HEADER BIOTIN-BINDING PROTEIN 15-JAN-16 5HLM TITLE CRYSTAL STRUCTURE OF AVIDIN COMPLEX WITH A FERROCENE BIOTIN 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 GLYCOPROTEIN, COMPLEX, BIOTIN-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.STRZELCZYK,G.BUJACZ REVDAT 5 09-OCT-24 5HLM 1 REMARK REVDAT 4 10-JAN-24 5HLM 1 HETSYN REVDAT 3 29-JUL-20 5HLM 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 07-MAR-18 5HLM 1 REMARK REVDAT 1 18-JAN-17 5HLM 0 JRNL AUTH A.BLAUZ,B.RYCHLIK,A.MAKAL,K.SZULC,P.STRZELCZYK,G.BUJACZ, JRNL AUTH 2 J.ZAKRZEWSKI,K.WOZNIAK,D.PLAZUK JRNL TITL FERROCENE-BIOTIN CONJUGATES: SYNTHESIS, STRUCTURE, CYTOTOXIC JRNL TITL 2 ACTIVITY AND INTERACTION WITH AVIDIN JRNL REF CHEMPLUSCHEM V. 81 1191 2016 JRNL REFN ESSN 2192-6506 JRNL DOI 10.1002/CPLU.201600320 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 14210 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 749 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1061 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 160 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.23000 REMARK 3 B22 (A**2) : 1.62000 REMARK 3 B33 (A**2) : 4.86000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.344 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.306 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.308 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3898 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3609 ; 0.010 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5225 ; 2.026 ; 1.863 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8288 ; 1.792 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 451 ; 7.637 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;30.971 ;24.037 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 635 ;18.810 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;14.159 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 605 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4259 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 955 ; 0.010 ; 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): 1834 ; 1.784 ; 2.619 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1833 ; 1.784 ; 2.619 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2275 ; 3.058 ; 3.912 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2276 ; 3.058 ; 3.913 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2064 ; 2.663 ; 3.198 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2065 ; 2.663 ; 3.200 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2951 ; 3.350 ; 4.562 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3919 ; 6.850 ;21.257 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3920 ; 6.849 ;21.270 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 3 123 B 3 123 11326 0.10 0.05 REMARK 3 2 A 3 123 C 3 123 11798 0.11 0.05 REMARK 3 3 A 3 123 D 3 123 11866 0.10 0.05 REMARK 3 4 B 3 123 C 3 123 11098 0.10 0.05 REMARK 3 5 B 3 123 D 3 123 11306 0.08 0.05 REMARK 3 6 C 3 123 D 3 123 12046 0.11 0.05 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 : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 46 REMARK 3 RESIDUE RANGE : A 47 A 95 REMARK 3 RESIDUE RANGE : A 96 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): -2.0810 41.2550 33.6280 REMARK 3 T TENSOR REMARK 3 T11: 0.3569 T22: 0.5783 REMARK 3 T33: 0.0404 T12: 0.0827 REMARK 3 T13: 0.0775 T23: -0.0311 REMARK 3 L TENSOR REMARK 3 L11: 5.7276 L22: 4.9051 REMARK 3 L33: 6.2714 L12: 0.0804 REMARK 3 L13: -1.7412 L23: -1.2352 REMARK 3 S TENSOR REMARK 3 S11: -0.0676 S12: -0.9587 S13: 0.2025 REMARK 3 S21: 0.7531 S22: 0.0700 S23: -0.0440 REMARK 3 S31: -0.2355 S32: -0.5545 S33: -0.0024 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 46 REMARK 3 RESIDUE RANGE : B 47 B 95 REMARK 3 RESIDUE RANGE : B 96 B 123 REMARK 3 ORIGIN FOR THE GROUP (A): -4.4830 52.1080 21.3860 REMARK 3 T TENSOR REMARK 3 T11: 0.3525 T22: 0.3717 REMARK 3 T33: 0.1293 T12: 0.2053 REMARK 3 T13: 0.0731 T23: -0.0450 REMARK 3 L TENSOR REMARK 3 L11: 3.0109 L22: 7.7510 REMARK 3 L33: 4.3403 L12: 0.7200 REMARK 3 L13: 1.8634 L23: 0.8274 REMARK 3 S TENSOR REMARK 3 S11: -0.1688 S12: -0.4900 S13: 0.4465 REMARK 3 S21: -0.1419 S22: -0.0754 S23: 0.2467 REMARK 3 S31: -0.5934 S32: -0.5088 S33: 0.2442 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 3 C 46 REMARK 3 RESIDUE RANGE : C 47 C 95 REMARK 3 RESIDUE RANGE : C 96 C 123 REMARK 3 ORIGIN FOR THE GROUP (A): 6.6160 33.6240 5.1060 REMARK 3 T TENSOR REMARK 3 T11: 0.2437 T22: 0.0876 REMARK 3 T33: 0.1775 T12: -0.0312 REMARK 3 T13: 0.1823 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 4.2741 L22: 4.5846 REMARK 3 L33: 8.6516 L12: -0.4354 REMARK 3 L13: 2.1203 L23: 0.6257 REMARK 3 S TENSOR REMARK 3 S11: 0.1873 S12: 0.2514 S13: -0.0080 REMARK 3 S21: -0.5020 S22: 0.0726 S23: -0.1584 REMARK 3 S31: 0.1809 S32: 0.0785 S33: -0.2599 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 3 D 46 REMARK 3 RESIDUE RANGE : D 47 D 95 REMARK 3 RESIDUE RANGE : D 96 D 123 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1830 22.3800 15.4810 REMARK 3 T TENSOR REMARK 3 T11: 0.3382 T22: 0.1687 REMARK 3 T33: 0.2079 T12: -0.1092 REMARK 3 T13: 0.0535 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 4.7916 L22: 6.9820 REMARK 3 L33: 4.7010 L12: -1.6679 REMARK 3 L13: 1.0041 L23: 0.0030 REMARK 3 S TENSOR REMARK 3 S11: 0.2252 S12: -0.2973 S13: -0.4159 REMARK 3 S21: 0.2008 S22: 0.0272 S23: -0.2592 REMARK 3 S31: 0.6705 S32: -0.0768 S33: -0.2524 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 5HLM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 1.07106 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 : 14959 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 91.8 REMARK 200 DATA REDUNDANCY : 2.930 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5700 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.53 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.860 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 (%): 40.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM THIOCYANATE, 0.1M BIS REMARK 280 -TRIS PH 6.5 AND 22% W/V POLYETHYLENE GLYCOL 3350, VAPOR REMARK 280 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 37.45500 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: 10820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 ALA A 39 REMARK 465 THR A 40 REMARK 465 SER A 41 REMARK 465 ILE A 56 REMARK 465 ASN A 57 REMARK 465 LYS A 58 REMARK 465 ARG A 59 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 2 REMARK 465 THR B 38 REMARK 465 ALA B 39 REMARK 465 THR B 40 REMARK 465 SER B 41 REMARK 465 ASN B 42 REMARK 465 GLU B 43 REMARK 465 ILE B 56 REMARK 465 ASN B 57 REMARK 465 LYS B 58 REMARK 465 ARG B 59 REMARK 465 THR B 60 REMARK 465 ARG B 87 REMARK 465 ASN B 88 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 THR C 38 REMARK 465 ALA C 39 REMARK 465 THR C 40 REMARK 465 SER C 41 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 2 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 PRO B 62 O HOH B 301 2.06 REMARK 500 SG CYS D 4 CB CYS D 83 2.11 REMARK 500 ND2 ASN B 17 O5 NAG B 202 2.12 REMARK 500 ND2 ASN A 17 O5 NAG A 202 2.12 REMARK 500 ND2 ASN D 17 O5 NAG D 202 2.18 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 LYS A 111 N - CA - CB ANGL. DEV. = -11.5 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 CYS A 4 68.96 -107.01 REMARK 500 GLU A 46 134.62 -33.77 REMARK 500 ARG A 87 -59.08 69.62 REMARK 500 GLU B 46 132.44 -35.04 REMARK 500 GLU C 46 131.47 -34.10 REMARK 500 ILE C 56 -70.20 -65.40 REMARK 500 CYS D 4 48.60 35.42 REMARK 500 THR D 40 -160.44 -119.57 REMARK 500 SER D 41 33.87 -92.19 REMARK 500 ASN D 42 -119.72 43.95 REMARK 500 GLU D 46 133.19 -33.62 REMARK 500 ASN D 57 78.62 46.96 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 5HLM A 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5HLM B 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5HLM C 1 128 UNP P02701 AVID_CHICK 25 152 DBREF 5HLM D 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 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 ILE 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 ILE 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 B9F A 201 26 HET NAG A 202 14 HET B9F B 201 26 HET NAG B 202 14 HET B9F C 301 26 HET NAG C 302 14 HET B9F D 201 26 HET NAG D 202 14 HETNAM B9F [(1,2,3,4,5-ETA)-CYCLOPENTADIENYL]{(1,2,3,4,5-ETA)-1- HETNAM 2 B9F [1-HYDROXY-5-(2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL- HETNAM 3 B9F 4-YL)PENTYL]CYCLOPENTADIENYL}IRON HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 B9F 4(C20 H26 FE N2 O2 S) FORMUL 6 NAG 4(C8 H15 N O6) FORMUL 13 HOH *36(H2 O) HELIX 1 AA1 ASP A 105 LYS A 111 5 7 HELIX 2 AA2 ASP B 105 LYS B 111 5 7 HELIX 3 AA3 ASP C 105 LYS C 111 5 7 HELIX 4 AA4 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 ILE A 34 -1 O ILE A 34 N ASN A 17 SHEET 4 AA1 9 SER A 47 GLN A 53 -1 O SER A 47 N TYR A 33 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 ASP A 86 -1 O PHE A 79 N PHE A 66 SHEET 7 AA1 9 LYS A 90 ARG A 100 -1 O VAL A 92 N PHE A 84 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 ILE B 20 N GLY B 8 SHEET 3 AA2 9 GLU B 28 ILE B 34 -1 O ILE 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 PHE B 84 -1 O PHE B 79 N PHE B 66 SHEET 7 AA2 9 VAL B 92 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 ILE C 34 -1 O ILE 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 ASN C 69 -1 O GLY C 65 N THR C 52 SHEET 6 AA3 9 THR C 76 ILE C 85 -1 O PHE C 79 N PHE C 66 SHEET 7 AA3 9 GLU C 91 ARG C 100 -1 O VAL C 92 N PHE C 84 SHEET 8 AA3 9 THR C 113 ARG C 122 -1 O ARG C 114 N LEU C 99 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 ILE D 34 -1 O ILE 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 GLY D 65 N THR D 52 SHEET 6 AA4 9 THR D 76 ILE D 85 -1 O PHE D 79 N PHE D 66 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 ARG D 114 N LEU D 99 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 2.05 SSBOND 2 CYS B 4 CYS B 83 1555 1555 2.06 SSBOND 3 CYS C 4 CYS C 83 1555 1555 2.06 SSBOND 4 CYS D 4 CYS D 83 1555 1555 1.93 LINK ND2 ASN A 17 C1 NAG A 202 1555 1555 1.23 LINK ND2 ASN B 17 C1 NAG B 202 1555 1555 1.31 LINK ND2 ASN C 17 C1 NAG C 302 1555 1555 1.30 LINK ND2 ASN D 17 C1 NAG D 202 1555 1555 1.30 CRYST1 43.200 74.910 76.180 90.00 106.17 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 0.023148 0.000000 0.006710 0.00000 SCALE2 0.000000 0.013349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013667 0.00000 CONECT 15 564 CONECT 112 3647 CONECT 564 15 CONECT 909 1427 CONECT 1006 3687 CONECT 1427 909 CONECT 1764 2342 CONECT 1861 3727 CONECT 2342 1764 CONECT 2687 3290 CONECT 2784 3767 CONECT 3290 2687 CONECT 3621 3622 CONECT 3622 3621 3623 3628 CONECT 3623 3622 3624 3627 3646 CONECT 3624 3623 3625 3646 CONECT 3625 3624 3626 3646 CONECT 3626 3625 3627 3646 CONECT 3627 3623 3626 3646 CONECT 3628 3622 3629 CONECT 3629 3628 3630 CONECT 3630 3629 3631 CONECT 3631 3630 3632 CONECT 3632 3631 3633 3637 CONECT 3633 3632 3634 3639 CONECT 3634 3633 3635 CONECT 3635 3634 3636 3640 CONECT 3636 3635 CONECT 3637 3632 3638 CONECT 3638 3637 3639 CONECT 3639 3633 3638 3640 CONECT 3640 3635 3639 CONECT 3641 3642 3645 3646 CONECT 3642 3641 3643 3646 CONECT 3643 3642 3644 3646 CONECT 3644 3643 3645 3646 CONECT 3645 3641 3644 3646 CONECT 3646 3623 3624 3625 3626 CONECT 3646 3627 3641 3642 3643 CONECT 3646 3644 3645 CONECT 3647 112 3648 3658 CONECT 3648 3647 3649 3655 CONECT 3649 3648 3650 3656 CONECT 3650 3649 3651 3657 CONECT 3651 3650 3652 3658 CONECT 3652 3651 3659 CONECT 3653 3654 3655 3660 CONECT 3654 3653 CONECT 3655 3648 3653 CONECT 3656 3649 CONECT 3657 3650 CONECT 3658 3647 3651 CONECT 3659 3652 CONECT 3660 3653 CONECT 3661 3662 CONECT 3662 3661 3663 3668 CONECT 3663 3662 3664 3667 3686 CONECT 3664 3663 3665 3686 CONECT 3665 3664 3666 3686 CONECT 3666 3665 3667 3686 CONECT 3667 3663 3666 3686 CONECT 3668 3662 3669 CONECT 3669 3668 3670 CONECT 3670 3669 3671 CONECT 3671 3670 3672 CONECT 3672 3671 3673 3677 CONECT 3673 3672 3674 3679 CONECT 3674 3673 3675 CONECT 3675 3674 3676 3680 CONECT 3676 3675 CONECT 3677 3672 3678 CONECT 3678 3677 3679 CONECT 3679 3673 3678 3680 CONECT 3680 3675 3679 CONECT 3681 3682 3685 3686 CONECT 3682 3681 3683 3686 CONECT 3683 3682 3684 3686 CONECT 3684 3683 3685 3686 CONECT 3685 3681 3684 3686 CONECT 3686 3663 3664 3665 3666 CONECT 3686 3667 3681 3682 3683 CONECT 3686 3684 3685 CONECT 3687 1006 3688 3698 CONECT 3688 3687 3689 3695 CONECT 3689 3688 3690 3696 CONECT 3690 3689 3691 3697 CONECT 3691 3690 3692 3698 CONECT 3692 3691 3699 CONECT 3693 3694 3695 3700 CONECT 3694 3693 CONECT 3695 3688 3693 CONECT 3696 3689 CONECT 3697 3690 CONECT 3698 3687 3691 CONECT 3699 3692 CONECT 3700 3693 CONECT 3701 3702 CONECT 3702 3701 3703 3708 CONECT 3703 3702 3704 3707 3726 CONECT 3704 3703 3705 3726 CONECT 3705 3704 3706 3726 CONECT 3706 3705 3707 3726 CONECT 3707 3703 3706 3726 CONECT 3708 3702 3709 CONECT 3709 3708 3710 CONECT 3710 3709 3711 CONECT 3711 3710 3712 CONECT 3712 3711 3713 3717 CONECT 3713 3712 3714 3719 CONECT 3714 3713 3715 CONECT 3715 3714 3716 3720 CONECT 3716 3715 CONECT 3717 3712 3718 CONECT 3718 3717 3719 CONECT 3719 3713 3718 3720 CONECT 3720 3715 3719 CONECT 3721 3722 3725 3726 CONECT 3722 3721 3723 3726 CONECT 3723 3722 3724 3726 CONECT 3724 3723 3725 3726 CONECT 3725 3721 3724 3726 CONECT 3726 3703 3704 3705 3706 CONECT 3726 3707 3721 3722 3723 CONECT 3726 3724 3725 CONECT 3727 1861 3728 3738 CONECT 3728 3727 3729 3735 CONECT 3729 3728 3730 3736 CONECT 3730 3729 3731 3737 CONECT 3731 3730 3732 3738 CONECT 3732 3731 3739 CONECT 3733 3734 3735 3740 CONECT 3734 3733 CONECT 3735 3728 3733 CONECT 3736 3729 CONECT 3737 3730 CONECT 3738 3727 3731 CONECT 3739 3732 CONECT 3740 3733 CONECT 3741 3742 CONECT 3742 3741 3743 3748 CONECT 3743 3742 3744 3747 3766 CONECT 3744 3743 3745 3766 CONECT 3745 3744 3746 3766 CONECT 3746 3745 3747 3766 CONECT 3747 3743 3746 3766 CONECT 3748 3742 3749 CONECT 3749 3748 3750 CONECT 3750 3749 3751 CONECT 3751 3750 3752 CONECT 3752 3751 3753 3757 CONECT 3753 3752 3754 3759 CONECT 3754 3753 3755 CONECT 3755 3754 3756 3760 CONECT 3756 3755 CONECT 3757 3752 3758 CONECT 3758 3757 3759 CONECT 3759 3753 3758 3760 CONECT 3760 3755 3759 CONECT 3761 3762 3765 3766 CONECT 3762 3761 3763 3766 CONECT 3763 3762 3764 3766 CONECT 3764 3763 3765 3766 CONECT 3765 3761 3764 3766 CONECT 3766 3743 3744 3745 3746 CONECT 3766 3747 3761 3762 3763 CONECT 3766 3764 3765 CONECT 3767 2784 3768 3778 CONECT 3768 3767 3769 3775 CONECT 3769 3768 3770 3776 CONECT 3770 3769 3771 3777 CONECT 3771 3770 3772 3778 CONECT 3772 3771 3779 CONECT 3773 3774 3775 3780 CONECT 3774 3773 CONECT 3775 3768 3773 CONECT 3776 3769 CONECT 3777 3770 CONECT 3778 3767 3771 CONECT 3779 3772 CONECT 3780 3773 MASTER 448 0 8 4 36 0 0 6 3812 4 180 40 END