HEADER BIOTIN-BINDING PROTEIN 14-FEB-07 2JGS TITLE CIRCULAR PERMUTANT OF AVIDIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CIRCULAR PERMUTANT OF AVIDIN; COMPND 3 CHAIN: A, B, C, D; 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 BIOTIN-BINDING PROTEIN, GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.E.MAATTA,V.P.HYTONEN,T.T.AIRENNE,E.NISKANEN,M.S.JOHNSON, AUTHOR 2 M.S.KULOMAA,H.R.NORDLUND REVDAT 4 13-DEC-23 2JGS 1 REMARK REVDAT 3 13-JUL-11 2JGS 1 VERSN REVDAT 2 24-FEB-09 2JGS 1 VERSN REVDAT 1 04-MAR-08 2JGS 0 JRNL AUTH J.A.E.MAATTA,T.T.AIRENNE,H.R.NORDLUND,J.JANIS,T.A.PALDANIUS, JRNL AUTH 2 P.VAINIOTALO,M.S.JOHNSON,M.S.KULOMAA,V.P.HYTONEN JRNL TITL RATIONAL MODIFICATION OF LIGAND-BINDING PREFERENCE OF AVIDIN JRNL TITL 2 BY CIRCULAR PERMUTATION AND MUTAGENESIS. JRNL REF CHEMBIOCHEM V. 9 1124 2008 JRNL REFN ISSN 1439-4227 JRNL PMID 18381715 JRNL DOI 10.1002/CBIC.200700671 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0021 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34607 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1818 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2546 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3528 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : UNVERIFIED REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 6.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.23000 REMARK 3 B22 (A**2) : -0.48000 REMARK 3 B33 (A**2) : -1.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.010 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3700 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5017 ; 1.648 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 8.407 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;33.291 ;23.567 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 620 ;17.277 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;20.596 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 577 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2726 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1467 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2484 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 214 ; 0.172 ; 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): 45 ; 0.227 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.168 ; 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): 2287 ; 0.724 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3620 ; 1.132 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1631 ; 1.735 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1394 ; 2.640 ; 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 130 REMARK 3 ORIGIN FOR THE GROUP (A): 28.6700 14.5360 47.5600 REMARK 3 T TENSOR REMARK 3 T11: -0.2297 T22: -0.1142 REMARK 3 T33: -0.0522 T12: -0.0533 REMARK 3 T13: 0.0540 T23: 0.0489 REMARK 3 L TENSOR REMARK 3 L11: 2.8906 L22: 3.2914 REMARK 3 L33: 3.2061 L12: -0.4915 REMARK 3 L13: 1.0439 L23: -0.8155 REMARK 3 S TENSOR REMARK 3 S11: -0.1385 S12: 0.1682 S13: 0.4352 REMARK 3 S21: 0.1493 S22: -0.0013 S23: -0.0856 REMARK 3 S31: -0.3988 S32: 0.1385 S33: 0.1398 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 130 REMARK 3 ORIGIN FOR THE GROUP (A): 27.3680 -14.1740 56.5520 REMARK 3 T TENSOR REMARK 3 T11: -0.0662 T22: -0.0734 REMARK 3 T33: -0.0535 T12: -0.0719 REMARK 3 T13: -0.0854 T23: 0.0681 REMARK 3 L TENSOR REMARK 3 L11: 2.3948 L22: 4.0066 REMARK 3 L33: 1.7368 L12: 0.6469 REMARK 3 L13: 0.5460 L23: -0.3347 REMARK 3 S TENSOR REMARK 3 S11: 0.2857 S12: -0.1608 S13: -0.4224 REMARK 3 S21: -0.0111 S22: -0.0775 S23: -0.0649 REMARK 3 S31: 0.4224 S32: -0.0868 S33: -0.2082 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 130 REMARK 3 ORIGIN FOR THE GROUP (A): 23.0370 -2.8910 66.4520 REMARK 3 T TENSOR REMARK 3 T11: -0.1152 T22: 0.0600 REMARK 3 T33: -0.0821 T12: -0.0999 REMARK 3 T13: 0.0136 T23: 0.0508 REMARK 3 L TENSOR REMARK 3 L11: 2.5581 L22: 2.3016 REMARK 3 L33: 4.4295 L12: 0.2930 REMARK 3 L13: 1.7753 L23: 0.3033 REMARK 3 S TENSOR REMARK 3 S11: 0.2186 S12: -0.6832 S13: -0.0660 REMARK 3 S21: 0.4114 S22: -0.0256 S23: 0.1219 REMARK 3 S31: 0.2235 S32: -0.5920 S33: -0.1931 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 1 D 130 REMARK 3 ORIGIN FOR THE GROUP (A): 27.7850 3.6870 37.5680 REMARK 3 T TENSOR REMARK 3 T11: -0.2154 T22: -0.0526 REMARK 3 T33: -0.1119 T12: 0.0041 REMARK 3 T13: 0.0430 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 2.4361 L22: 2.5189 REMARK 3 L33: 3.1297 L12: -0.4512 REMARK 3 L13: 0.2097 L23: 0.2065 REMARK 3 S TENSOR REMARK 3 S11: 0.1282 S12: 0.3813 S13: -0.0394 REMARK 3 S21: -0.3128 S22: 0.0125 S23: -0.0089 REMARK 3 S31: 0.1663 S32: 0.2163 S33: -0.1407 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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. REMARK 4 REMARK 4 2JGS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1290031449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-06 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36425 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2AVI REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 39.65450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.8 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 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 45 REMARK 465 ASN A 46 REMARK 465 GLY A 47 REMARK 465 LEU A 81 REMARK 465 ARG A 82 REMARK 465 THR A 83 REMARK 465 GLN A 84 REMARK 465 LYS A 85 REMARK 465 GLU A 86 REMARK 465 GLY A 87 REMARK 465 GLY A 88 REMARK 465 SER A 89 REMARK 465 GLY A 90 REMARK 465 GLY A 91 REMARK 465 SER A 92 REMARK 465 ALA A 93 REMARK 465 ARG A 94 REMARK 465 LYS A 95 REMARK 465 ARG B 82 REMARK 465 THR B 83 REMARK 465 GLN B 84 REMARK 465 LYS B 85 REMARK 465 GLU B 86 REMARK 465 GLY B 87 REMARK 465 GLY B 88 REMARK 465 SER B 89 REMARK 465 GLY B 90 REMARK 465 GLY B 91 REMARK 465 SER B 92 REMARK 465 ALA B 93 REMARK 465 ARG B 94 REMARK 465 LYS B 95 REMARK 465 GLY C 1 REMARK 465 SER C 2 REMARK 465 LYS C 3 REMARK 465 LEU C 81 REMARK 465 ARG C 82 REMARK 465 THR C 83 REMARK 465 GLN C 84 REMARK 465 LYS C 85 REMARK 465 GLU C 86 REMARK 465 GLY C 87 REMARK 465 GLY C 88 REMARK 465 SER C 89 REMARK 465 GLY C 90 REMARK 465 GLY C 91 REMARK 465 SER C 92 REMARK 465 ALA C 93 REMARK 465 ARG C 94 REMARK 465 LYS C 95 REMARK 465 GLY D 1 REMARK 465 SER D 2 REMARK 465 LYS D 3 REMARK 465 ARG D 82 REMARK 465 THR D 83 REMARK 465 GLN D 84 REMARK 465 LYS D 85 REMARK 465 GLU D 86 REMARK 465 GLY D 87 REMARK 465 GLY D 88 REMARK 465 SER D 89 REMARK 465 GLY D 90 REMARK 465 GLY D 91 REMARK 465 SER D 92 REMARK 465 ALA D 93 REMARK 465 ARG D 94 REMARK 465 LYS D 95 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 B 2014 O HOH C 2023 2.15 REMARK 500 O PRO D 20 O HOH D 2007 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 41 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 GLY B 47 N - CA - C ANGL. DEV. = 23.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 15 -161.43 58.23 REMARK 500 LYS A 16 -77.06 -26.71 REMARK 500 ILE B 14 -57.38 -120.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 16 ARG A 17 -36.26 REMARK 500 ASN B 46 GLY B 47 -93.42 REMARK 500 GLY B 47 LYS B 48 -136.62 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 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 700 THE SHEETS PRESENTED AS "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 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 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-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 A1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTN B1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTN C1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTN D1001 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: 1VYO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AVIDIN REMARK 900 RELATED ID: 2A5B RELATED DB: PDB REMARK 900 AVIDIN COMPLEXED WITH 8-OXODEOXYGUANOSINE REMARK 900 RELATED ID: 2A5C RELATED DB: PDB REMARK 900 STRUCTURE OF AVIDIN IN COMPLEX WITH THE LIGAND 8-OXODEOXYADENOSINE REMARK 900 RELATED ID: 2A8G RELATED DB: PDB REMARK 900 STRUCTURE OF AVIDIN IN COMPLEX WITH THE LIGANDDEOXYGUANOSINE REMARK 900 RELATED ID: 2AVI RELATED DB: PDB REMARK 900 AVIDIN COMPLEX WITH BIOTIN REMARK 900 RELATED ID: 2C4I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ENGINEERED AVIDIN REMARK 900 RELATED ID: 2CAM RELATED DB: PDB REMARK 900 AVIDIN MUTANT (K3E,K9E,R26D,R124L) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE DEPOSITED IS A CIRCULAR PERMUTANT (ARTIFICIAL LOCATION REMARK 999 OF N- AND C-TERMINI & SHORT LINKER REGIONS ETC) OF AVIDIN. HOWEVER, REMARK 999 THE SEQUENCE FOR THIS ENGINEERED AVIDIN IS NOT YET DEPOSITED TO E.G. REMARK 999 UNIPROT. THERE WILL BE A SEQUENCE ENTRY MATCHING THE DEPOSITED REMARK 999 STRUCTURE (EXCEPT THE N76 TO M MUTATION), BUT IT IS NOT YET REMARK 999 AVAILABLE. THIS SEQUENCE IS RELATED TO AVIDIN. DBREF 2JGS A 1 130 PDB 2JGS 2JGS 1 130 DBREF 2JGS B 1 130 PDB 2JGS 2JGS 1 130 DBREF 2JGS C 1 130 PDB 2JGS 2JGS 1 130 DBREF 2JGS D 1 130 PDB 2JGS 2JGS 1 130 SEQRES 1 A 130 GLY SER LYS GLU SER PRO LEU HIS GLY THR GLN ASN THR SEQRES 2 A 130 ILE ASN LYS ARG THR GLN PRO THR PHE GLY PHE THR VAL SEQRES 3 A 130 ASN TRP LYS PHE SER GLU SER THR THR VAL PHE THR GLY SEQRES 4 A 130 GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU VAL LEU LYS SEQRES 5 A 130 THR MET TRP LEU LEU ARG SER SER VAL ASN ASP ILE GLY SEQRES 6 A 130 ASP ASP TRP LYS ALA THR ARG VAL GLY ILE MET ILE PHE SEQRES 7 A 130 THR ARG LEU ARG THR GLN LYS GLU GLY GLY SER GLY GLY SEQRES 8 A 130 SER ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN SEQRES 9 A 130 ASP LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER SEQRES 10 A 130 ARG GLY GLU PHE THR GLY THR TYR ILE THR ALA VAL THR SEQRES 1 B 130 GLY SER LYS GLU SER PRO LEU HIS GLY THR GLN ASN THR SEQRES 2 B 130 ILE ASN LYS ARG THR GLN PRO THR PHE GLY PHE THR VAL SEQRES 3 B 130 ASN TRP LYS PHE SER GLU SER THR THR VAL PHE THR GLY SEQRES 4 B 130 GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU VAL LEU LYS SEQRES 5 B 130 THR MET TRP LEU LEU ARG SER SER VAL ASN ASP ILE GLY SEQRES 6 B 130 ASP ASP TRP LYS ALA THR ARG VAL GLY ILE MET ILE PHE SEQRES 7 B 130 THR ARG LEU ARG THR GLN LYS GLU GLY GLY SER GLY GLY SEQRES 8 B 130 SER ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN SEQRES 9 B 130 ASP LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER SEQRES 10 B 130 ARG GLY GLU PHE THR GLY THR TYR ILE THR ALA VAL THR SEQRES 1 C 130 GLY SER LYS GLU SER PRO LEU HIS GLY THR GLN ASN THR SEQRES 2 C 130 ILE ASN LYS ARG THR GLN PRO THR PHE GLY PHE THR VAL SEQRES 3 C 130 ASN TRP LYS PHE SER GLU SER THR THR VAL PHE THR GLY SEQRES 4 C 130 GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU VAL LEU LYS SEQRES 5 C 130 THR MET TRP LEU LEU ARG SER SER VAL ASN ASP ILE GLY SEQRES 6 C 130 ASP ASP TRP LYS ALA THR ARG VAL GLY ILE MET ILE PHE SEQRES 7 C 130 THR ARG LEU ARG THR GLN LYS GLU GLY GLY SER GLY GLY SEQRES 8 C 130 SER ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN SEQRES 9 C 130 ASP LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER SEQRES 10 C 130 ARG GLY GLU PHE THR GLY THR TYR ILE THR ALA VAL THR SEQRES 1 D 130 GLY SER LYS GLU SER PRO LEU HIS GLY THR GLN ASN THR SEQRES 2 D 130 ILE ASN LYS ARG THR GLN PRO THR PHE GLY PHE THR VAL SEQRES 3 D 130 ASN TRP LYS PHE SER GLU SER THR THR VAL PHE THR GLY SEQRES 4 D 130 GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU VAL LEU LYS SEQRES 5 D 130 THR MET TRP LEU LEU ARG SER SER VAL ASN ASP ILE GLY SEQRES 6 D 130 ASP ASP TRP LYS ALA THR ARG VAL GLY ILE MET ILE PHE SEQRES 7 D 130 THR ARG LEU ARG THR GLN LYS GLU GLY GLY SER GLY GLY SEQRES 8 D 130 SER ALA ARG LYS CYS SER LEU THR GLY LYS TRP THR ASN SEQRES 9 D 130 ASP LEU GLY SER ASN MET THR ILE GLY ALA VAL ASN SER SEQRES 10 D 130 ARG GLY GLU PHE THR GLY THR TYR ILE THR ALA VAL THR HET BTN A1001 16 HET BTN B1001 16 HET BTN C1001 16 HET BTN D1001 16 HETNAM BTN BIOTIN FORMUL 5 BTN 4(C10 H16 N2 O3 S) FORMUL 9 HOH *172(H2 O) HELIX 1 1 ASP A 63 LYS A 69 5 7 HELIX 2 2 ASP B 63 LYS B 69 5 7 HELIX 3 3 ASP C 63 LYS C 69 5 7 HELIX 4 4 ASP D 63 LYS D 69 5 7 SHEET 1 AA10 SER A 5 GLN A 11 0 SHEET 2 AA10 GLU A 120 ILE A 126 -1 O PHE A 121 N GLY A 9 SHEET 3 AA10 ASN A 109 ILE A 112 -1 O ASN A 109 N ILE A 126 SHEET 4 AA10 GLY A 100 THR A 103 -1 O GLY A 100 N ILE A 112 SHEET 5 AA10 THR A 71 THR A 79 -1 O THR A 79 N THR A 103 SHEET 6 AA10 GLU A 49 ARG A 58 -1 O LEU A 51 N PHE A 78 SHEET 7 AA10 THR A 34 ILE A 43 -1 O THR A 34 N ARG A 58 SHEET 8 AA10 THR A 21 ASN A 27 -1 O PHE A 22 N GLY A 39 SHEET 9 AA10 SER A 5 GLN A 11 -1 O PRO A 6 N ASN A 27 SHEET 10 AA10 SER A 5 GLN A 11 0 SHEET 1 BA10 SER B 5 ASN B 12 0 SHEET 2 BA10 GLU B 120 ILE B 126 -1 O PHE B 121 N GLY B 9 SHEET 3 BA10 ASN B 109 ILE B 112 -1 O ASN B 109 N ILE B 126 SHEET 4 BA10 GLY B 100 THR B 103 -1 O GLY B 100 N ILE B 112 SHEET 5 BA10 THR B 71 ARG B 80 -1 O THR B 79 N THR B 103 SHEET 6 BA10 GLU B 49 ARG B 58 -1 O GLU B 49 N ARG B 80 SHEET 7 BA10 THR B 34 ILE B 43 -1 O THR B 34 N ARG B 58 SHEET 8 BA10 THR B 21 ASN B 27 -1 O PHE B 22 N GLY B 39 SHEET 9 BA10 SER B 5 ASN B 12 -1 O PRO B 6 N ASN B 27 SHEET 10 BA10 SER B 5 ASN B 12 0 SHEET 1 CA22 SER C 5 GLN C 11 0 SHEET 2 CA22 GLU C 120 ILE C 126 -1 O PHE C 121 N GLY C 9 SHEET 3 CA22 ASN C 109 ILE C 112 -1 O ASN C 109 N ILE C 126 SHEET 4 CA22 GLY C 100 THR C 103 -1 O GLY C 100 N ILE C 112 SHEET 5 CA22 THR C 71 THR C 79 -1 O THR C 79 N THR C 103 SHEET 6 CA22 GLU C 49 ARG C 58 -1 O LEU C 51 N PHE C 78 SHEET 7 CA22 THR C 34 ILE C 43 -1 O THR C 34 N ARG C 58 SHEET 8 CA22 THR C 21 ASN C 27 -1 O PHE C 22 N GLY C 39 SHEET 9 CA22 THR C 21 ASN C 27 0 SHEET 10 CA22 SER C 5 GLN C 11 -1 O PRO C 6 N ASN C 27 SHEET 11 CA22 THR C 34 ILE C 43 0 SHEET 12 CA22 THR C 21 ASN C 27 -1 O PHE C 22 N GLY C 39 SHEET 13 CA22 GLU C 49 ARG C 58 0 SHEET 14 CA22 THR C 34 ILE C 43 -1 O THR C 34 N ARG C 58 SHEET 15 CA22 THR C 71 THR C 79 0 SHEET 16 CA22 GLU C 49 ARG C 58 -1 O LEU C 51 N PHE C 78 SHEET 17 CA22 GLY C 100 THR C 103 0 SHEET 18 CA22 THR C 71 THR C 79 -1 O THR C 79 N THR C 103 SHEET 19 CA22 ASN C 109 ILE C 112 0 SHEET 20 CA22 GLY C 100 THR C 103 -1 O GLY C 100 N ILE C 112 SHEET 21 CA22 GLU C 120 ILE C 126 0 SHEET 22 CA22 SER C 5 GLN C 11 -1 O SER C 5 N TYR C 125 SHEET 1 DA16 SER D 5 GLN D 11 0 SHEET 2 DA16 GLU D 120 ILE D 126 -1 O PHE D 121 N GLY D 9 SHEET 3 DA16 THR D 21 ASN D 27 0 SHEET 4 DA16 SER D 5 GLN D 11 -1 O PRO D 6 N ASN D 27 SHEET 5 DA16 THR D 34 ILE D 43 0 SHEET 6 DA16 THR D 21 ASN D 27 -1 O PHE D 22 N GLY D 39 SHEET 7 DA16 GLU D 49 ARG D 58 0 SHEET 8 DA16 THR D 34 ILE D 43 -1 O THR D 34 N ARG D 58 SHEET 9 DA16 THR D 71 ARG D 80 0 SHEET 10 DA16 GLU D 49 ARG D 58 -1 O GLU D 49 N ARG D 80 SHEET 11 DA16 GLY D 100 THR D 103 0 SHEET 12 DA16 THR D 71 ARG D 80 -1 O THR D 79 N THR D 103 SHEET 13 DA16 ASN D 109 ILE D 112 0 SHEET 14 DA16 GLY D 100 THR D 103 -1 O GLY D 100 N ILE D 112 SHEET 15 DA16 GLU D 120 ILE D 126 0 SHEET 16 DA16 SER D 5 GLN D 11 -1 O SER D 5 N TYR D 125 SSBOND 1 CYS A 41 CYS A 96 1555 1555 2.02 SSBOND 2 CYS B 41 CYS B 96 1555 1555 2.05 SSBOND 3 CYS C 41 CYS C 96 1555 1555 2.01 SSBOND 4 CYS D 41 CYS D 96 1555 1555 2.05 SITE 1 AC1 11 TRP A 28 SER A 31 SER A 33 THR A 35 SITE 2 AC1 11 TRP A 55 MET A 76 SER A 108 TYR A 125 SITE 3 AC1 11 THR A 127 VAL A 129 TRP B 68 SITE 1 AC2 11 TRP A 68 TRP B 28 SER B 31 SER B 33 SITE 2 AC2 11 THR B 35 TRP B 55 MET B 76 SER B 108 SITE 3 AC2 11 TYR B 125 THR B 127 VAL B 129 SITE 1 AC3 13 TRP C 28 SER C 31 SER C 33 THR C 35 SITE 2 AC3 13 TRP C 55 MET C 76 SER C 108 TYR C 125 SITE 3 AC3 13 THR C 127 VAL C 129 THR C 130 HOH C2038 SITE 4 AC3 13 TRP D 68 SITE 1 AC4 14 TRP C 68 ARG D 17 TRP D 28 PHE D 30 SITE 2 AC4 14 SER D 31 SER D 33 THR D 35 TRP D 55 SITE 3 AC4 14 MET D 76 SER D 108 TYR D 125 THR D 127 SITE 4 AC4 14 THR D 130 HOH D2055 CRYST1 41.768 79.309 71.727 90.00 98.73 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 0.023942 0.000000 0.003676 0.00000 SCALE2 0.000000 0.012609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014105 0.00000 MTRIX1 1 0.938770 0.008810 0.344430 -16.54458 1 MTRIX2 1 0.012520 -0.999890 -0.008540 1.13228 1 MTRIX3 1 0.344320 0.012330 -0.938770 91.86986 1 MTRIX1 2 -0.973790 -0.169100 -0.152140 60.36687 1 MTRIX2 2 -0.169900 0.096020 0.980770 -46.21220 1 MTRIX3 2 -0.151240 0.980910 -0.122230 62.29931 1 MTRIX1 3 -0.972890 0.159520 -0.167430 61.00995 1 MTRIX2 3 0.154410 -0.090900 -0.983820 47.88213 1 MTRIX3 3 -0.172160 -0.983000 0.063800 53.96689 1 MTRIX1 4 -0.967310 0.186930 -0.171380 61.38431 1 MTRIX2 4 0.157200 -0.088330 -0.983610 47.68832 1 MTRIX3 4 -0.199010 -0.978390 0.056050 54.67527 1 MTRIX1 5 -0.969650 -0.194650 -0.147970 60.38112 1 MTRIX2 5 -0.166450 0.082200 0.982620 -46.48714 1 MTRIX3 5 -0.179100 0.977420 -0.112100 62.13909 1 MTRIX1 6 0.947430 0.005470 0.319930 -15.30696 1 MTRIX2 6 0.007800 -0.999950 -0.006000 0.90837 1 MTRIX3 6 0.319880 0.008180 -0.947420 93.22396 1