HEADER GLYCOPROTEIN 03-MAY-04 1VYO TITLE CRYSTAL STRUCTURE OF AVIDIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AVIDIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOPROTEIN, BIOTIN EXPDTA X-RAY DIFFRACTION AUTHOR T.T.AIRENNE,M.S.JOHNSON,T.A.SALMINEN REVDAT 6 13-DEC-23 1VYO 1 REMARK REVDAT 5 16-OCT-19 1VYO 1 REMARK REVDAT 4 24-JUL-19 1VYO 1 REMARK REVDAT 3 24-FEB-09 1VYO 1 VERSN REVDAT 2 25-SEP-07 1VYO 1 JRNL REVDAT 1 20-JUL-05 1VYO 0 JRNL AUTH S.REPO,T.A.PALDANIUS,V.P.HYTONEN,T.K.NYHOLM,K.K.HALLING, JRNL AUTH 2 J.HUUSKONEN,O.T.PENTIKAINEN,K.RISSANEN,J.P.SLOTTE, JRNL AUTH 3 T.T.AIRENNE,T.A.SALMINEN,M.S.KULOMAA,M.S.JOHNSON JRNL TITL BINDING PROPERTIES OF HABA-TYPE AZO DERIVATIVES TO AVIDIN JRNL TITL 2 AND AVIDIN-RELATED PROTEIN 4. JRNL REF CHEM.BIOL. V. 13 1029 2006 JRNL REFN ISSN 1074-5521 JRNL PMID 17052607 JRNL DOI 10.1016/J.CHEMBIOL.2006.08.006 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 39720 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2091 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2878 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 152 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1905 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.13000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : -0.77000 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): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.213 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2134 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1914 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2887 ; 1.483 ; 1.924 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4477 ; 0.849 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 6.972 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 343 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2290 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 427 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 373 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2260 ; 0.257 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1330 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 96 ; 0.149 ; 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): 49 ; 0.247 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 197 ; 0.303 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.141 ; 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): 1285 ; 0.700 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2114 ; 1.226 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 849 ; 2.013 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 773 ; 3.246 ; 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 : 8 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 34 A 45 REMARK 3 ORIGIN FOR THE GROUP (A): -3.4540 16.0290 -8.8550 REMARK 3 T TENSOR REMARK 3 T11: 0.1457 T22: 0.1811 REMARK 3 T33: 0.1539 T12: -0.0046 REMARK 3 T13: -0.0004 T23: 0.0402 REMARK 3 L TENSOR REMARK 3 L11: 2.7193 L22: 7.3288 REMARK 3 L33: 7.9231 L12: -1.0747 REMARK 3 L13: 1.8585 L23: 4.2408 REMARK 3 S TENSOR REMARK 3 S11: 0.1245 S12: 0.2604 S13: -0.1580 REMARK 3 S21: -0.6367 S22: -0.0683 S23: 0.0551 REMARK 3 S31: -0.0939 S32: -0.1316 S33: -0.0562 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 : B 34 B 45 REMARK 3 ORIGIN FOR THE GROUP (A): 16.6310 0.3080 23.6920 REMARK 3 T TENSOR REMARK 3 T11: 0.3140 T22: 0.2734 REMARK 3 T33: 0.2825 T12: -0.0490 REMARK 3 T13: -0.0116 T23: 0.0137 REMARK 3 L TENSOR REMARK 3 L11: 2.7157 L22: -2.3362 REMARK 3 L33: 9.1222 L12: -0.6074 REMARK 3 L13: -2.0201 L23: -0.8251 REMARK 3 S TENSOR REMARK 3 S11: 0.0724 S12: -0.2556 S13: -0.1887 REMARK 3 S21: -0.0443 S22: 0.0822 S23: 0.3024 REMARK 3 S31: -0.0972 S32: -0.2961 S33: -0.1546 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 3 A 33 REMARK 3 ORIGIN FOR THE GROUP (A): -7.8990 21.0980 8.3210 REMARK 3 T TENSOR REMARK 3 T11: 0.1190 T22: 0.0919 REMARK 3 T33: 0.1117 T12: 0.0169 REMARK 3 T13: -0.0170 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 2.8240 L22: 2.4720 REMARK 3 L33: 2.3247 L12: -0.7272 REMARK 3 L13: -0.6585 L23: 0.1604 REMARK 3 S TENSOR REMARK 3 S11: -0.0537 S12: -0.1329 S13: 0.1732 REMARK 3 S21: 0.2474 S22: 0.0376 S23: -0.0850 REMARK 3 S31: -0.1689 S32: 0.0435 S33: 0.0161 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 2 B 33 REMARK 3 ORIGIN FOR THE GROUP (A): 22.6080 -2.1560 5.7250 REMARK 3 T TENSOR REMARK 3 T11: 0.0323 T22: 0.1782 REMARK 3 T33: 0.1465 T12: -0.0155 REMARK 3 T13: -0.0218 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 2.4131 L22: 3.2377 REMARK 3 L33: 1.9020 L12: 0.0282 REMARK 3 L13: 0.2973 L23: -0.7874 REMARK 3 S TENSOR REMARK 3 S11: -0.0131 S12: 0.1185 S13: 0.0345 REMARK 3 S21: -0.0093 S22: -0.0988 S23: -0.2690 REMARK 3 S31: -0.0877 S32: 0.2624 S33: 0.1119 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 46 A 84 REMARK 3 ORIGIN FOR THE GROUP (A): -8.7650 13.9800 8.8010 REMARK 3 T TENSOR REMARK 3 T11: 0.0373 T22: 0.0458 REMARK 3 T33: 0.0670 T12: 0.0177 REMARK 3 T13: 0.0010 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.1466 L22: 1.2939 REMARK 3 L33: 3.2830 L12: -0.1127 REMARK 3 L13: 0.3049 L23: -0.0495 REMARK 3 S TENSOR REMARK 3 S11: -0.0388 S12: -0.0226 S13: 0.1076 REMARK 3 S21: 0.1080 S22: 0.0334 S23: -0.0002 REMARK 3 S31: -0.3145 S32: -0.0491 S33: 0.0054 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 85 A 90 REMARK 3 ORIGIN FOR THE GROUP (A): 6.7480 22.8110 18.4860 REMARK 3 T TENSOR REMARK 3 T11: 0.3773 T22: 0.3438 REMARK 3 T33: 0.3408 T12: -0.0462 REMARK 3 T13: -0.0002 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 62.4165 L22: 78.8520 REMARK 3 L33: 45.6776 L12: 48.4600 REMARK 3 L13: 7.4959 L23: -38.0122 REMARK 3 S TENSOR REMARK 3 S11: -0.1495 S12: -0.2498 S13: -1.4287 REMARK 3 S21: -0.0179 S22: -0.3422 S23: -2.3601 REMARK 3 S31: 0.6404 S32: 1.6184 S33: 0.4917 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 91 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8280 6.7080 2.4940 REMARK 3 T TENSOR REMARK 3 T11: 0.0027 T22: 0.0622 REMARK 3 T33: 0.0351 T12: 0.0093 REMARK 3 T13: 0.0086 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 2.1887 L22: 4.3045 REMARK 3 L33: 1.8954 L12: 0.9889 REMARK 3 L13: 0.6102 L23: 1.1112 REMARK 3 S TENSOR REMARK 3 S11: -0.0152 S12: 0.1155 S13: 0.0410 REMARK 3 S21: -0.0475 S22: 0.0201 S23: -0.0694 REMARK 3 S31: -0.1114 S32: 0.0590 S33: -0.0049 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 : B 46 B 123 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2390 -2.0940 8.0760 REMARK 3 T TENSOR REMARK 3 T11: 0.0184 T22: 0.0616 REMARK 3 T33: 0.0616 T12: -0.0042 REMARK 3 T13: -0.0188 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.2312 L22: 1.3649 REMARK 3 L33: 1.8257 L12: -0.1023 REMARK 3 L13: -0.3327 L23: -0.3209 REMARK 3 S TENSOR REMARK 3 S11: -0.0169 S12: -0.0182 S13: 0.0623 REMARK 3 S21: 0.0994 S22: 0.0110 S23: -0.0798 REMARK 3 S31: -0.0726 S32: 0.1413 S33: 0.0059 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. THE PEPTIDE BONDS BETWEEN RESIDUES A41 AND A42 AND REMARK 3 BETWEEN B41 AND B42 HAVE BEEN DETERMINED TO BE CIS- BONDS. THESE REMARK 3 RESIDUES ARE NOT EXPECTED TO ADOPT THE CIS- CONFORMATION. THIS REMARK 3 IS DUE TO THE POOR ELECTRON DENSITY IN THESE REGIONS OF THE REMARK 3 ELECTRON DENSITY MAP. RESIDUES 34-46 OF BOTH CHAINS FORM LOOPS REMARK 3 WITH TWO ALTERNATE CONFORMATIONS. BOTH ALTERNATE CONFORMATIONS REMARK 3 CAN BE DETERMINED FOR RESIDUES 34-36 AND 42-46, BUT DUE TO POOR REMARK 3 ELECTRON DENSITY RESIDUES 37-41 CAN BE ASSIGNED ONLY A SINGLE REMARK 3 CONFORMATION. REMARK 4 REMARK 4 1VYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1290015155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.804 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41811 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1AVD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EQUAL VOLUMES (1 UL) OF PROTEIN (0.5 REMARK 280 MG/ML) IN 50 MM NA ACETATE (PH 4) + 20 MM NACL AND WELL SOLUTION REMARK 280 OF 0.1 M MES (PH 6.6) + 24% PEG 8000 + 0.2 M MG ACETATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 36.47450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.38600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.47450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.38600 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 FUNCTION: THE BIOLOGICAL FUNCTION OF AVIDIN IS NOT KNOWN. FORMS A REMARK 400 STRONG NON-COVALENT SPECIFIC COMPLEX WITH BIOTIN (ONE MOLECULE OF REMARK 400 BIOTIN PER SUBUNIT OF AVIDIN). 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 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 GLN A 53 O HOH A 2029 2.13 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 ASP B 105 CB - CG - OD2 ANGL. DEV. = 6.8 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 GLU A 43 -100.42 165.29 REMARK 500 SER B 41 44.01 -102.01 REMARK 500 GLU B 43 -133.22 93.47 REMARK 500 GLU B 46 130.85 -35.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AVD RELATED DB: PDB REMARK 900 AVIDIN COMPLEX WITH BIOTIN REMARK 900 RELATED ID: 1AVE RELATED DB: PDB REMARK 900 AVIDIN (APO FORM) REMARK 900 RELATED ID: 1IJ8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX REMARK 900 RELATED ID: 1LDO RELATED DB: PDB REMARK 900 AVIDIN-NORBIOITN COMPLEX REMARK 900 RELATED ID: 1LDQ RELATED DB: PDB REMARK 900 AVIDIN-HOMOBIOTIN COMPLEX REMARK 900 RELATED ID: 1LEL RELATED DB: PDB REMARK 900 THE AVIDIN BCAP COMPLEX REMARK 900 RELATED ID: 1NQN RELATED DB: PDB REMARK 900 STRAYCTURE OF AVM-W110K (W110K MUTANT OF AVIDIN) REMARK 900 RELATED ID: 1RAV RELATED DB: PDB REMARK 900 RECOMBINANT AVIDIN REMARK 900 RELATED ID: 2AVI RELATED DB: PDB REMARK 900 AVIDIN COMPLEX WITH BIOTIN REMARK 900 RELATED ID: 2CAM RELATED DB: PDB REMARK 900 AVIDIN MUTANT (K3E,K9E,R26D,R124L) DBREF 1VYO A 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 1VYO B 1 128 UNP P02701 AVID_CHICK 25 152 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 ILE 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 ILE 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 HET GOL A 501 6 HET GOL A 502 6 HET GOL A 503 6 HET GOL A 504 6 HET GOL B 501 6 HET GOL B 502 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 6(C3 H8 O3) FORMUL 9 HOH *149(H2 O) HELIX 1 1 THR A 55 ARG A 59 5 5 HELIX 2 2 ASP A 105 LYS A 111 5 7 HELIX 3 3 THR B 55 ARG B 59 5 5 HELIX 4 4 ASP B 105 LYS B 111 5 7 SHEET 1 AA10 GLY A 8 ASN A 12 0 SHEET 2 AA10 ASN A 17 ILE A 20 -1 O MET A 18 N TRP A 10 SHEET 3 AA10 GLU A 28 ILE A 34 -1 O THR A 32 N THR A 19 SHEET 4 AA10 SER A 47 GLN A 53 -1 O SER A 47 N TYR A 33 SHEET 5 AA10 THR A 63 ASN A 69 -1 O GLY A 65 N THR A 52 SHEET 6 AA10 THR A 76 ILE A 85 -1 O THR A 77 N VAL A 68 SHEET 7 AA10 GLU A 91 ARG A 100 -1 O VAL A 92 N PHE A 84 SHEET 8 AA10 THR A 113 ARG A 122 -1 O ARG A 114 N LEU A 99 SHEET 9 AA10 GLY A 8 ASN A 12 -1 O THR A 11 N THR A 121 SHEET 10 AA10 GLY A 8 ASN A 12 0 SHEET 1 BA10 GLY B 8 ASN B 12 0 SHEET 2 BA10 ASN B 17 ILE B 20 -1 O MET B 18 N TRP B 10 SHEET 3 BA10 GLU B 28 ILE B 34 -1 O THR B 32 N THR B 19 SHEET 4 BA10 SER B 47 GLN B 53 -1 O SER B 47 N TYR B 33 SHEET 5 BA10 THR B 63 VAL B 68 -1 O GLY B 65 N THR B 52 SHEET 6 BA10 THR B 76 ILE B 85 -1 O THR B 77 N VAL B 68 SHEET 7 BA10 GLU B 91 ARG B 100 -1 O VAL B 92 N PHE B 84 SHEET 8 BA10 THR B 113 ARG B 122 -1 O ARG B 114 N LEU B 99 SHEET 9 BA10 GLY B 8 ASN B 12 -1 O THR B 11 N THR B 121 SHEET 10 BA10 GLY B 8 ASN B 12 0 SSBOND 1 CYS A 4 CYS A 83 1555 1555 2.02 SSBOND 2 CYS B 4 CYS B 83 1555 1555 2.01 SITE 1 AC1 7 TRP A 70 THR A 77 TRP A 97 TRP A 110 SITE 2 AC1 7 ASN A 118 GOL A 502 HOH A2008 SITE 1 AC2 8 VAL A 37 THR A 38 ALA A 39 TRP A 70 SITE 2 AC2 8 PHE A 72 SER A 73 SER A 75 GOL A 501 SITE 1 AC3 9 LEU A 14 ASP A 109 TRP A 110 GLY A 116 SITE 2 AC3 9 ILE A 117 HOH A2066 HOH A2067 HOH A2068 SITE 3 AC3 9 LYS B 94 SITE 1 AC4 5 ALA A 22 ASN A 24 GLU A 28 THR A 30 SITE 2 AC4 5 HOH B2053 SITE 1 AC5 6 TRP B 70 THR B 77 TRP B 97 ASN B 118 SITE 2 AC5 6 GOL B 502 HOH B2080 SITE 1 AC6 8 VAL B 37 THR B 38 ALA B 39 TRP B 70 SITE 2 AC6 8 SER B 73 SER B 75 LEU B 99 GOL B 501 CRYST1 72.949 78.772 43.010 90.00 90.00 90.00 P 21 21 2 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 0.013708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023250 0.00000 MTRIX1 1 -0.239100 0.971000 0.001600 0.01690 1 MTRIX2 1 0.971000 0.239100 -0.003700 0.07190 1 MTRIX3 1 -0.004000 0.000700 -1.000000 14.88210 1