HEADER BIOTIN BINDING PROTEIN 05-SEP-14 3WYQ TITLE CRYSTAL STRUCTURE OF THE LOW-IMMUNOGENIC CORE STREPTAVIDIN MUTANT TITLE 2 LISA-314 (Y22S/Y83S/R84K/E101D/R103K/E116N) AT 1.0 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTAVIDIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 37-163; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AVIDINII; SOURCE 3 ORGANISM_TAXID: 1895; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21STAR(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPAL7 KEYWDS BETA-BARREL, BIOTIN BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KAWATO,E.MIZOHATA,T.MESHIZUKA,H.DOI,T.KAWAMURA,H.MATSUMURA, AUTHOR 2 K.YUMURA,K.TSUMOTO,T.KODAMA,T.INOUE,A.SUGIYAMA REVDAT 3 29-MAY-24 3WYQ 1 REMARK REVDAT 2 24-AUG-22 3WYQ 1 JRNL REMARK SEQADV REVDAT 1 24-DEC-14 3WYQ 0 JRNL AUTH T.KAWATO,E.MIZOHATA,T.MESHIZUKA,H.DOI,T.KAWAMURA, JRNL AUTH 2 H.MATSUMURA,K.YUMURA,K.TSUMOTO,T.KODAMA,T.INOUE,A.SUGIYAMA JRNL TITL CRYSTAL STRUCTURE OF STREPTAVIDIN MUTANT WITH LOW JRNL TITL 2 IMMUNOGENICITY. JRNL REF J.BIOSCI.BIOENG. V. 119 642 2015 JRNL REFN ISSN 1389-1723 JRNL PMID 25434833 JRNL DOI 10.1016/J.JBIOSC.2014.10.025 REMARK 2 REMARK 2 RESOLUTION. 1.00 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 101796 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) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5363 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) : 1.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6979 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 392 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1770 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 254 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.023 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.025 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.017 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.755 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1950 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2655 ; 2.426 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 254 ; 8.571 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;26.740 ;24.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 261 ;12.695 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;14.278 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 297 ; 0.407 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1428 ; 0.012 ; 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): 1205 ; 2.587 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1919 ; 3.552 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 745 ; 5.265 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 731 ; 6.695 ; 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): 1950 ; 2.879 ; 3.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 13 A 134 REMARK 3 RESIDUE RANGE : A 1001 A 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 26.2696 7.1977 13.2888 REMARK 3 T TENSOR REMARK 3 T11: 0.0156 T22: 0.0080 REMARK 3 T33: 0.0098 T12: -0.0021 REMARK 3 T13: -0.0036 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.3296 L22: 0.3769 REMARK 3 L33: 0.3232 L12: -0.0577 REMARK 3 L13: -0.0922 L23: -0.0642 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: 0.0169 S13: 0.0215 REMARK 3 S21: -0.0050 S22: 0.0021 S23: -0.0050 REMARK 3 S31: -0.0270 S32: 0.0028 S33: -0.0096 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 14 B 133 REMARK 3 RESIDUE RANGE : B 1001 B 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 20.3753 -7.4408 11.3740 REMARK 3 T TENSOR REMARK 3 T11: 0.0264 T22: 0.0272 REMARK 3 T33: 0.0147 T12: -0.0045 REMARK 3 T13: -0.0083 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.4463 L22: 0.3941 REMARK 3 L33: 0.2439 L12: -0.0845 REMARK 3 L13: -0.1833 L23: -0.0744 REMARK 3 S TENSOR REMARK 3 S11: -0.0325 S12: 0.0208 S13: -0.0473 REMARK 3 S21: -0.0159 S22: 0.0037 S23: 0.0060 REMARK 3 S31: 0.0384 S32: -0.0140 S33: 0.0288 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 3WYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000096960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.82000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107216 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 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 (%) : 95.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 30.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29600 REMARK 200 FOR SHELL : 3.610 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE TRIHYDRATE, 24% POLYETHYLENE GLYCOL 4000, PH 5.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 31.61150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.53300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.61150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.53300 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: 16720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 37.91561 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.36193 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B1120 LIES ON A SPECIAL POSITION. 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 PRO A 135 REMARK 465 SER A 136 REMARK 465 ALA A 137 REMARK 465 ALA A 138 REMARK 465 SER A 139 REMARK 465 ALA B 13 REMARK 465 LYS B 134 REMARK 465 PRO B 135 REMARK 465 SER B 136 REMARK 465 ALA B 137 REMARK 465 ALA B 138 REMARK 465 SER B 139 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 1142 O HOH A 1203 1.44 REMARK 500 O HOH A 1188 O HOH A 1202 1.72 REMARK 500 C1 GOL B 1003 O HOH B 1200 1.82 REMARK 500 O HOH A 1202 O HOH A 1203 1.93 REMARK 500 O HOH B 1208 O HOH B 1219 2.04 REMARK 500 OE2 GLU A 14 O1 GOL A 1007 2.18 REMARK 500 O HOH A 1220 O HOH A 1221 2.18 REMARK 500 O HOH A 1191 O HOH A 1198 2.18 REMARK 500 O HOH A 1194 O HOH A 1195 2.19 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 HOH B 1210 O HOH B 1210 2655 1.89 REMARK 500 CG1 VAL B 97 O HOH B 1191 3545 1.92 REMARK 500 O HOH A 1214 O HOH B 1194 4555 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 44 CD GLU A 44 OE1 -0.084 REMARK 500 GLN A 95 CD GLN A 95 OE1 0.136 REMARK 500 GLN B 95 CB GLN B 95 CG -0.216 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 134 N - CA - CB ANGL. DEV. = 11.9 DEGREES REMARK 500 ARG B 53 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 GLN B 95 CA - CB - CG ANGL. DEV. = 14.6 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 SER A 52 -161.67 62.44 REMARK 500 SER A 52 -163.62 66.64 REMARK 500 ASP A 101 63.03 -118.82 REMARK 500 SER B 52 -164.25 67.28 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 VAL A 133 LYS A 134 118.74 REMARK 500 GLU B 14 ALA B 15 -137.66 REMARK 500 REMARK 500 REMARK: NULL 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 GOL A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WYP RELATED DB: PDB DBREF 3WYQ A 13 139 UNP P22629 SAV_STRAV 37 163 DBREF 3WYQ B 13 139 UNP P22629 SAV_STRAV 37 163 SEQADV 3WYQ SER A 22 UNP P22629 TYR 46 ENGINEERED MUTATION SEQADV 3WYQ SER A 83 UNP P22629 TYR 107 ENGINEERED MUTATION SEQADV 3WYQ LYS A 84 UNP P22629 ARG 108 ENGINEERED MUTATION SEQADV 3WYQ ASP A 101 UNP P22629 GLU 125 ENGINEERED MUTATION SEQADV 3WYQ LYS A 103 UNP P22629 ARG 127 ENGINEERED MUTATION SEQADV 3WYQ ASN A 116 UNP P22629 GLU 140 ENGINEERED MUTATION SEQADV 3WYQ SER B 22 UNP P22629 TYR 46 ENGINEERED MUTATION SEQADV 3WYQ SER B 83 UNP P22629 TYR 107 ENGINEERED MUTATION SEQADV 3WYQ LYS B 84 UNP P22629 ARG 108 ENGINEERED MUTATION SEQADV 3WYQ ASP B 101 UNP P22629 GLU 125 ENGINEERED MUTATION SEQADV 3WYQ LYS B 103 UNP P22629 ARG 127 ENGINEERED MUTATION SEQADV 3WYQ ASN B 116 UNP P22629 GLU 140 ENGINEERED MUTATION SEQRES 1 A 127 ALA GLU ALA GLY ILE THR GLY THR TRP SER ASN GLN LEU SEQRES 2 A 127 GLY SER THR PHE ILE VAL THR ALA GLY ALA ASP GLY ALA SEQRES 3 A 127 LEU THR GLY THR TYR GLU SER ALA VAL GLY ASN ALA GLU SEQRES 4 A 127 SER ARG TYR VAL LEU THR GLY ARG TYR ASP SER ALA PRO SEQRES 5 A 127 ALA THR ASP GLY SER GLY THR ALA LEU GLY TRP THR VAL SEQRES 6 A 127 ALA TRP LYS ASN ASN SER LYS ASN ALA HIS SER ALA THR SEQRES 7 A 127 THR TRP SER GLY GLN TYR VAL GLY GLY ALA ASP ALA LYS SEQRES 8 A 127 ILE ASN THR GLN TRP LEU LEU THR SER GLY THR THR ASN SEQRES 9 A 127 ALA ASN ALA TRP LYS SER THR LEU VAL GLY HIS ASP THR SEQRES 10 A 127 PHE THR LYS VAL LYS PRO SER ALA ALA SER SEQRES 1 B 127 ALA GLU ALA GLY ILE THR GLY THR TRP SER ASN GLN LEU SEQRES 2 B 127 GLY SER THR PHE ILE VAL THR ALA GLY ALA ASP GLY ALA SEQRES 3 B 127 LEU THR GLY THR TYR GLU SER ALA VAL GLY ASN ALA GLU SEQRES 4 B 127 SER ARG TYR VAL LEU THR GLY ARG TYR ASP SER ALA PRO SEQRES 5 B 127 ALA THR ASP GLY SER GLY THR ALA LEU GLY TRP THR VAL SEQRES 6 B 127 ALA TRP LYS ASN ASN SER LYS ASN ALA HIS SER ALA THR SEQRES 7 B 127 THR TRP SER GLY GLN TYR VAL GLY GLY ALA ASP ALA LYS SEQRES 8 B 127 ILE ASN THR GLN TRP LEU LEU THR SER GLY THR THR ASN SEQRES 9 B 127 ALA ASN ALA TRP LYS SER THR LEU VAL GLY HIS ASP THR SEQRES 10 B 127 PHE THR LYS VAL LYS PRO SER ALA ALA SER HET BTN A1001 16 HET GOL A1002 12 HET GOL A1003 6 HET GOL A1004 12 HET GOL A1005 6 HET GOL A1006 6 HET GOL A1007 6 HET SO4 A1008 5 HET BTN B1001 16 HET GOL B1002 6 HET GOL B1003 6 HET GOL B1004 6 HET GOL B1005 6 HETNAM BTN BIOTIN HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 BTN 2(C10 H16 N2 O3 S) FORMUL 4 GOL 10(C3 H8 O3) FORMUL 10 SO4 O4 S 2- FORMUL 16 HOH *254(H2 O) HELIX 1 1 THR A 115 LYS A 121 5 7 HELIX 2 2 THR B 115 LYS B 121 5 7 SHEET 1 A 9 GLY A 19 ASN A 23 0 SHEET 2 A 9 THR A 28 ALA A 33 -1 O PHE A 29 N TRP A 21 SHEET 3 A 9 ALA A 38 GLU A 44 -1 O THR A 42 N ILE A 30 SHEET 4 A 9 TYR A 54 TYR A 60 -1 O TYR A 54 N TYR A 43 SHEET 5 A 9 THR A 71 LYS A 80 -1 O THR A 76 N THR A 57 SHEET 6 A 9 ASN A 85 VAL A 97 -1 O TYR A 96 N THR A 71 SHEET 7 A 9 LYS A 103 SER A 112 -1 O GLN A 107 N SER A 93 SHEET 8 A 9 THR A 123 LYS A 134 -1 O PHE A 130 N ILE A 104 SHEET 9 A 9 GLY A 19 ASN A 23 -1 N THR A 20 O VAL A 133 SHEET 1 B 9 GLY B 19 ASN B 23 0 SHEET 2 B 9 THR B 28 ALA B 33 -1 O PHE B 29 N TRP B 21 SHEET 3 B 9 ALA B 38 GLU B 44 -1 O THR B 42 N ILE B 30 SHEET 4 B 9 TYR B 54 TYR B 60 -1 O GLY B 58 N LEU B 39 SHEET 5 B 9 THR B 71 LYS B 80 -1 O THR B 76 N THR B 57 SHEET 6 B 9 ASN B 85 VAL B 97 -1 O GLY B 94 N LEU B 73 SHEET 7 B 9 LYS B 103 SER B 112 -1 O GLN B 107 N SER B 93 SHEET 8 B 9 THR B 123 LYS B 132 -1 O PHE B 130 N ILE B 104 SHEET 9 B 9 GLY B 19 ASN B 23 -1 N SER B 22 O THR B 131 SITE 1 AC1 14 ASN A 23 LEU A 25 SER A 27 TYR A 43 SITE 2 AC1 14 SER A 45 VAL A 47 GLY A 48 ASN A 49 SITE 3 AC1 14 TRP A 79 SER A 88 THR A 90 TRP A 108 SITE 4 AC1 14 ASP A 128 GOL A1006 SITE 1 AC2 10 GLN A 95 ASN A 105 THR A 106 GLN A 107 SITE 2 AC2 10 HIS A 127 GOL A1005 HOH A1157 HOH A1158 SITE 3 AC2 10 HOH A1193 SER B 122 SITE 1 AC3 8 LEU A 25 VAL A 47 THR A 115 ASN A 116 SITE 2 AC3 8 ALA A 117 HOH A1129 GLY B 68 ALA B 117 SITE 1 AC4 9 GLY A 34 ALA A 35 ASP A 36 ALA A 38 SITE 2 AC4 9 ARG A 53 SO4 A1008 HOH A1113 HOH A1115 SITE 3 AC4 9 HOH A1179 SITE 1 AC5 9 GLN A 24 LEU A 25 GLY A 126 HIS A 127 SITE 2 AC5 9 GOL A1002 HOH A1158 HOH A1174 TRP B 120 SITE 3 AC5 9 HOH B1164 SITE 1 AC6 5 BTN A1001 HOH A1188 HOH A1225 TRP B 120 SITE 2 AC6 5 HOH B1204 SITE 1 AC7 5 GLU A 14 GLY A 16 TYR A 96 GLY A 99 SITE 2 AC7 5 ARG B 53 SITE 1 AC8 9 ALA A 13 GLY A 34 ALA A 35 SER A 52 SITE 2 AC8 9 ARG A 53 GOL A1004 HOH A1143 HOH A1179 SITE 3 AC8 9 HOH A1227 SITE 1 AC9 14 ASN B 23 LEU B 25 SER B 27 TYR B 43 SITE 2 AC9 14 SER B 45 VAL B 47 ASN B 49 TRP B 79 SITE 3 AC9 14 SER B 88 THR B 90 TRP B 108 ASP B 128 SITE 4 AC9 14 GOL B1005 HOH B1157 SITE 1 BC1 10 HOH A1209 SER B 69 GLY B 70 THR B 71 SITE 2 BC1 10 TYR B 96 VAL B 97 GLY B 98 THR B 115 SITE 3 BC1 10 ASN B 116 ALA B 117 SITE 1 BC2 9 TRP A 120 HOH A1172 GLN B 24 LEU B 25 SITE 2 BC2 9 TRP B 108 GLY B 126 HIS B 127 ASP B 128 SITE 3 BC2 9 HOH B1200 SITE 1 BC3 8 SER A 69 GLY B 99 ALA B 100 GLY B 113 SITE 2 BC3 8 THR B 114 THR B 115 ASN B 118 HOH B1220 SITE 1 BC4 4 BTN B1001 HOH B1152 HOH B1157 HOH B1161 CRYST1 63.223 67.066 56.363 90.00 116.68 90.00 C 1 2 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 0.015817 0.000000 0.007949 0.00000 SCALE2 0.000000 0.014911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019856 0.00000