HEADER BIOTIN-BINDING PROTEIN 27-JAN-17 5MYQ TITLE CRYSTAL STRUCTURE OF AVIDIN IN COMPLEX WITH FERROCENE HOMOBIOTIN TITLE 2 DERIVATIVE 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 4 13-NOV-24 5MYQ 1 REMARK REVDAT 3 17-JAN-24 5MYQ 1 HETSYN REVDAT 2 29-JUL-20 5MYQ 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 14-FEB-18 5MYQ 0 JRNL AUTH P.STRZELCZYK,D.PLAZUK,G.BUJACZ JRNL TITL STRUCTURAL INVESTIGATION OF THE INTERACTIONS OF FERROCENE JRNL TITL 2 HOMOBIOTIN DERIVATIVE WITH AVIDIN. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 38729 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1229 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) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2650 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3190 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 : 181 REMARK 3 SOLVENT ATOMS : 337 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.25000 REMARK 3 B22 (A**2) : -2.08000 REMARK 3 B33 (A**2) : 1.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.161 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.551 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4112 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3808 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5756 ; 2.185 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8740 ; 1.115 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 484 ; 7.412 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;33.508 ;23.721 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 676 ;15.088 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;21.482 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4532 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1020 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1948 ; 1.264 ; 1.832 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1947 ; 1.261 ; 1.830 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2428 ; 2.133 ; 2.729 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2429 ; 2.134 ; 2.731 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2164 ; 1.559 ; 2.161 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2165 ; 1.558 ; 2.162 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3173 ; 2.139 ; 3.188 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4613 ; 6.609 ;16.105 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4614 ; 6.609 ;16.112 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 : 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): 0.2209 58.9844 9.0705 REMARK 3 T TENSOR REMARK 3 T11: 0.0510 T22: 0.0256 REMARK 3 T33: 0.0720 T12: 0.0118 REMARK 3 T13: 0.0202 T23: 0.0362 REMARK 3 L TENSOR REMARK 3 L11: 4.6588 L22: 3.9226 REMARK 3 L33: 4.1382 L12: -1.6991 REMARK 3 L13: 1.3927 L23: -0.5061 REMARK 3 S TENSOR REMARK 3 S11: -0.0630 S12: 0.1791 S13: 0.4196 REMARK 3 S21: 0.1269 S22: 0.0221 S23: -0.0873 REMARK 3 S31: -0.3227 S32: -0.0741 S33: 0.0409 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): -6.9273 55.5001 13.0805 REMARK 3 T TENSOR REMARK 3 T11: 0.0505 T22: 0.0632 REMARK 3 T33: 0.0989 T12: 0.0473 REMARK 3 T13: 0.0305 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 5.0935 L22: 2.9603 REMARK 3 L33: 2.6316 L12: -0.2403 REMARK 3 L13: -0.4139 L23: 0.0679 REMARK 3 S TENSOR REMARK 3 S11: 0.0434 S12: -0.0488 S13: 0.4886 REMARK 3 S21: 0.1712 S22: -0.0287 S23: 0.2987 REMARK 3 S31: -0.2993 S32: -0.3476 S33: -0.0148 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): 5.0238 42.5177 13.7069 REMARK 3 T TENSOR REMARK 3 T11: 0.0124 T22: 0.0383 REMARK 3 T33: 0.0364 T12: 0.0189 REMARK 3 T13: -0.0173 T23: -0.0258 REMARK 3 L TENSOR REMARK 3 L11: 2.1012 L22: 6.5870 REMARK 3 L33: 2.7320 L12: -0.9512 REMARK 3 L13: 0.5622 L23: -0.3061 REMARK 3 S TENSOR REMARK 3 S11: -0.0421 S12: 0.0614 S13: 0.0131 REMARK 3 S21: 0.1628 S22: 0.2043 S23: -0.3739 REMARK 3 S31: 0.1305 S32: 0.2607 S33: -0.1622 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): -11.4103 39.3536 1.8533 REMARK 3 T TENSOR REMARK 3 T11: 0.0777 T22: 0.1511 REMARK 3 T33: 0.0682 T12: -0.0050 REMARK 3 T13: -0.0486 T23: -0.0380 REMARK 3 L TENSOR REMARK 3 L11: 2.1752 L22: 4.3417 REMARK 3 L33: 2.1181 L12: -0.6628 REMARK 3 L13: 0.6927 L23: -0.8551 REMARK 3 S TENSOR REMARK 3 S11: 0.0249 S12: 0.2801 S13: -0.1782 REMARK 3 S21: -0.2929 S22: 0.0276 S23: 0.3452 REMARK 3 S31: 0.0011 S32: -0.2428 S33: -0.0525 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): -2.8666 39.9604 3.2343 REMARK 3 T TENSOR REMARK 3 T11: 0.0726 T22: 0.0842 REMARK 3 T33: 0.0122 T12: -0.0113 REMARK 3 T13: -0.0024 T23: -0.0244 REMARK 3 L TENSOR REMARK 3 L11: 1.9242 L22: 3.0263 REMARK 3 L33: 2.1994 L12: -0.7313 REMARK 3 L13: 0.0139 L23: 0.0379 REMARK 3 S TENSOR REMARK 3 S11: 0.0849 S12: 0.3346 S13: -0.1232 REMARK 3 S21: -0.4612 S22: 0.0044 S23: 0.0233 REMARK 3 S31: 0.0312 S32: -0.0334 S33: -0.0893 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): -9.1733 43.8084 19.0307 REMARK 3 T TENSOR REMARK 3 T11: 0.0201 T22: 0.0827 REMARK 3 T33: 0.0599 T12: 0.0244 REMARK 3 T13: 0.0288 T23: 0.0455 REMARK 3 L TENSOR REMARK 3 L11: 1.9281 L22: 4.9088 REMARK 3 L33: 6.9235 L12: -0.5585 REMARK 3 L13: 0.1628 L23: 2.8396 REMARK 3 S TENSOR REMARK 3 S11: -0.0663 S12: -0.2921 S13: -0.0269 REMARK 3 S21: 0.2951 S22: 0.2227 S23: 0.3569 REMARK 3 S31: 0.0699 S32: -0.1964 S33: -0.1564 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): 5.9857 22.9733 28.2173 REMARK 3 T TENSOR REMARK 3 T11: 0.1329 T22: 0.0409 REMARK 3 T33: 0.1319 T12: 0.0266 REMARK 3 T13: -0.0157 T23: 0.0603 REMARK 3 L TENSOR REMARK 3 L11: 2.7361 L22: 4.5204 REMARK 3 L33: 6.3213 L12: -0.5108 REMARK 3 L13: 0.3080 L23: 0.0046 REMARK 3 S TENSOR REMARK 3 S11: -0.0394 S12: -0.1775 S13: -0.2382 REMARK 3 S21: -0.1022 S22: -0.0058 S23: -0.1653 REMARK 3 S31: 0.1916 S32: 0.1713 S33: 0.0452 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): -1.7940 26.6967 28.9122 REMARK 3 T TENSOR REMARK 3 T11: 0.0972 T22: 0.0927 REMARK 3 T33: 0.0979 T12: -0.0258 REMARK 3 T13: 0.0307 T23: 0.0608 REMARK 3 L TENSOR REMARK 3 L11: 5.5985 L22: 4.3869 REMARK 3 L33: 3.4932 L12: 0.4004 REMARK 3 L13: -0.4740 L23: -0.3021 REMARK 3 S TENSOR REMARK 3 S11: -0.0160 S12: -0.3251 S13: -0.4134 REMARK 3 S21: 0.1212 S22: -0.0023 S23: 0.3515 REMARK 3 S31: 0.4829 S32: -0.3227 S33: 0.0182 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): 7.6541 39.5353 21.6086 REMARK 3 T TENSOR REMARK 3 T11: 0.0281 T22: 0.0550 REMARK 3 T33: 0.0400 T12: 0.0157 REMARK 3 T13: -0.0003 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 3.3174 L22: 7.9244 REMARK 3 L33: 2.1948 L12: 3.0405 REMARK 3 L13: 0.0906 L23: -0.0276 REMARK 3 S TENSOR REMARK 3 S11: -0.0782 S12: 0.0610 S13: -0.0189 REMARK 3 S21: -0.1155 S22: 0.1488 S23: -0.1596 REMARK 3 S31: -0.0229 S32: 0.1971 S33: -0.0705 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): 1.5382 42.6808 40.8854 REMARK 3 T TENSOR REMARK 3 T11: 0.2132 T22: 0.2330 REMARK 3 T33: 0.0336 T12: 0.0069 REMARK 3 T13: -0.0064 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 2.8552 L22: 4.0935 REMARK 3 L33: 2.9700 L12: -0.7326 REMARK 3 L13: -0.0742 L23: -0.5511 REMARK 3 S TENSOR REMARK 3 S11: 0.1075 S12: -0.5906 S13: -0.1847 REMARK 3 S21: 0.4080 S22: -0.0101 S23: 0.2172 REMARK 3 S31: -0.0394 S32: -0.1124 S33: -0.0974 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): 7.5630 42.0353 34.5955 REMARK 3 T TENSOR REMARK 3 T11: 0.0878 T22: 0.1269 REMARK 3 T33: 0.0614 T12: 0.0270 REMARK 3 T13: -0.0470 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 3.7367 L22: 3.4088 REMARK 3 L33: 2.0869 L12: 1.3966 REMARK 3 L13: -0.3779 L23: -0.0260 REMARK 3 S TENSOR REMARK 3 S11: 0.0122 S12: -0.3872 S13: -0.2073 REMARK 3 S21: 0.4487 S22: 0.1077 S23: -0.4193 REMARK 3 S31: -0.0048 S32: 0.1555 S33: -0.1200 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): -6.9937 38.4945 25.7713 REMARK 3 T TENSOR REMARK 3 T11: 0.0157 T22: 0.1059 REMARK 3 T33: 0.0880 T12: 0.0319 REMARK 3 T13: 0.0362 T23: 0.0690 REMARK 3 L TENSOR REMARK 3 L11: 4.0108 L22: 4.5963 REMARK 3 L33: 6.0411 L12: 2.0397 REMARK 3 L13: 2.4016 L23: 2.6249 REMARK 3 S TENSOR REMARK 3 S11: -0.0894 S12: -0.0967 S13: -0.1726 REMARK 3 S21: 0.1160 S22: 0.1688 S23: 0.3779 REMARK 3 S31: -0.0720 S32: -0.5191 S33: -0.0794 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 5MYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1200003265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91840 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42387 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 71.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 1.920 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3600 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 (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.42300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.970 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: 1VYO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM IODIDE, 22 % W/V PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 41.04050 REMARK 290 SMTRY3 2 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 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 ARG D 124 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 O HOH A 456 O HOH A 467 1.33 REMARK 500 O HOH C 357 O HOH C 360 1.92 REMARK 500 O HOH A 480 O HOH A 483 2.12 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 CYS B 83 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 CYS D 83 CA - CB - SG ANGL. DEV. = 8.2 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 ALA A 39 24.31 -147.55 REMARK 500 ALA B 39 32.42 -140.50 REMARK 500 ASN B 57 8.39 58.74 REMARK 500 ALA C 39 18.44 -154.19 REMARK 500 ASN D 57 15.13 56.66 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 A 485 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH B 402 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH B 403 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH B 404 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH B 405 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH B 406 DISTANCE = 7.30 ANGSTROMS REMARK 525 HOH D 379 DISTANCE = 6.23 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VYO RELATED DB: PDB REMARK 900 AVIDIN, FREE-LIGAND STRUCTURE REMARK 900 RELATED ID: 3VGW RELATED DB: PDB REMARK 900 MONOAC-BIOTIN - AVIDIN COMPLEX REMARK 900 RELATED ID: 4I60 RELATED DB: PDB REMARK 900 AVIDIN - BIOTINYLRUTHENOCENE COMPLEX DBREF 5MYQ A 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5MYQ B 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5MYQ C 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5MYQ D 1 128 UNP P02701 AVID_CHICK 25 152 SEQADV 5MYQ THR A 34 UNP P02701 ILE 58 CONFLICT SEQADV 5MYQ THR B 34 UNP P02701 ILE 58 CONFLICT SEQADV 5MYQ THR C 34 UNP P02701 ILE 58 CONFLICT SEQADV 5MYQ 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 HBF A 301 26 HET NAG A 302 14 HET IOD A 303 1 HET IOD A 304 1 HET IOD A 305 1 HET IOD A 306 1 HET HBF B 201 26 HET NAG B 202 14 HET IOD B 203 1 HET IOD B 204 1 HET IOD B 205 1 HET IOD B 206 1 HET IOD B 207 1 HET IOD B 208 1 HET HBF C 201 26 HET NAG C 202 14 HET IOD C 203 1 HET IOD C 204 1 HET IOD C 205 1 HET IOD C 206 1 HET IOD C 207 1 HET HBF D 201 26 HET NAG D 202 14 HET IOD D 203 1 HET IOD D 204 1 HET IOD D 205 1 HET IOD D 206 1 HET IOD D 207 1 HET IOD D 208 1 HETNAM HBF FERROCENE HOMOBIOTIN DERIVATIVE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM IOD IODIDE ION 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 HBF 4(C21 H17 FE N2 O S 1-) FORMUL 6 NAG 4(C8 H15 N O6) FORMUL 7 IOD 21(I 1-) FORMUL 34 HOH *337(H2 O) HELIX 1 AA1 ASP A 105 LYS A 111 5 7 HELIX 2 AA2 THR B 55 ARG B 59 5 5 HELIX 3 AA3 ASP B 105 LYS B 111 5 7 HELIX 4 AA4 ASP C 105 LYS C 111 5 7 HELIX 5 AA5 THR D 55 ARG D 59 5 5 HELIX 6 AA6 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 ASN A 54 -1 O GLY A 51 N PHE A 29 SHEET 5 AA1 9 THR A 63 ASN A 69 -1 O THR A 63 N ASN A 54 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 ARG A 114 N LEU A 99 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 MET B 18 N TRP B 10 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 THR B 67 N HIS B 50 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 GLY C 51 N PHE C 29 SHEET 5 AA3 9 THR C 63 VAL C 68 -1 O THR C 67 N HIS C 50 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 VAL D 92 N PHE D 84 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 2.01 SSBOND 2 CYS B 4 CYS B 83 1555 1555 1.99 SSBOND 3 CYS C 4 CYS C 83 1555 1555 2.03 SSBOND 4 CYS D 4 CYS D 83 1555 1555 2.01 LINK ND2 ASN A 17 C1 NAG A 302 1555 1555 1.34 LINK ND2 ASN B 17 C1 NAG B 202 1555 1555 1.33 LINK ND2 ASN C 17 C1 NAG C 202 1555 1555 1.33 LINK ND2 ASN D 17 C1 NAG D 202 1555 1555 1.31 CRYST1 43.933 82.081 74.601 90.00 106.29 90.00 P 1 21 1 8 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 0.022762 0.000000 0.006653 0.00000 SCALE2 0.000000 0.012183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013966 0.00000