HEADER BIOTIN BINDING PROTEIN 05-SEP-14 3WYP TITLE CRYSTAL STRUCTURE OF WILD-TYPE CORE STREPTAVIDIN IN COMPLEX WITH D- TITLE 2 BIOTIN/BIOTIN-D-SULFOXIDE AT 1.3 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTAVIDIN; COMPND 3 CHAIN: A, B, D, C; COMPND 4 FRAGMENT: UNP RESIDUES 37-163; COMPND 5 ENGINEERED: 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 08-NOV-23 3WYP 1 REMARK REVDAT 2 24-AUG-22 3WYP 1 JRNL REMARK REVDAT 1 24-DEC-14 3WYP 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 104885 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) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5538 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7352 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 345 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3630 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 136 REMARK 3 SOLVENT ATOMS : 480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.666 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 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): 3921 ; 0.025 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5357 ; 2.232 ; 1.926 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 494 ; 7.602 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;28.516 ;23.631 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 532 ;12.279 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;23.126 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 599 ; 0.166 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2942 ; 0.013 ; 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): 2393 ; 2.642 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3822 ; 3.668 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1528 ; 4.735 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1531 ; 6.191 ; 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): 3921 ; 2.681 ; 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 : 4 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 15 A 134 REMARK 3 RESIDUE RANGE : A 1001 A 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 2.3168 -6.6082 21.0316 REMARK 3 T TENSOR REMARK 3 T11: 0.0216 T22: 0.0324 REMARK 3 T33: 0.0137 T12: 0.0002 REMARK 3 T13: -0.0028 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.3488 L22: 0.5288 REMARK 3 L33: 0.2697 L12: -0.0768 REMARK 3 L13: -0.0838 L23: 0.0894 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: 0.0042 S13: 0.0537 REMARK 3 S21: -0.0322 S22: 0.0032 S23: -0.0059 REMARK 3 S31: -0.0384 S32: 0.0025 S33: -0.0222 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 135 REMARK 3 RESIDUE RANGE : B 1001 B 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 13.5891 -17.1422 26.4744 REMARK 3 T TENSOR REMARK 3 T11: 0.0109 T22: 0.0382 REMARK 3 T33: 0.0141 T12: -0.0017 REMARK 3 T13: -0.0121 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.3026 L22: 0.4943 REMARK 3 L33: 0.4970 L12: -0.0603 REMARK 3 L13: -0.1822 L23: 0.0314 REMARK 3 S TENSOR REMARK 3 S11: -0.0015 S12: -0.0286 S13: 0.0154 REMARK 3 S21: 0.0282 S22: 0.0265 S23: -0.0532 REMARK 3 S31: 0.0091 S32: 0.0133 S33: -0.0250 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 13 C 134 REMARK 3 RESIDUE RANGE : C 1001 C 1001 REMARK 3 ORIGIN FOR THE GROUP (A): -2.013 -25.464 1.808 REMARK 3 T TENSOR REMARK 3 T11: 0.0203 T22: 0.0385 REMARK 3 T33: 0.0197 T12: 0.0014 REMARK 3 T13: -0.0034 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.3501 L22: 0.7425 REMARK 3 L33: 0.3499 L12: 0.0759 REMARK 3 L13: -0.1871 L23: -0.0034 REMARK 3 S TENSOR REMARK 3 S11: -0.0411 S12: -0.0160 S13: -0.0616 REMARK 3 S21: 0.0051 S22: 0.0102 S23: -0.0233 REMARK 3 S31: 0.0579 S32: 0.0179 S33: 0.0309 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 14 D 135 REMARK 3 RESIDUE RANGE : D 1001 D 1001 REMARK 3 ORIGIN FOR THE GROUP (A): -1.962 -35.753 14.389 REMARK 3 T TENSOR REMARK 3 T11: 0.0284 T22: 0.0384 REMARK 3 T33: 0.0032 T12: -0.0029 REMARK 3 T13: -0.0072 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.6663 L22: 0.4799 REMARK 3 L33: 0.1838 L12: 0.0617 REMARK 3 L13: -0.0221 L23: -0.0279 REMARK 3 S TENSOR REMARK 3 S11: -0.0240 S12: 0.0359 S13: -0.0137 REMARK 3 S21: -0.0664 S22: 0.0234 S23: -0.0034 REMARK 3 S31: 0.0055 S32: -0.0209 S33: 0.0006 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 3WYP 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_1000096959. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-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) : 0.90000 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 : 110519 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 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 (%) : 96.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34500 REMARK 200 FOR SHELL : 2.910 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: 2F01 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 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: 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 48.84800 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: 14580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C 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 13 REMARK 465 GLU A 14 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 SER B 136 REMARK 465 ALA B 137 REMARK 465 ALA B 138 REMARK 465 SER B 139 REMARK 465 ALA D 13 REMARK 465 SER D 136 REMARK 465 ALA D 137 REMARK 465 ALA D 138 REMARK 465 SER D 139 REMARK 465 PRO C 135 REMARK 465 SER C 136 REMARK 465 ALA C 137 REMARK 465 ALA C 138 REMARK 465 SER C 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 C 1167 O HOH C 1193 1.90 REMARK 500 O HOH D 1196 O HOH D 1197 2.07 REMARK 500 OE2 GLU B 14 O HOH B 1146 2.07 REMARK 500 C3 GOL D 1003 O HOH D 1202 2.10 REMARK 500 O HOH D 1183 O HOH D 1215 2.10 REMARK 500 O HOH D 1157 O HOH D 1217 2.11 REMARK 500 O HOH B 1201 O HOH B 1206 2.12 REMARK 500 O HOH B 1178 O HOH B 1179 2.15 REMARK 500 OG1 THR D 91 OG SER C 93 2.16 REMARK 500 O HOH C 1182 O HOH C 1198 2.16 REMARK 500 O HOH A 1163 O HOH A 1203 2.17 REMARK 500 O ASP C 36 O3 GOL D 1004 2.18 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 B 14 CD GLU B 14 OE1 0.074 REMARK 500 ARG D 84 CZ ARG D 84 NH2 0.078 REMARK 500 GLU C 51 CB GLU C 51 CG -0.133 REMARK 500 LYS C 132 CE LYS C 132 NZ 0.196 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 128 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG B 103 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 103 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG D 84 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 LYS C 132 CD - CE - NZ ANGL. DEV. = 14.0 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 -159.75 62.45 REMARK 500 GLU A 101 72.13 -119.20 REMARK 500 SER B 52 -158.32 61.72 REMARK 500 GLU B 101 50.60 -117.28 REMARK 500 ALA D 15 109.81 -169.59 REMARK 500 SER D 52 -152.24 57.68 REMARK 500 SER C 52 -157.33 58.78 REMARK 500 GLU C 101 57.78 -115.93 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 ALA D 15 GLY D 16 146.47 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 BSO B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTN D 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BSO C 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WYQ RELATED DB: PDB DBREF 3WYP A 13 139 UNP P22629 SAV_STRAV 37 163 DBREF 3WYP B 13 139 UNP P22629 SAV_STRAV 37 163 DBREF 3WYP D 13 139 UNP P22629 SAV_STRAV 37 163 DBREF 3WYP C 13 139 UNP P22629 SAV_STRAV 37 163 SEQRES 1 A 127 ALA GLU ALA GLY ILE THR GLY THR TRP TYR 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 TYR ARG ASN ALA HIS SER ALA THR SEQRES 7 A 127 THR TRP SER GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG SEQRES 8 A 127 ILE ASN THR GLN TRP LEU LEU THR SER GLY THR THR GLU 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 TYR 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 TYR ARG ASN ALA HIS SER ALA THR SEQRES 7 B 127 THR TRP SER GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG SEQRES 8 B 127 ILE ASN THR GLN TRP LEU LEU THR SER GLY THR THR GLU 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 SEQRES 1 D 127 ALA GLU ALA GLY ILE THR GLY THR TRP TYR ASN GLN LEU SEQRES 2 D 127 GLY SER THR PHE ILE VAL THR ALA GLY ALA ASP GLY ALA SEQRES 3 D 127 LEU THR GLY THR TYR GLU SER ALA VAL GLY ASN ALA GLU SEQRES 4 D 127 SER ARG TYR VAL LEU THR GLY ARG TYR ASP SER ALA PRO SEQRES 5 D 127 ALA THR ASP GLY SER GLY THR ALA LEU GLY TRP THR VAL SEQRES 6 D 127 ALA TRP LYS ASN ASN TYR ARG ASN ALA HIS SER ALA THR SEQRES 7 D 127 THR TRP SER GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG SEQRES 8 D 127 ILE ASN THR GLN TRP LEU LEU THR SER GLY THR THR GLU SEQRES 9 D 127 ALA ASN ALA TRP LYS SER THR LEU VAL GLY HIS ASP THR SEQRES 10 D 127 PHE THR LYS VAL LYS PRO SER ALA ALA SER SEQRES 1 C 127 ALA GLU ALA GLY ILE THR GLY THR TRP TYR ASN GLN LEU SEQRES 2 C 127 GLY SER THR PHE ILE VAL THR ALA GLY ALA ASP GLY ALA SEQRES 3 C 127 LEU THR GLY THR TYR GLU SER ALA VAL GLY ASN ALA GLU SEQRES 4 C 127 SER ARG TYR VAL LEU THR GLY ARG TYR ASP SER ALA PRO SEQRES 5 C 127 ALA THR ASP GLY SER GLY THR ALA LEU GLY TRP THR VAL SEQRES 6 C 127 ALA TRP LYS ASN ASN TYR ARG ASN ALA HIS SER ALA THR SEQRES 7 C 127 THR TRP SER GLY GLN TYR VAL GLY GLY ALA GLU ALA ARG SEQRES 8 C 127 ILE ASN THR GLN TRP LEU LEU THR SER GLY THR THR GLU SEQRES 9 C 127 ALA ASN ALA TRP LYS SER THR LEU VAL GLY HIS ASP THR SEQRES 10 C 127 PHE THR LYS VAL LYS PRO SER ALA ALA SER HET BTN A1001 16 HET GOL A1002 6 HET GOL A1003 6 HET GOL A1004 6 HET BSO B1001 17 HET GOL B1002 6 HET GOL B1003 6 HET SO4 B1004 5 HET BTN D1001 16 HET GOL D1002 6 HET GOL D1003 6 HET GOL D1004 6 HET BSO C1001 17 HET GOL C1002 6 HET GOL C1003 6 HET SO4 C1004 5 HETNAM BTN BIOTIN HETNAM GOL GLYCEROL HETNAM BSO BIOTIN-D-SULFOXIDE HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN BSO 5-[(3AR,4R,6AS)-5-OXIDO-2-OXOHEXAHYDRO-1H-THIENO[3,4- HETSYN 2 BSO D]IMIDAZOL-4-YL]PENTANOIC ACID FORMUL 5 BTN 2(C10 H16 N2 O3 S) FORMUL 6 GOL 10(C3 H8 O3) FORMUL 9 BSO 2(C10 H16 N2 O4 S) FORMUL 12 SO4 2(O4 S 2-) FORMUL 21 HOH *480(H2 O) HELIX 1 1 THR A 115 LYS A 121 5 7 HELIX 2 2 ASN B 118 LYS B 121 5 4 HELIX 3 3 ASN D 118 LYS D 121 5 4 HELIX 4 4 GLU C 14 THR C 18 5 5 HELIX 5 5 THR C 115 LYS C 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 GLY A 58 N LEU A 39 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 SER A 88 N TRP A 79 SHEET 7 A 9 ARG A 103 SER A 112 -1 O ARG A 103 N VAL A 97 SHEET 8 A 9 THR A 123 THR A 131 -1 O PHE A 130 N ILE A 104 SHEET 9 A 9 GLY A 19 ASN A 23 -1 N TYR A 22 O THR A 131 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 TYR B 54 N TYR B 43 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 SER B 88 N TRP B 79 SHEET 7 B 9 ARG B 103 SER B 112 -1 O THR B 111 N ALA B 89 SHEET 8 B 9 THR B 123 THR B 131 -1 O PHE B 130 N ILE B 104 SHEET 9 B 9 GLY B 19 ASN B 23 -1 N TYR B 22 O THR B 131 SHEET 1 C 9 GLY D 19 ASN D 23 0 SHEET 2 C 9 THR D 28 ALA D 33 -1 O PHE D 29 N TRP D 21 SHEET 3 C 9 ALA D 38 GLU D 44 -1 O THR D 42 N ILE D 30 SHEET 4 C 9 TYR D 54 TYR D 60 -1 O GLY D 58 N LEU D 39 SHEET 5 C 9 THR D 71 LYS D 80 -1 O THR D 76 N THR D 57 SHEET 6 C 9 ASN D 85 VAL D 97 -1 O GLY D 94 N LEU D 73 SHEET 7 C 9 ARG D 103 SER D 112 -1 O ARG D 103 N VAL D 97 SHEET 8 C 9 THR D 123 THR D 131 -1 O LEU D 124 N LEU D 110 SHEET 9 C 9 GLY D 19 ASN D 23 -1 N TYR D 22 O THR D 131 SHEET 1 D 9 GLY C 19 TYR C 22 0 SHEET 2 D 9 THR C 28 ALA C 33 -1 O PHE C 29 N TRP C 21 SHEET 3 D 9 ALA C 38 GLU C 44 -1 O THR C 42 N ILE C 30 SHEET 4 D 9 TYR C 54 TYR C 60 -1 O TYR C 54 N TYR C 43 SHEET 5 D 9 THR C 71 LYS C 80 -1 O THR C 76 N THR C 57 SHEET 6 D 9 ASN C 85 VAL C 97 -1 O GLY C 94 N LEU C 73 SHEET 7 D 9 ARG C 103 SER C 112 -1 O ARG C 103 N VAL C 97 SHEET 8 D 9 THR C 123 THR C 131 -1 O PHE C 130 N ILE C 104 SHEET 9 D 9 GLY C 19 TYR C 22 -1 N TYR C 22 O THR C 131 CISPEP 1 ALA A 15 GLY A 16 0 18.76 CISPEP 2 GLU D 14 ALA D 15 0 -7.61 CISPEP 3 ALA D 100 GLU D 101 0 -16.96 SITE 1 AC1 16 ASN A 23 LEU A 25 SER A 27 TYR A 43 SITE 2 AC1 16 SER A 45 VAL A 47 GLY A 48 ASN A 49 SITE 3 AC1 16 TRP A 79 SER A 88 THR A 90 TRP A 108 SITE 4 AC1 16 ASP A 128 HOH A1170 TRP D 120 GOL D1002 SITE 1 AC2 8 GLN A 24 LEU A 25 GLY A 126 HIS A 127 SITE 2 AC2 8 GOL A1004 HOH A1123 HOH A1145 HOH A1163 SITE 1 AC3 5 GLY A 26 SER A 27 THR A 28 GLU A 44 SITE 2 AC3 5 ALA A 46 SITE 1 AC4 7 HIS A 127 GOL A1002 HOH A1189 HOH A1203 SITE 2 AC4 7 HOH A1213 THR C 129 HOH C1119 SITE 1 AC5 16 ASN B 23 LEU B 25 SER B 27 TYR B 43 SITE 2 AC5 16 SER B 45 VAL B 47 ASN B 49 TRP B 79 SITE 3 AC5 16 SER B 88 THR B 90 TRP B 108 LEU B 110 SITE 4 AC5 16 ASP B 128 HOH B1147 HOH B1212 TRP C 120 SITE 1 AC6 6 GLN B 24 LEU B 25 GLY B 126 HIS B 127 SITE 2 AC6 6 HOH B1124 HOH B1132 SITE 1 AC7 4 GLY B 26 SER B 27 THR B 28 GLU B 44 SITE 1 AC8 6 HIS A 87 ALA B 65 THR B 66 HOH B1167 SITE 2 AC8 6 HOH B1168 HOH B1211 SITE 1 AC9 16 TRP A 120 ASN D 23 LEU D 25 SER D 27 SITE 2 AC9 16 TYR D 43 SER D 45 VAL D 47 GLY D 48 SITE 3 AC9 16 ASN D 49 TRP D 79 SER D 88 THR D 90 SITE 4 AC9 16 TRP D 108 ASP D 128 HOH D1127 HOH D1224 SITE 1 BC1 4 BTN A1001 HOH A1170 HOH D1139 HOH D1170 SITE 1 BC2 9 GLN D 24 LEU D 25 GLY D 126 HIS D 127 SITE 2 BC2 9 HOH D1121 HOH D1148 HOH D1174 HOH D1202 SITE 3 BC2 9 HOH D1222 SITE 1 BC3 7 ASP C 36 ARG C 59 SER C 62 HOH C1115 SITE 2 BC3 7 LYS D 80 ASN D 81 ASN D 82 SITE 1 BC4 15 TRP B 120 ASN C 23 LEU C 25 SER C 27 SITE 2 BC4 15 TYR C 43 SER C 45 VAL C 47 ASN C 49 SITE 3 BC4 15 TRP C 79 SER C 88 THR C 90 TRP C 108 SITE 4 BC4 15 LEU C 110 ASP C 128 GOL C1003 SITE 1 BC5 6 TRP B 120 GLN C 24 LEU C 25 GLY C 126 SITE 2 BC5 6 HIS C 127 HOH C1125 SITE 1 BC6 3 SER C 112 BSO C1001 HOH C1134 SITE 1 BC7 11 GLY B 48 HOH B1148 HOH B1164 ALA C 65 SITE 2 BC7 11 THR C 66 ASP C 67 LYS C 121 HOH C1137 SITE 3 BC7 11 HOH C1143 HOH C1178 HOH C1199 CRYST1 50.354 97.696 52.570 90.00 112.29 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 0.019859 0.000000 0.008139 0.00000 SCALE2 0.000000 0.010236 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020558 0.00000