HEADER PROTEIN BINDING 06-APR-11 3RFS TITLE DESIGN OF A BINDING SCAFFOLD BASED ON VARIABLE LYMPHOCYTE RECEPTORS OF TITLE 2 JAWLESS VERTEBRATES BY MODULE ENGINEERING COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERNALIN B, REPEAT MODULES, VARIABLE LYMPHOCYTE RECEPTOR COMPND 3 B; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CHIMERA OF INTERNALIN B, REPEAT MODULES, VARIABLE COMPND 7 LYMPHOCYTE RECEPTOR B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES, EPTATRETUS BURGERI, SOURCE 3 SYNTHETIC; SOURCE 4 ORGANISM_COMMON: INSHORE HAGFISH; SOURCE 5 ORGANISM_TAXID: 637381, 7764, 32630; SOURCE 6 STRAIN: 08-5923; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LRR, PROTEIN BINDING, PLASMA EXPDTA X-RAY DIFFRACTION AUTHOR H.J.KIM,H.K.CHEONG,Y.H.JEON REVDAT 3 20-NOV-24 3RFS 1 REMARK SEQADV LINK REVDAT 2 16-AUG-17 3RFS 1 SOURCE REMARK REVDAT 1 14-MAR-12 3RFS 0 JRNL AUTH S.C.LEE,K.PARK,J.HAN,J.J.LEE,H.J.KIM,S.HONG,W.HEU,Y.J.KIM, JRNL AUTH 2 J.S.HA,S.G.LEE,H.K.CHEONG,Y.H.JEON,D.KIM,H.S.KIM JRNL TITL DESIGN OF A BINDING SCAFFOLD BASED ON VARIABLE LYMPHOCYTE JRNL TITL 2 RECEPTORS OF JAWLESS VERTEBRATES BY MODULE ENGINEERING JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 3299 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22328160 JRNL DOI 10.1073/PNAS.1113193109 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 49492 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2657 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3526 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 201 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4120 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.04000 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): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.288 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4196 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5710 ; 2.097 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 524 ; 6.611 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;40.860 ;26.304 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 752 ;16.068 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;25.036 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 678 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3098 ; 0.011 ; 0.021 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): 2624 ; 1.246 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4268 ; 2.179 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1572 ; 3.746 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1442 ; 5.988 ; 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 : NULL 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 3RFS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000064876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49492 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 33.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 30%(W/V) POLYETHYLENE REMARK 280 GLYCOL 4000, 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, PH 8.5, VAPOR REMARK 280 DIFFUSION, 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 53.84650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 1 REMARK 465 PRO A 265 REMARK 465 THR A 266 REMARK 465 HIS A 267 REMARK 465 HIS A 268 REMARK 465 HIS A 269 REMARK 465 HIS A 270 REMARK 465 HIS A 271 REMARK 465 HIS A 272 REMARK 465 GLU B 1 REMARK 465 PRO B 265 REMARK 465 THR B 266 REMARK 465 HIS B 267 REMARK 465 HIS B 268 REMARK 465 HIS B 269 REMARK 465 HIS B 270 REMARK 465 HIS B 271 REMARK 465 HIS B 272 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 OD2 ASP A 214 O HOH A 308 1.95 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 OG SER A 206 O HOH A 308 1455 1.97 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 LYS A 54 CE LYS A 54 NZ 0.175 REMARK 500 LYS B 27 CB LYS B 27 CG -0.238 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 27 CD - CE - NZ ANGL. DEV. = -15.8 DEGREES REMARK 500 LYS A 54 CD - CE - NZ ANGL. DEV. = 17.1 DEGREES REMARK 500 ASP A 126 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 LEU A 135 CB - CG - CD2 ANGL. DEV. = -11.5 DEGREES REMARK 500 LEU A 159 CB - CG - CD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 GLY A 254 C - N - CA ANGL. DEV. = -13.1 DEGREES REMARK 500 ARG A 260 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 260 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ASN B 119 CB - CA - C ANGL. DEV. = 13.3 DEGREES REMARK 500 ASN B 119 N - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 ARG B 239 CG - CD - NE ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG B 239 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG B 239 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 239 NE - CZ - NH2 ANGL. DEV. = 6.3 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 LEU A 62 72.62 -112.88 REMARK 500 ASN A 73 -156.32 -104.70 REMARK 500 ASN A 95 -160.33 -106.50 REMARK 500 ASN A 119 -160.74 -103.57 REMARK 500 ASN A 143 -160.79 -118.29 REMARK 500 ASN A 167 -165.06 -111.25 REMARK 500 ASN A 191 -167.58 -128.26 REMARK 500 ALA A 246 70.38 -154.93 REMARK 500 ALA B 48 56.79 -141.13 REMARK 500 LEU B 62 76.42 -115.63 REMARK 500 ASN B 73 -156.49 -98.21 REMARK 500 ASN B 119 -160.45 -111.14 REMARK 500 LEU B 132 60.54 -100.77 REMARK 500 ASN B 143 -160.99 -127.73 REMARK 500 ASN B 167 -163.15 -125.87 REMARK 500 ALA B 246 82.11 -164.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 292 O REMARK 620 2 HOH A 335 O 88.9 REMARK 620 3 HOH A 387 O 86.1 95.4 REMARK 620 4 HOH A 388 O 92.3 174.8 79.6 REMARK 620 5 HOH A 389 O 175.5 87.1 96.3 91.9 REMARK 620 6 HOH B 366 O 85.6 88.1 170.9 97.1 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 373 O REMARK 620 2 HOH B 278 O 172.7 REMARK 620 3 HOH B 352 O 86.7 88.9 REMARK 620 4 HOH B 363 O 92.8 92.0 175.9 REMARK 620 5 HOH B 364 O 88.0 86.0 87.8 96.2 REMARK 620 6 HOH B 365 O 88.6 97.0 87.2 88.8 174.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RFJ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUE 66-179 REPRESENTS CONSENSUS DESIGNED REPEAT MODULES. REMARK 999 THE SEQUENCES OF REPEAT MOLDUES IS BASED ON VARIABLE LYMPHOCYTE REMARK 999 RECEPTORS. DBREF 3RFS A 1 65 UNP D2P9A6 D2P9A6_LISM2 36 100 DBREF 3RFS A 66 179 PDB 3RFS 3RFS 66 179 DBREF 3RFS A 180 266 UNP Q4G1L3 Q4G1L3_EPTBU 146 232 DBREF 3RFS B 1 65 UNP D2P9A6 D2P9A6_LISM2 36 100 DBREF 3RFS B 66 179 PDB 3RFS 3RFS 66 179 DBREF 3RFS B 180 266 UNP Q4G1L3 Q4G1L3_EPTBU 146 232 SEQADV 3RFS ALA A 24 UNP D2P9A6 ASP 59 CONFLICT SEQADV 3RFS HIS A 267 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS A 268 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS A 269 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS A 270 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS A 271 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS A 272 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS ALA B 24 UNP D2P9A6 ASP 59 CONFLICT SEQADV 3RFS HIS B 267 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS B 268 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS B 269 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS B 270 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS B 271 UNP Q4G1L3 EXPRESSION TAG SEQADV 3RFS HIS B 272 UNP Q4G1L3 EXPRESSION TAG SEQRES 1 A 272 GLU THR ILE THR VAL SER THR PRO ILE LYS GLN ILE PHE SEQRES 2 A 272 PRO ASP ASP ALA PHE ALA GLU THR ILE LYS ALA ASN LEU SEQRES 3 A 272 LYS LYS LYS SER VAL THR ASP ALA VAL THR GLN ASN GLU SEQRES 4 A 272 LEU ASN SER ILE ASP GLN ILE ILE ALA ASN ASN SER ASP SEQRES 5 A 272 ILE LYS SER VAL GLN GLY ILE GLN TYR LEU PRO ASN VAL SEQRES 6 A 272 ARG TYR LEU ALA LEU GLY GLY ASN LYS LEU HIS ASP ILE SEQRES 7 A 272 SER ALA LEU LYS GLU LEU THR ASN LEU THR TYR LEU ILE SEQRES 8 A 272 LEU THR GLY ASN GLN LEU GLN SER LEU PRO ASN GLY VAL SEQRES 9 A 272 PHE ASP LYS LEU THR ASN LEU LYS GLU LEU VAL LEU VAL SEQRES 10 A 272 GLU ASN GLN LEU GLN SER LEU PRO ASP GLY VAL PHE ASP SEQRES 11 A 272 LYS LEU THR ASN LEU THR TYR LEU ASN LEU ALA HIS ASN SEQRES 12 A 272 GLN LEU GLN SER LEU PRO LYS GLY VAL PHE ASP LYS LEU SEQRES 13 A 272 THR ASN LEU THR GLU LEU ASP LEU SER TYR ASN GLN LEU SEQRES 14 A 272 GLN SER LEU PRO GLU GLY VAL PHE ASP LYS LEU THR GLN SEQRES 15 A 272 LEU LYS ASP LEU ARG LEU TYR GLN ASN GLN LEU LYS SER SEQRES 16 A 272 VAL PRO ASP GLY VAL PHE ASP ARG LEU THR SER LEU GLN SEQRES 17 A 272 TYR ILE TRP LEU HIS ASP ASN PRO TRP ASP CYS THR CYS SEQRES 18 A 272 PRO GLY ILE ARG TYR LEU SER GLU TRP ILE ASN LYS HIS SEQRES 19 A 272 SER GLY VAL VAL ARG ASN SER ALA GLY SER VAL ALA PRO SEQRES 20 A 272 ASP SER ALA LYS CYS SER GLY SER GLY LYS PRO VAL ARG SEQRES 21 A 272 SER ILE ILE CYS PRO THR HIS HIS HIS HIS HIS HIS SEQRES 1 B 272 GLU THR ILE THR VAL SER THR PRO ILE LYS GLN ILE PHE SEQRES 2 B 272 PRO ASP ASP ALA PHE ALA GLU THR ILE LYS ALA ASN LEU SEQRES 3 B 272 LYS LYS LYS SER VAL THR ASP ALA VAL THR GLN ASN GLU SEQRES 4 B 272 LEU ASN SER ILE ASP GLN ILE ILE ALA ASN ASN SER ASP SEQRES 5 B 272 ILE LYS SER VAL GLN GLY ILE GLN TYR LEU PRO ASN VAL SEQRES 6 B 272 ARG TYR LEU ALA LEU GLY GLY ASN LYS LEU HIS ASP ILE SEQRES 7 B 272 SER ALA LEU LYS GLU LEU THR ASN LEU THR TYR LEU ILE SEQRES 8 B 272 LEU THR GLY ASN GLN LEU GLN SER LEU PRO ASN GLY VAL SEQRES 9 B 272 PHE ASP LYS LEU THR ASN LEU LYS GLU LEU VAL LEU VAL SEQRES 10 B 272 GLU ASN GLN LEU GLN SER LEU PRO ASP GLY VAL PHE ASP SEQRES 11 B 272 LYS LEU THR ASN LEU THR TYR LEU ASN LEU ALA HIS ASN SEQRES 12 B 272 GLN LEU GLN SER LEU PRO LYS GLY VAL PHE ASP LYS LEU SEQRES 13 B 272 THR ASN LEU THR GLU LEU ASP LEU SER TYR ASN GLN LEU SEQRES 14 B 272 GLN SER LEU PRO GLU GLY VAL PHE ASP LYS LEU THR GLN SEQRES 15 B 272 LEU LYS ASP LEU ARG LEU TYR GLN ASN GLN LEU LYS SER SEQRES 16 B 272 VAL PRO ASP GLY VAL PHE ASP ARG LEU THR SER LEU GLN SEQRES 17 B 272 TYR ILE TRP LEU HIS ASP ASN PRO TRP ASP CYS THR CYS SEQRES 18 B 272 PRO GLY ILE ARG TYR LEU SER GLU TRP ILE ASN LYS HIS SEQRES 19 B 272 SER GLY VAL VAL ARG ASN SER ALA GLY SER VAL ALA PRO SEQRES 20 B 272 ASP SER ALA LYS CYS SER GLY SER GLY LYS PRO VAL ARG SEQRES 21 B 272 SER ILE ILE CYS PRO THR HIS HIS HIS HIS HIS HIS HET MG A 302 1 HET MG B 301 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *218(H2 O) HELIX 1 1 ILE A 9 PHE A 13 1 5 HELIX 2 2 ASP A 15 LYS A 27 1 13 HELIX 3 3 THR A 36 ASN A 41 1 6 HELIX 4 4 GLY A 58 LEU A 62 5 5 HELIX 5 5 ILE A 78 LYS A 82 5 5 HELIX 6 6 ILE A 224 HIS A 234 1 11 HELIX 7 7 SER A 235 VAL A 238 5 4 HELIX 8 8 ALA A 246 ALA A 250 5 5 HELIX 9 9 PRO A 258 ILE A 262 5 5 HELIX 10 10 ILE B 9 PHE B 13 1 5 HELIX 11 11 ASP B 15 LYS B 27 1 13 HELIX 12 12 THR B 36 ASN B 41 1 6 HELIX 13 13 GLY B 58 LEU B 62 5 5 HELIX 14 14 ILE B 78 LEU B 84 5 7 HELIX 15 15 ILE B 224 HIS B 234 1 11 HELIX 16 16 SER B 235 VAL B 238 5 4 HELIX 17 17 ALA B 246 ALA B 250 5 5 HELIX 18 18 PRO B 258 ILE B 262 5 5 SHEET 1 A 2 THR A 7 PRO A 8 0 SHEET 2 A 2 ALA A 34 VAL A 35 -1 O VAL A 35 N THR A 7 SHEET 1 B 8 GLN A 45 ILE A 47 0 SHEET 2 B 8 TYR A 67 ALA A 69 1 O ALA A 69 N ILE A 46 SHEET 3 B 8 TYR A 89 ILE A 91 1 O ILE A 91 N LEU A 68 SHEET 4 B 8 GLU A 113 VAL A 115 1 O VAL A 115 N LEU A 90 SHEET 5 B 8 TYR A 137 ASN A 139 1 O TYR A 137 N LEU A 114 SHEET 6 B 8 GLU A 161 ASP A 163 1 O ASP A 163 N LEU A 138 SHEET 7 B 8 ASP A 185 ARG A 187 1 O ASP A 185 N LEU A 162 SHEET 8 B 8 TYR A 209 TRP A 211 1 O TYR A 209 N LEU A 186 SHEET 1 C 2 THR B 7 PRO B 8 0 SHEET 2 C 2 ALA B 34 VAL B 35 -1 O VAL B 35 N THR B 7 SHEET 1 D 8 GLN B 45 ILE B 47 0 SHEET 2 D 8 TYR B 67 ALA B 69 1 O ALA B 69 N ILE B 46 SHEET 3 D 8 TYR B 89 ILE B 91 1 O ILE B 91 N LEU B 68 SHEET 4 D 8 GLU B 113 VAL B 115 1 O VAL B 115 N LEU B 90 SHEET 5 D 8 TYR B 137 ASN B 139 1 O ASN B 139 N LEU B 114 SHEET 6 D 8 GLU B 161 ASP B 163 1 O ASP B 163 N LEU B 138 SHEET 7 D 8 ASP B 185 ARG B 187 1 O ASP B 185 N LEU B 162 SHEET 8 D 8 TYR B 209 TRP B 211 1 O TYR B 209 N LEU B 186 SSBOND 1 CYS A 219 CYS A 252 1555 1555 2.01 SSBOND 2 CYS A 221 CYS A 264 1555 1555 2.10 SSBOND 3 CYS B 219 CYS B 252 1555 1555 2.00 SSBOND 4 CYS B 221 CYS B 264 1555 1555 2.08 LINK O HOH A 292 MG MG A 302 1555 1555 2.03 LINK MG MG A 302 O HOH A 335 1555 1555 2.32 LINK MG MG A 302 O HOH A 387 1555 1555 2.12 LINK MG MG A 302 O HOH A 388 1555 1555 1.89 LINK MG MG A 302 O HOH A 389 1555 1555 1.95 LINK MG MG A 302 O HOH B 366 1555 1555 2.15 LINK O HOH A 373 MG MG B 301 1555 1555 2.09 LINK O HOH B 278 MG MG B 301 1555 1555 2.06 LINK MG MG B 301 O HOH B 352 1555 1555 2.34 LINK MG MG B 301 O HOH B 363 1555 1555 2.08 LINK MG MG B 301 O HOH B 364 1555 1555 1.91 LINK MG MG B 301 O HOH B 365 1555 1555 1.96 CISPEP 1 CYS A 221 PRO A 222 0 3.15 CISPEP 2 CYS B 221 PRO B 222 0 9.50 SITE 1 AC1 6 HOH A 292 HOH A 335 HOH A 387 HOH A 388 SITE 2 AC1 6 HOH A 389 HOH B 366 SITE 1 AC2 6 HOH A 373 HOH B 278 HOH B 352 HOH B 363 SITE 2 AC2 6 HOH B 364 HOH B 365 CRYST1 31.733 107.693 71.277 90.00 91.06 90.00 P 1 21 1 4 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 0.031513 0.000000 0.000585 0.00000 SCALE2 0.000000 0.009286 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014032 0.00000