GLN ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY SEQRES 6 B 128 PHE THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL SEQRES 7 B 128 PHE THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU SEQRES 8 B 128 VAL LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN SEQRES 9 B 128 ASP ILE GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE SEQRES 10 B 128 ASN ILE PHE THR ARG LEU ARG THR GLN LYS GLU SEQRES 1 C 128 ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP SEQRES 2 C 128 LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG SEQRES 3 C 128 GLY GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA SEQRES 4 C 128 THR SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR SEQRES 5 C 128 GLN ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY SEQRES 6 C 128 PHE THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL SEQRES 7 C 128 PHE THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU SEQRES 8 C 128 VAL LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN SEQRES 9 C 128 ASP ILE GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE SEQRES 10 C 128 ASN ILE PHE THR ARG LEU ARG THR GLN LYS GLU SEQRES 1 D 128 ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP SEQRES 2 D 128 LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER ARG SEQRES 3 D 128 GLY GLU PHE THR GLY THR TYR THR THR ALA VAL THR ALA SEQRES 4 D 128 THR SER ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR SEQRES 5 D 128 GLN ASN THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY SEQRES 6 D 128 PHE THR VAL ASN TRP LYS PHE SER GLU SER THR THR VAL SEQRES 7 D 128 PHE THR GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU SEQRES 8 D 128 VAL LEU LYS THR MET TRP LEU LEU ARG SER SER VAL ASN SEQRES 9 D 128 ASP ILE GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE SEQRES 10 D 128 ASN ILE PHE THR ARG LEU ARG THR GLN LYS GLU HET NAG A 201 14 HET B9P A 202 31 HET NAG B 201 14 HET B9P B 202 31 HET NAG C 201 14 HET B9P C 202 31 HET NAG D 201 14 HET B9P D 202 31 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM B9P 1-BIOTINYLPYRENE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 5 NAG 4(C8 H15 N O6) FORMUL 6 B9P 4(C26 H24 N2 O2 S) FORMUL 13 HOH *227(H2 O) HELIX 1 AA1 THR A 55 ARG A 59 5 5 HELIX 2 AA2 ASP A 105 LYS A 111 5 7 HELIX 3 AA3 THR B 55 ARG B 59 5 5 HELIX 4 AA4 ASP B 105 LYS B 111 5 7 HELIX 5 AA5 THR C 55 ARG C 59 5 5 HELIX 6 AA6 ASP C 105 LYS C 111 5 7 HELIX 7 AA7 THR D 55 ARG D 59 5 5 HELIX 8 AA8 ASP D 105 LYS D 111 5 7 SHEET 1 AA1 9 GLY A 8 ASN A 12 0 SHEET 2 AA1 9 ASN A 17 ILE A 20 -1 O ILE A 20 N GLY A 8 SHEET 3 AA1 9 GLU A 28 THR A 34 -1 O THR A 34 N ASN A 17 SHEET 4 AA1 9 SER A 47 GLN A 53 -1 O GLY A 51 N PHE A 29 SHEET 5 AA1 9 THR A 63 ASN A 69 -1 O GLY A 65 N THR A 52 SHEET 6 AA1 9 THR A 76 ILE A 85 -1 O THR A 77 N VAL A 68 SHEET 7 AA1 9 GLU A 91 ARG A 100 -1 O ARG A 100 N THR A 76 SHEET 8 AA1 9 THR A 113 ARG A 122 -1 O GLY A 116 N TRP A 97 SHEET 9 AA1 9 GLY A 8 ASN A 12 -1 N THR A 11 O THR A 121 SHEET 1 AA2 9 GLY B 8 ASN B 12 0 SHEET 2 AA2 9 ASN B 17 ILE B 20 -1 O ILE B 20 N GLY B 8 SHEET 3 AA2 9 GLU B 28 THR B 34 -1 O THR B 34 N ASN B 17 SHEET 4 AA2 9 SER B 47 GLN B 53 -1 O SER B 47 N TYR B 33 SHEET 5 AA2 9 THR B 63 ASN B 69 -1 O GLY B 65 N THR B 52 SHEET 6 AA2 9 THR B 76 ILE B 85 -1 O THR B 77 N VAL B 68 SHEET 7 AA2 9 GLU B 91 ARG B 100 -1 O VAL B 92 N PHE B 84 SHEET 8 AA2 9 THR B 113 ARG B 122 -1 O ARG B 114 N LEU B 99 SHEET 9 AA2 9 GLY B 8 ASN B 12 -1 N THR B 11 O THR B 121 SHEET 1 AA3 9 GLY C 8 ASN C 12 0 SHEET 2 AA3 9 ASN C 17 ILE C 20 -1 O ILE C 20 N GLY C 8 SHEET 3 AA3 9 GLU C 28 THR C 34 -1 O THR C 34 N ASN C 17 SHEET 4 AA3 9 SER C 47 GLN C 53 -1 O SER C 47 N TYR C 33 SHEET 5 AA3 9 THR C 63 ASN C 69 -1 O GLY C 65 N THR C 52 SHEET 6 AA3 9 THR C 76 ILE C 85 -1 O THR C 77 N VAL C 68 SHEET 7 AA3 9 GLU C 91 ARG C 100 -1 O ARG C 100 N THR C 76 SHEET 8 AA3 9 THR C 113 ARG C 122 -1 O GLY C 116 N TRP C 97 SHEET 9 AA3 9 GLY C 8 ASN C 12 -1 N THR C 11 O THR C 121 SHEET 1 AA4 9 GLY D 8 ASN D 12 0 SHEET 2 AA4 9 ASN D 17 ILE D 20 -1 O ILE D 20 N GLY D 8 SHEET 3 AA4 9 GLU D 28 THR D 34 -1 O THR D 34 N ASN D 17 SHEET 4 AA4 9 SER D 47 GLN D 53 -1 O SER D 47 N TYR D 33 SHEET 5 AA4 9 THR D 63 ASN D 69 -1 O THR D 67 N HIS D 50 SHEET 6 AA4 9 THR D 76 ILE D 85 -1 O THR D 77 N VAL D 68 SHEET 7 AA4 9 GLU D 91 ARG D 100 -1 O ARG D 100 N THR D 76 SHEET 8 AA4 9 THR D 113 ARG D 122 -1 O GLY D 116 N TRP D 97 SHEET 9 AA4 9 GLY D 8 ASN D 12 -1 N THR D 11 O THR D 121 SSBOND 1 CYS A 4 CYS A 83 1555 1555 1.98 SSBOND 2 CYS B 4 CYS B 83 1555 1555 1.98 SSBOND 3 CYS C 4 CYS C 83 1555 1555 1.98 SSBOND 4 CYS D 4 CYS D 83 1555 1555 1.95 LINK ND2 ASN A 17 C1 NAG A 201 1555 1555 1.46 LINK ND2 ASN B 17 C1 NAG B 201 1555 1555 1.46 LINK ND2 ASN C 17 C1 NAG C 201 1555 1555 1.44 LINK ND2 ASN D 17 C1 NAG D 201 1555 1555 1.44 CRYST1 57.160 81.950 107.890 90.00 90.00 90.00 P 21 21 21 16 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 0.017495 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009269 0.00000