HEADER BIOTIN-BINDING PROTEIN 27-SEP-12 4BBO TITLE CRYSTAL STRUCTURE OF CORE-BRADAVIDIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BLR5658 PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESIDUES 26-143; COMPND 5 SYNONYM: BRADAVIDIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM JAPONICUM; SOURCE 3 ORGANISM_TAXID: 375; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BIOTIN-BINDING PROTEIN, AVIDINS EXPDTA X-RAY DIFFRACTION AUTHOR T.T.AIRENNE,M.S.JOHNSON,J.A.E.MAATTA,V.H.HYTONEN,M.S.KULOMAA REVDAT 4 20-DEC-23 4BBO 1 REMARK REVDAT 3 08-MAY-19 4BBO 1 REMARK REVDAT 2 17-JAN-18 4BBO 1 REMARK REVDAT 1 16-OCT-13 4BBO 0 JRNL AUTH T.T.AIRENNE,J.A.E.MAATTA,H.NORDLUND,M.S.KULOMAA,M.S.JOHNSON JRNL TITL CRYSTAL STRUCTURE OF CORE-BRADAVIDIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 50108 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) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2690 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3640 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 211 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3313 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 368 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.11000 REMARK 3 B22 (A**2) : -0.78000 REMARK 3 B33 (A**2) : -0.33000 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): 0.079 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.959 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3569 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4924 ; 1.457 ; 1.896 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 475 ; 6.071 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;34.969 ;25.733 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 437 ;10.920 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 558 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2776 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2237 ; 0.626 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3571 ; 1.224 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1332 ; 1.838 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1337 ; 2.715 ; 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 : 4 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 120 REMARK 3 ORIGIN FOR THE GROUP (A): 43.0320 7.4860 2.4440 REMARK 3 T TENSOR REMARK 3 T11: 0.0512 T22: 0.1107 REMARK 3 T33: 0.0767 T12: -0.0014 REMARK 3 T13: -0.0069 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.5102 L22: 0.7930 REMARK 3 L33: 0.7375 L12: 0.0159 REMARK 3 L13: -0.2543 L23: -0.0567 REMARK 3 S TENSOR REMARK 3 S11: 0.0007 S12: -0.0471 S13: -0.0015 REMARK 3 S21: 0.0514 S22: -0.0079 S23: -0.0497 REMARK 3 S31: 0.0080 S32: 0.0085 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 : B 1 B 120 REMARK 3 ORIGIN FOR THE GROUP (A): 44.3840 3.3090 -28.1420 REMARK 3 T TENSOR REMARK 3 T11: 0.0655 T22: 0.1102 REMARK 3 T33: 0.0800 T12: -0.0045 REMARK 3 T13: 0.0064 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.3006 L22: 0.7536 REMARK 3 L33: 1.1648 L12: -0.1611 REMARK 3 L13: -0.0359 L23: 0.2207 REMARK 3 S TENSOR REMARK 3 S11: -0.0298 S12: 0.0163 S13: -0.0047 REMARK 3 S21: -0.0802 S22: -0.0015 S23: -0.0209 REMARK 3 S31: 0.0386 S32: -0.0261 S33: 0.0313 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 : C 1 C 120 REMARK 3 ORIGIN FOR THE GROUP (A): 43.6990 18.2580 -22.1970 REMARK 3 T TENSOR REMARK 3 T11: 0.0881 T22: 0.1069 REMARK 3 T33: 0.0824 T12: 0.0005 REMARK 3 T13: 0.0064 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.8153 L22: 1.3840 REMARK 3 L33: 1.0890 L12: -0.2424 REMARK 3 L13: -0.1994 L23: 0.3539 REMARK 3 S TENSOR REMARK 3 S11: -0.0015 S12: -0.0005 S13: 0.0773 REMARK 3 S21: -0.1381 S22: -0.0110 S23: 0.0177 REMARK 3 S31: -0.1827 S32: -0.0397 S33: 0.0126 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 : D 3 D 120 REMARK 3 ORIGIN FOR THE GROUP (A): 51.6350 -4.3220 -3.5330 REMARK 3 T TENSOR REMARK 3 T11: 0.0697 T22: 0.1252 REMARK 3 T33: 0.1088 T12: 0.0166 REMARK 3 T13: 0.0047 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.5448 L22: 0.9465 REMARK 3 L33: 1.0075 L12: 0.0271 REMARK 3 L13: -0.1586 L23: 0.0169 REMARK 3 S TENSOR REMARK 3 S11: -0.0549 S12: -0.0423 S13: -0.1062 REMARK 3 S21: -0.0244 S22: -0.0163 S23: -0.1215 REMARK 3 S31: 0.1601 S32: 0.1112 S33: 0.0712 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 4BBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1290053961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-05 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 : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.063 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52798 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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 2Y32 REMARK 200 REMARK 200 REMARK: CORE REGION OF 2Y32 WAS USED FOR MOLECULAR REPLACEMENT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ONE MICROLITER OF THE PROTEIN SOLUTION REMARK 280 (LESS THAN 1 MG PER ML AND IN 50 MM SODIUM ACETATE, 100 MM NACL, REMARK 280 PH 4) WAS CRYSTALLIZED BY ADDING ONE MICROLITER OF THE WELL REMARK 280 SOLUTION (0.1 M HEPES PH 7.4, 0.8 M K,NA TARTRATE).HANGING DROPS REMARK 280 AND VAPOUR DIFFUSION METHOD WAS USED AT RT. BEFORE REMARK 280 CRYSTALLIZATION, 25 MICROLITERS OF THE PROTEIN SAMPLE WAS REMARK 280 INCUBATED WITH 1 MICRO LITER OF BIOTIN SOLUTION (1 MG PER ML AND REMARK 280 IN 5 MM TRIS PH 8.8, 8 MM CHES PH 9.5) FOR 3.5 HOURS AT 37 REMARK 280 DEGREES OF CELCIUS., VAPOR DIFFUSION, HANGING DROP 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 24.97300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.32350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.97300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.32350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.9 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 GLY A 114 REMARK 465 ASP A 115 REMARK 465 LYS A 116 REMARK 465 ALA A 117 REMARK 465 LEU A 118 REMARK 465 GLY B 114 REMARK 465 ASP B 115 REMARK 465 LYS B 116 REMARK 465 ALA B 117 REMARK 465 LEU B 118 REMARK 465 SER C 113 REMARK 465 GLY C 114 REMARK 465 ASP C 115 REMARK 465 LYS C 116 REMARK 465 ALA C 117 REMARK 465 LEU C 118 REMARK 465 GLN D 1 REMARK 465 SER D 2 REMARK 465 SER D 113 REMARK 465 GLY D 114 REMARK 465 ASP D 115 REMARK 465 LYS D 116 REMARK 465 ALA D 117 REMARK 465 LEU D 118 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 2081 O HOH A 2082 1.90 REMARK 500 O HOH C 2014 O HOH C 2056 2.09 REMARK 500 O HOH A 2084 O HOH A 2085 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O GLN A 10 O HOH A 2084 4455 2.18 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 ASN A 9 -169.73 -101.93 REMARK 500 ASN B 9 -169.70 -104.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-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 BTN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTN C 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTN D 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT D 1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1114 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y32 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BRADAVIDIN DBREF 4BBO A 1 118 UNP Q89IH6 Q89IH6_BRAJA 26 143 DBREF 4BBO B 1 118 UNP Q89IH6 Q89IH6_BRAJA 26 143 DBREF 4BBO C 1 118 UNP Q89IH6 Q89IH6_BRAJA 26 143 DBREF 4BBO D 1 118 UNP Q89IH6 Q89IH6_BRAJA 26 143 SEQRES 1 A 118 GLN SER VAL ASN TRP THR TRP THR ASN GLN TYR GLY SER SEQRES 2 A 118 THR LEU ALA ILE THR SER PHE ASN SER ASN THR GLY ALA SEQRES 3 A 118 ILE THR GLY THR TYR THR ASN ASN ALA ALA ASN SER CYS SEQRES 4 A 118 ASP GLU GLY LYS PRO GLN GLY VAL THR GLY TRP LEU ALA SEQRES 5 A 118 TYR GLY ASN THR GLY THR ALA ILE SER PHE SER VAL ASN SEQRES 6 A 118 PHE LEU GLY CYS GLY SER THR THR VAL TRP THR GLY GLN SEQRES 7 A 118 LEU ASN ASN ALA THR GLY PHE GLN GLY LEU TRP TYR LEU SEQRES 8 A 118 SER LEU ALA GLU ALA VAL ALA TRP ASN GLY ILE SER ALA SEQRES 9 A 118 GLY ALA ASP THR PHE THR PHE SER SER GLY ASP LYS ALA SEQRES 10 A 118 LEU SEQRES 1 B 118 GLN SER VAL ASN TRP THR TRP THR ASN GLN TYR GLY SER SEQRES 2 B 118 THR LEU ALA ILE THR SER PHE ASN SER ASN THR GLY ALA SEQRES 3 B 118 ILE THR GLY THR TYR THR ASN ASN ALA ALA ASN SER CYS SEQRES 4 B 118 ASP GLU GLY LYS PRO GLN GLY VAL THR GLY TRP LEU ALA SEQRES 5 B 118 TYR GLY ASN THR GLY THR ALA ILE SER PHE SER VAL ASN SEQRES 6 B 118 PHE LEU GLY CYS GLY SER THR THR VAL TRP THR GLY GLN SEQRES 7 B 118 LEU ASN ASN ALA THR GLY PHE GLN GLY LEU TRP TYR LEU SEQRES 8 B 118 SER LEU ALA GLU ALA VAL ALA TRP ASN GLY ILE SER ALA SEQRES 9 B 118 GLY ALA ASP THR PHE THR PHE SER SER GLY ASP LYS ALA SEQRES 10 B 118 LEU SEQRES 1 C 118 GLN SER VAL ASN TRP THR TRP THR ASN GLN TYR GLY SER SEQRES 2 C 118 THR LEU ALA ILE THR SER PHE ASN SER ASN THR GLY ALA SEQRES 3 C 118 ILE THR GLY THR TYR THR ASN ASN ALA ALA ASN SER CYS SEQRES 4 C 118 ASP GLU GLY LYS PRO GLN GLY VAL THR GLY TRP LEU ALA SEQRES 5 C 118 TYR GLY ASN THR GLY THR ALA ILE SER PHE SER VAL ASN SEQRES 6 C 118 PHE LEU GLY CYS GLY SER THR THR VAL TRP THR GLY GLN SEQRES 7 C 118 LEU ASN ASN ALA THR GLY PHE GLN GLY LEU TRP TYR LEU SEQRES 8 C 118 SER LEU ALA GLU ALA VAL ALA TRP ASN GLY ILE SER ALA SEQRES 9 C 118 GLY ALA ASP THR PHE THR PHE SER SER GLY ASP LYS ALA SEQRES 10 C 118 LEU SEQRES 1 D 118 GLN SER VAL ASN TRP THR TRP THR ASN GLN TYR GLY SER SEQRES 2 D 118 THR LEU ALA ILE THR SER PHE ASN SER ASN THR GLY ALA SEQRES 3 D 118 ILE THR GLY THR TYR THR ASN ASN ALA ALA ASN SER CYS SEQRES 4 D 118 ASP GLU GLY LYS PRO GLN GLY VAL THR GLY TRP LEU ALA SEQRES 5 D 118 TYR GLY ASN THR GLY THR ALA ILE SER PHE SER VAL ASN SEQRES 6 D 118 PHE LEU GLY CYS GLY SER THR THR VAL TRP THR GLY GLN SEQRES 7 D 118 LEU ASN ASN ALA THR GLY PHE GLN GLY LEU TRP TYR LEU SEQRES 8 D 118 SER LEU ALA GLU ALA VAL ALA TRP ASN GLY ILE SER ALA SEQRES 9 D 118 GLY ALA ASP THR PHE THR PHE SER SER GLY ASP LYS ALA SEQRES 10 D 118 LEU HET BTN A1001 16 HET GOL A1114 6 HET BTN B1001 16 HET ACT B1114 4 HET BTN C1001 16 HET ACT C1113 4 HET BTN D1001 16 HET ACT D1113 4 HETNAM BTN BIOTIN HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 BTN 4(C10 H16 N2 O3 S) FORMUL 6 GOL C3 H8 O3 FORMUL 8 ACT 3(C2 H3 O2 1-) FORMUL 13 HOH *368(H2 O) SHEET 1 AA 9 SER A 2 THR A 8 0 SHEET 2 AA 9 THR A 14 PHE A 20 -1 O LEU A 15 N TRP A 7 SHEET 3 AA 9 ALA A 26 THR A 32 -1 O THR A 28 N THR A 18 SHEET 4 AA 9 PRO A 44 TYR A 53 -1 O GLN A 45 N TYR A 31 SHEET 5 AA 9 THR A 58 PHE A 66 -1 O ALA A 59 N ALA A 52 SHEET 6 AA 9 SER A 71 GLN A 78 -1 O SER A 71 N PHE A 66 SHEET 7 AA 9 PHE A 85 LEU A 93 -1 N GLN A 86 O GLN A 78 SHEET 8 AA 9 ILE A 102 SER A 112 -1 O SER A 103 N LEU A 91 SHEET 9 AA 9 SER A 2 THR A 8 -1 O THR A 6 N SER A 112 SHEET 1 BA 9 SER B 2 THR B 8 0 SHEET 2 BA 9 THR B 14 PHE B 20 -1 O LEU B 15 N TRP B 7 SHEET 3 BA 9 ALA B 26 THR B 32 -1 O THR B 28 N THR B 18 SHEET 4 BA 9 GLN B 45 TYR B 53 -1 O GLN B 45 N TYR B 31 SHEET 5 BA 9 THR B 58 PHE B 66 -1 O ALA B 59 N ALA B 52 SHEET 6 BA 9 SER B 71 GLN B 78 -1 O SER B 71 N PHE B 66 SHEET 7 BA 9 PHE B 85 LEU B 93 -1 N GLN B 86 O GLN B 78 SHEET 8 BA 9 ILE B 102 SER B 112 -1 O SER B 103 N LEU B 91 SHEET 9 BA 9 SER B 2 THR B 8 -1 O THR B 6 N SER B 112 SHEET 1 CA 9 SER C 2 THR C 8 0 SHEET 2 CA 9 THR C 14 PHE C 20 -1 O LEU C 15 N TRP C 7 SHEET 3 CA 9 ALA C 26 THR C 32 -1 O THR C 28 N THR C 18 SHEET 4 CA 9 PRO C 44 TYR C 53 -1 O GLN C 45 N TYR C 31 SHEET 5 CA 9 THR C 58 PHE C 66 -1 O ALA C 59 N ALA C 52 SHEET 6 CA 9 SER C 71 GLN C 78 -1 O SER C 71 N PHE C 66 SHEET 7 CA 9 PHE C 85 LEU C 93 -1 N GLN C 86 O GLN C 78 SHEET 8 CA 9 ILE C 102 SER C 112 -1 O SER C 103 N LEU C 91 SHEET 9 CA 9 SER C 2 THR C 8 -1 O THR C 6 N SER C 112 SHEET 1 DA 9 TRP D 5 THR D 8 0 SHEET 2 DA 9 THR D 14 PHE D 20 -1 O LEU D 15 N TRP D 7 SHEET 3 DA 9 ALA D 26 THR D 32 -1 O THR D 28 N THR D 18 SHEET 4 DA 9 GLN D 45 TYR D 53 -1 O GLN D 45 N TYR D 31 SHEET 5 DA 9 THR D 58 PHE D 66 -1 O ALA D 59 N ALA D 52 SHEET 6 DA 9 SER D 71 GLN D 78 -1 O SER D 71 N PHE D 66 SHEET 7 DA 9 PHE D 85 LEU D 93 -1 N GLN D 86 O GLN D 78 SHEET 8 DA 9 ILE D 102 SER D 112 -1 O SER D 103 N LEU D 91 SHEET 9 DA 9 TRP D 5 THR D 8 -1 O THR D 6 N SER D 112 SSBOND 1 CYS A 39 CYS A 69 1555 1555 2.08 SSBOND 2 CYS B 39 CYS B 69 1555 1555 2.04 SSBOND 3 CYS C 39 CYS C 69 1555 1555 2.08 SSBOND 4 CYS D 39 CYS D 69 1555 1555 2.05 SITE 1 AC1 16 ASN A 9 TYR A 11 SER A 13 TYR A 31 SITE 2 AC1 16 ASN A 33 SER A 38 CYS A 39 PHE A 66 SITE 3 AC1 16 SER A 71 THR A 73 TRP A 75 TRP A 89 SITE 4 AC1 16 ASP A 107 HOH A2071 HOH A2115 HOH A2116 SITE 1 AC2 16 TRP A 99 ASN B 9 SER B 13 TYR B 31 SITE 2 AC2 16 ASN B 33 SER B 38 CYS B 39 PHE B 66 SITE 3 AC2 16 SER B 71 THR B 73 TRP B 75 TRP B 89 SITE 4 AC2 16 LEU B 91 ASP B 107 HOH B2056 HOH B2091 SITE 1 AC3 17 ASN C 9 TYR C 11 SER C 13 TYR C 31 SITE 2 AC3 17 ASN C 33 SER C 38 CYS C 39 PHE C 66 SITE 3 AC3 17 SER C 71 THR C 73 TRP C 75 TRP C 89 SITE 4 AC3 17 ASP C 107 HOH C2061 HOH C2089 HOH C2090 SITE 5 AC3 17 TRP D 99 SITE 1 AC4 16 TRP C 99 ASN D 9 SER D 13 TYR D 31 SITE 2 AC4 16 ASN D 33 SER D 38 CYS D 39 PHE D 66 SITE 3 AC4 16 SER D 71 THR D 73 TRP D 75 TRP D 89 SITE 4 AC4 16 ASP D 107 HOH D2050 HOH D2070 HOH D2071 SITE 1 AC5 2 TRP A 5 TYR A 53 SITE 1 AC6 5 ASN C 80 GLY C 84 THR C 110 HOH C2067 SITE 2 AC6 5 HOH C2070 SITE 1 AC7 1 LEU D 79 SITE 1 AC8 2 TRP B 5 TRP B 7 CRYST1 49.946 78.647 100.120 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 0.020022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009988 0.00000 MTRIX1 1 0.795120 0.606430 -0.005250 5.51383 1 MTRIX2 1 0.606380 -0.795130 -0.008610 -16.66453 1 MTRIX3 1 -0.009400 0.003660 -0.999950 -25.09087 1 MTRIX1 2 -0.818740 -0.536380 -0.204840 83.37444 1 MTRIX2 2 -0.516200 0.531430 0.671660 34.93614 1 MTRIX3 2 -0.251410 0.655650 -0.711980 -14.56345 1 MTRIX1 3 -0.965550 -0.099640 0.240400 93.25267 1 MTRIX2 3 -0.084140 -0.754630 -0.650740 6.20110 1 MTRIX3 3 0.246250 -0.648540 0.720240 -10.77602 1 MTRIX1 4 -0.975180 -0.068920 0.210400 92.90064 1 MTRIX2 4 -0.091000 -0.741560 -0.664680 6.38820 1 MTRIX3 4 0.201830 -0.667330 0.716890 -8.83114 1 MTRIX1 5 -0.829230 -0.508550 -0.231860 83.53468 1 MTRIX2 5 -0.521510 0.554810 0.648240 34.59206 1 MTRIX3 5 -0.201020 0.658450 -0.725280 -16.89169 1 MTRIX1 6 0.794620 0.607090 0.005190 5.85409 1 MTRIX2 6 0.607110 -0.794530 -0.011740 -16.83226 1 MTRIX3 6 -0.003000 0.012480 -0.999920 -25.56830 1