HEADER IMMUNE SYSTEM 14-FEB-13 4J8R TITLE STRUCTURE OF AN OCTAPEPTIDE REPEAT OF THE PRION PROTEIN BOUND TO THE TITLE 2 POM2 FAB ANTIBODY FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF POM2 FAB; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 67-82; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF POM2 FAB; COMPND 7 CHAIN: B, D; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: MAJOR PRION PROTEIN; COMPND 10 CHAIN: I, J; COMPND 11 SYNONYM: PRP, PRP27-30, PRP33-35C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 6 ORGANISM_TAXID: 10090; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090 KEYWDS IMMUNOGLOBULIN FOLD, FAB, ANTIBODY, OCTAPEPTIDE REPEAT, MOUSE PRION KEYWDS 2 PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.SWAYAMPAKULA,P.K.BARAL,N.N.V.KAV,A.AGUZZI,M.N.G.JAMES REVDAT 5 06-NOV-24 4J8R 1 REMARK REVDAT 4 20-SEP-23 4J8R 1 REMARK REVDAT 3 26-NOV-14 4J8R 1 REMARK REVDAT 2 24-JUL-13 4J8R 1 JRNL REVDAT 1 22-MAY-13 4J8R 0 JRNL AUTH M.SWAYAMPAKULA,P.K.BARAL,A.AGUZZI,N.N.KAV,M.N.JAMES JRNL TITL THE CRYSTAL STRUCTURE OF AN OCTAPEPTIDE REPEAT OF THE PRION JRNL TITL 2 PROTEIN IN COMPLEX WITH A FAB FRAGMENT OF THE POM2 ANTIBODY. JRNL REF PROTEIN SCI. V. 22 893 2013 JRNL REFN ISSN 0961-8368 JRNL PMID 23629842 JRNL DOI 10.1002/PRO.2270 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 44006 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2215 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.6031 - 5.7973 1.00 2841 137 0.2326 0.2358 REMARK 3 2 5.7973 - 4.6037 1.00 2684 138 0.2000 0.1984 REMARK 3 3 4.6037 - 4.0224 1.00 2650 131 0.1912 0.1686 REMARK 3 4 4.0224 - 3.6550 1.00 2625 150 0.2184 0.2266 REMARK 3 5 3.6550 - 3.3931 1.00 2625 134 0.2383 0.2548 REMARK 3 6 3.3931 - 3.1932 1.00 2590 161 0.2567 0.2991 REMARK 3 7 3.1932 - 3.0333 1.00 2578 149 0.2743 0.3208 REMARK 3 8 3.0333 - 2.9013 1.00 2623 130 0.2808 0.3067 REMARK 3 9 2.9013 - 2.7897 1.00 2605 124 0.2982 0.3204 REMARK 3 10 2.7897 - 2.6934 1.00 2564 146 0.3104 0.3293 REMARK 3 11 2.6934 - 2.6092 1.00 2567 140 0.3172 0.3035 REMARK 3 12 2.6092 - 2.5346 1.00 2600 130 0.3169 0.3446 REMARK 3 13 2.5346 - 2.4679 1.00 2574 132 0.3287 0.3402 REMARK 3 14 2.4679 - 2.4077 1.00 2569 138 0.3401 0.3955 REMARK 3 15 2.4077 - 2.3530 1.00 2592 137 0.3498 0.3209 REMARK 3 16 2.3530 - 2.3029 0.98 2504 138 0.3406 0.3471 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.028 6797 REMARK 3 ANGLE : 1.933 9247 REMARK 3 CHIRALITY : 0.167 1040 REMARK 3 PLANARITY : 0.013 1179 REMARK 3 DIHEDRAL : 15.780 2403 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.0193 -13.5080 27.3858 REMARK 3 T TENSOR REMARK 3 T11: 0.3912 T22: 0.3517 REMARK 3 T33: 0.4468 T12: -0.0266 REMARK 3 T13: -0.0370 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: -0.1498 L22: 0.3556 REMARK 3 L33: 0.0682 L12: -0.1973 REMARK 3 L13: 0.0299 L23: -0.1949 REMARK 3 S TENSOR REMARK 3 S11: -0.0202 S12: 0.0084 S13: -0.0082 REMARK 3 S21: -0.0262 S22: 0.0210 S23: 0.0284 REMARK 3 S31: -0.0098 S32: -0.0005 S33: -0.0011 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE RMEAS FOR THE DATA COLLECTION IS REMARK 3 0.161 (OVERALL DATA) REMARK 4 REMARK 4 4J8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOXDS REMARK 200 DATA SCALING SOFTWARE : AUTOXDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44080 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 39.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.240 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4DGI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 1000, 0.1M HEPES, 0.2M CALCIUM REMARK 280 CHLORIDE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 32.70750 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 103.79600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.70750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.79600 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, J 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 210 REMARK 465 HIS I 10 REMARK 465 GLY I 11 REMARK 465 GLY I 12 REMARK 465 SER I 13 REMARK 465 TRP I 14 REMARK 465 GLY I 15 REMARK 465 GLN I 16 REMARK 465 PRO J 9 REMARK 465 HIS J 10 REMARK 465 GLY J 11 REMARK 465 GLY J 12 REMARK 465 SER J 13 REMARK 465 TRP J 14 REMARK 465 GLY J 15 REMARK 465 GLN J 16 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 CG GLU C 183 NH2 ARG C 186 1.74 REMARK 500 OE1 GLN B 170 OG1 THR B 175 2.19 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 TRP C 34 CB TRP C 34 CG -0.112 REMARK 500 GLU C 183 CD GLU C 183 OE1 -0.096 REMARK 500 GLU C 183 CD GLU C 183 OE2 -0.077 REMARK 500 THR C 191 C CYS C 192 N 0.175 REMARK 500 CYS C 192 C GLU C 193 N 0.155 REMARK 500 PRO D 183 CD PRO D 183 N -0.087 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 GLU A 183 OE1 - CD - OE2 ANGL. DEV. = -9.5 DEGREES REMARK 500 CYS B 22 CA - CB - SG ANGL. DEV. = 9.4 DEGREES REMARK 500 PRO B 126 C - N - CD ANGL. DEV. = -16.1 DEGREES REMARK 500 CYS B 139 CA - CB - SG ANGL. DEV. = 8.6 DEGREES REMARK 500 ASP B 172 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 172 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 LYS C 9 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 CYS C 132 CA - CB - SG ANGL. DEV. = 10.0 DEGREES REMARK 500 GLU C 183 N - CA - CB ANGL. DEV. = 11.1 DEGREES REMARK 500 THR C 191 CA - C - N ANGL. DEV. = -17.5 DEGREES REMARK 500 THR C 191 O - C - N ANGL. DEV. = 15.0 DEGREES REMARK 500 CYS C 192 CA - CB - SG ANGL. DEV. = 11.4 DEGREES REMARK 500 CYS C 192 CA - C - N ANGL. DEV. = -14.2 DEGREES REMARK 500 CYS C 192 O - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 GLU C 193 C - N - CA ANGL. DEV. = -15.4 DEGREES REMARK 500 PRO D 183 C - N - CD ANGL. DEV. = -13.9 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 ALA A 50 -49.21 77.30 REMARK 500 SER A 83 -168.11 170.12 REMARK 500 SER A 92 -167.72 -124.42 REMARK 500 SER B 95 -154.77 -135.60 REMARK 500 ALA B 130 179.86 64.36 REMARK 500 SER B 171 -123.00 177.48 REMARK 500 TRP I 6 -160.49 74.01 REMARK 500 ALA C 50 -54.47 72.82 REMARK 500 SER C 92 -168.67 -120.19 REMARK 500 ALA D 88 -179.05 -171.56 REMARK 500 SER D 95 -162.91 -126.51 REMARK 500 ALA D 127 -155.24 88.70 REMARK 500 SER D 133 -90.67 -112.43 REMARK 500 SER D 171 -127.59 60.38 REMARK 500 HIS J 2 110.65 -162.35 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 GLY A 29 THR A 30 148.48 REMARK 500 ASP B 172 LEU B 173 -144.67 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 CHAIN I OF MAJOR PRION PROTEIN REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN J OF MAJOR PRION PROTEIN DBREF 4J8R I 1 16 UNP P04925 PRIO_MOUSE 67 82 DBREF 4J8R J 1 16 UNP P04925 PRIO_MOUSE 67 82 DBREF 4J8R A 1 210 PDB 4J8R 4J8R 1 210 DBREF 4J8R C 1 210 PDB 4J8R 4J8R 1 210 DBREF 4J8R B 2 212 PDB 4J8R 4J8R 2 212 DBREF 4J8R D 2 212 PDB 4J8R 4J8R 2 212 SEQRES 1 A 210 ASP ILE VAL MET THR GLN SER HIS LYS PHE MET SER THR SEQRES 2 A 210 SER VAL GLY ASP ARG VAL SER ILE THR CYS LYS ALA SER SEQRES 3 A 210 GLN VAL GLY THR ALA LEU ALA TRP TYR GLN GLN LYS PRO SEQRES 4 A 210 GLY GLN SER PRO LYS LEU LEU ILE TYR TRP ALA SER THR SEQRES 5 A 210 ARG HIS THR GLY VAL PRO ASP ARG PHE THR GLY SER GLY SEQRES 6 A 210 SER GLY THR ASP PHE THR LEU THR ILE SER ASN VAL GLN SEQRES 7 A 210 SER GLU ASP LEU SER ASP TYR PHE CYS GLN GLN TYR SER SEQRES 8 A 210 SER TYR PRO THR PHE GLY GLY GLY THR LYS LEU GLU ILE SEQRES 9 A 210 LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE PRO SEQRES 10 A 210 PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER VAL SEQRES 11 A 210 VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE ASN SEQRES 12 A 210 VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN GLY SEQRES 13 A 210 VAL LEU ASN SER GLU THR ASP GLN ASP SER LYS ASP SER SEQRES 14 A 210 THR TYR SER MET SER SER THR LEU THR LEU THR LYS ASP SEQRES 15 A 210 GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA THR SEQRES 16 A 210 HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE ASN SEQRES 17 A 210 ARG ALA SEQRES 1 B 220 VAL LYS LEU GLN GLU SER GLY GLY GLU VAL VAL ARG PRO SEQRES 2 B 220 GLY THR SER VAL LYS VAL SER CYS LYS ALA SER GLY TYR SEQRES 3 B 220 ALA PHE THR ASN TYR LEU ILE GLU TRP VAL LYS GLN ARG SEQRES 4 B 220 PRO GLY GLN GLY LEU GLU TRP ILE GLY VAL ILE ASN PRO SEQRES 5 B 220 GLY SER GLY ASP THR ASN TYR ASN GLU LYS PHE LYS GLY SEQRES 6 B 220 LYS ALA THR LEU THR ALA ASP LYS SER SER SER THR ALA SEQRES 7 B 220 TYR MET GLN LEU ASN SER LEU THR SER ASP ASP SER ALA SEQRES 8 B 220 VAL TYR PHE CYS ALA ARG SER GLY ALA ALA ALA PRO THR SEQRES 9 B 220 TYR TYR ALA MET ASP TYR TRP GLY GLN GLY VAL SER VAL SEQRES 10 B 220 THR VAL SER SER ALA LYS THR THR PRO PRO SER VAL TYR SEQRES 11 B 220 PRO LEU ALA PRO ALA ALA ALA ALA ALA ASN SER MET VAL SEQRES 12 B 220 THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO SEQRES 13 B 220 VAL THR VAL THR TRP ASN SER GLY SER LEU SER GLY GLY SEQRES 14 B 220 VAL HIS THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR SEQRES 15 B 220 THR LEU SER SER SER VAL THR VAL PRO SER SER THR TRP SEQRES 16 B 220 PRO SER GLU THR VAL THR CYS ASN VAL ALA HIS PRO ALA SEQRES 17 B 220 SER SER THR LYS VAL ASP LYS LYS ILE VAL PRO ARG SEQRES 1 I 16 PRO HIS GLY GLY SER TRP GLY GLN PRO HIS GLY GLY SER SEQRES 2 I 16 TRP GLY GLN SEQRES 1 C 210 ASP ILE VAL MET THR GLN SER HIS LYS PHE MET SER THR SEQRES 2 C 210 SER VAL GLY ASP ARG VAL SER ILE THR CYS LYS ALA SER SEQRES 3 C 210 GLN VAL GLY THR ALA LEU ALA TRP TYR GLN GLN LYS PRO SEQRES 4 C 210 GLY GLN SER PRO LYS LEU LEU ILE TYR TRP ALA SER THR SEQRES 5 C 210 ARG HIS THR GLY VAL PRO ASP ARG PHE THR GLY SER GLY SEQRES 6 C 210 SER GLY THR ASP PHE THR LEU THR ILE SER ASN VAL GLN SEQRES 7 C 210 SER GLU ASP LEU SER ASP TYR PHE CYS GLN GLN TYR SER SEQRES 8 C 210 SER TYR PRO THR PHE GLY GLY GLY THR LYS LEU GLU ILE SEQRES 9 C 210 LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE PHE PRO SEQRES 10 C 210 PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SER VAL SEQRES 11 C 210 VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP ILE ASN SEQRES 12 C 210 VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN ASN GLY SEQRES 13 C 210 VAL LEU ASN SER GLU THR ASP GLN ASP SER LYS ASP SER SEQRES 14 C 210 THR TYR SER MET SER SER THR LEU THR LEU THR LYS ASP SEQRES 15 C 210 GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU ALA THR SEQRES 16 C 210 HIS LYS THR SER THR SER PRO ILE VAL LYS SER PHE ASN SEQRES 17 C 210 ARG ALA SEQRES 1 D 220 VAL LYS LEU GLN GLU SER GLY GLY GLU VAL VAL ARG PRO SEQRES 2 D 220 GLY THR SER VAL LYS VAL SER CYS LYS ALA SER GLY TYR SEQRES 3 D 220 ALA PHE THR ASN TYR LEU ILE GLU TRP VAL LYS GLN ARG SEQRES 4 D 220 PRO GLY GLN GLY LEU GLU TRP ILE GLY VAL ILE ASN PRO SEQRES 5 D 220 GLY SER GLY ASP THR ASN TYR ASN GLU LYS PHE LYS GLY SEQRES 6 D 220 LYS ALA THR LEU THR ALA ASP LYS SER SER SER THR ALA SEQRES 7 D 220 TYR MET GLN LEU ASN SER LEU THR SER ASP ASP SER ALA SEQRES 8 D 220 VAL TYR PHE CYS ALA ARG SER GLY ALA ALA ALA PRO THR SEQRES 9 D 220 TYR TYR ALA MET ASP TYR TRP GLY GLN GLY VAL SER VAL SEQRES 10 D 220 THR VAL SER SER ALA LYS THR THR PRO PRO SER VAL TYR SEQRES 11 D 220 PRO LEU ALA PRO ALA ALA ALA ALA ALA ASN SER MET VAL SEQRES 12 D 220 THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO SEQRES 13 D 220 VAL THR VAL THR TRP ASN SER GLY SER LEU SER GLY GLY SEQRES 14 D 220 VAL HIS THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR SEQRES 15 D 220 THR LEU SER SER SER VAL THR VAL PRO SER SER THR TRP SEQRES 16 D 220 PRO SER GLU THR VAL THR CYS ASN VAL ALA HIS PRO ALA SEQRES 17 D 220 SER SER THR LYS VAL ASP LYS LYS ILE VAL PRO ARG SEQRES 1 J 16 PRO HIS GLY GLY SER TRP GLY GLN PRO HIS GLY GLY SER SEQRES 2 J 16 TRP GLY GLN FORMUL 7 HOH *165(H2 O) HELIX 1 1 GLN A 78 LEU A 82 5 5 HELIX 2 2 SER A 119 SER A 125 1 7 HELIX 3 3 LYS A 181 HIS A 187 1 7 HELIX 4 4 ALA B 28 THR B 30 5 3 HELIX 5 5 GLU B 61 LYS B 64 5 4 HELIX 6 6 THR B 83 SER B 87 5 5 HELIX 7 7 SER B 155 SER B 157 5 3 HELIX 8 8 SER B 185 GLU B 190 1 6 HELIX 9 9 GLN C 78 LEU C 82 5 5 HELIX 10 10 SER C 119 THR C 124 1 6 HELIX 11 11 LYS C 181 HIS C 187 1 7 HELIX 12 12 ALA D 28 THR D 30 5 3 HELIX 13 13 GLU D 61 LYS D 64 5 4 HELIX 14 14 THR D 83 SER D 87 5 5 HELIX 15 15 PRO D 183 TRP D 187 5 5 SHEET 1 A 4 MET A 4 THR A 5 0 SHEET 2 A 4 VAL A 19 ALA A 25 -1 O LYS A 24 N THR A 5 SHEET 3 A 4 ASP A 69 ILE A 74 -1 O LEU A 72 N ILE A 21 SHEET 4 A 4 PHE A 61 SER A 66 -1 N THR A 62 O THR A 73 SHEET 1 B 6 PHE A 10 THR A 13 0 SHEET 2 B 6 THR A 100 ILE A 104 1 O GLU A 103 N MET A 11 SHEET 3 B 6 ASP A 84 GLN A 89 -1 N TYR A 85 O THR A 100 SHEET 4 B 6 LEU A 32 GLN A 37 -1 N ALA A 33 O GLN A 88 SHEET 5 B 6 LYS A 44 TYR A 48 -1 O LEU A 46 N TRP A 34 SHEET 6 B 6 THR A 52 ARG A 53 -1 O THR A 52 N TYR A 48 SHEET 1 C 4 PHE A 10 THR A 13 0 SHEET 2 C 4 THR A 100 ILE A 104 1 O GLU A 103 N MET A 11 SHEET 3 C 4 ASP A 84 GLN A 89 -1 N TYR A 85 O THR A 100 SHEET 4 C 4 THR A 95 PHE A 96 -1 O THR A 95 N GLN A 89 SHEET 1 D 4 THR A 112 PHE A 116 0 SHEET 2 D 4 GLY A 127 PHE A 137 -1 O PHE A 133 N SER A 114 SHEET 3 D 4 TYR A 171 THR A 180 -1 O MET A 173 N LEU A 134 SHEET 4 D 4 VAL A 157 GLU A 161 -1 N SER A 160 O SER A 174 SHEET 1 E 4 SER A 151 GLU A 152 0 SHEET 2 E 4 ASN A 143 ILE A 148 -1 N ILE A 148 O SER A 151 SHEET 3 E 4 SER A 189 HIS A 196 -1 O GLU A 193 N LYS A 145 SHEET 4 E 4 SER A 199 ASN A 208 -1 O LYS A 205 N CYS A 192 SHEET 1 F 4 LYS B 3 GLU B 6 0 SHEET 2 F 4 VAL B 18 SER B 25 -1 O LYS B 23 N GLN B 5 SHEET 3 F 4 THR B 77 LEU B 82 -1 O MET B 80 N VAL B 20 SHEET 4 F 4 ALA B 67 ASP B 72 -1 N THR B 70 O TYR B 79 SHEET 1 G 6 GLU B 10 VAL B 12 0 SHEET 2 G 6 VAL B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 G 6 ALA B 88 ALA B 97 -1 N ALA B 88 O VAL B 109 SHEET 4 G 6 TYR B 32 GLN B 39 -1 N GLU B 35 O ALA B 93 SHEET 5 G 6 GLU B 46 ILE B 51 -1 O GLU B 46 N LYS B 38 SHEET 6 G 6 THR B 57 TYR B 59 -1 O ASN B 58 N VAL B 50 SHEET 1 H 4 GLU B 10 VAL B 12 0 SHEET 2 H 4 VAL B 107 VAL B 111 1 O THR B 110 N VAL B 12 SHEET 3 H 4 ALA B 88 ALA B 97 -1 N ALA B 88 O VAL B 109 SHEET 4 H 4 TYR B 102 TRP B 103 -1 O TYR B 102 N ARG B 94 SHEET 1 I 4 SER B 120 LEU B 124 0 SHEET 2 I 4 MET B 134 TYR B 144 -1 O LYS B 142 N SER B 120 SHEET 3 I 4 TYR B 174 PRO B 183 -1 O VAL B 180 N LEU B 137 SHEET 4 I 4 VAL B 162 THR B 164 -1 N HIS B 163 O SER B 179 SHEET 1 J 4 SER B 120 LEU B 124 0 SHEET 2 J 4 MET B 134 TYR B 144 -1 O LYS B 142 N SER B 120 SHEET 3 J 4 TYR B 174 PRO B 183 -1 O VAL B 180 N LEU B 137 SHEET 4 J 4 VAL B 168 LEU B 169 -1 N VAL B 168 O THR B 175 SHEET 1 K 3 THR B 150 TRP B 153 0 SHEET 2 K 3 THR B 193 HIS B 198 -1 O ASN B 195 N THR B 152 SHEET 3 K 3 THR B 203 LYS B 208 -1 O THR B 203 N HIS B 198 SHEET 1 L 4 MET C 4 THR C 5 0 SHEET 2 L 4 VAL C 19 ALA C 25 -1 O LYS C 24 N THR C 5 SHEET 3 L 4 ASP C 69 ILE C 74 -1 O LEU C 72 N ILE C 21 SHEET 4 L 4 PHE C 61 SER C 64 -1 N THR C 62 O THR C 73 SHEET 1 M 6 PHE C 10 THR C 13 0 SHEET 2 M 6 THR C 100 ILE C 104 1 O GLU C 103 N MET C 11 SHEET 3 M 6 ASP C 84 GLN C 89 -1 N TYR C 85 O THR C 100 SHEET 4 M 6 LEU C 32 GLN C 37 -1 N ALA C 33 O GLN C 88 SHEET 5 M 6 LYS C 44 TYR C 48 -1 O LEU C 46 N TRP C 34 SHEET 6 M 6 THR C 52 ARG C 53 -1 O THR C 52 N TYR C 48 SHEET 1 N 4 PHE C 10 THR C 13 0 SHEET 2 N 4 THR C 100 ILE C 104 1 O GLU C 103 N MET C 11 SHEET 3 N 4 ASP C 84 GLN C 89 -1 N TYR C 85 O THR C 100 SHEET 4 N 4 THR C 95 PHE C 96 -1 O THR C 95 N GLN C 89 SHEET 1 O 4 THR C 112 PHE C 116 0 SHEET 2 O 4 GLY C 127 PHE C 137 -1 O VAL C 131 N PHE C 116 SHEET 3 O 4 TYR C 171 THR C 180 -1 O MET C 173 N LEU C 134 SHEET 4 O 4 VAL C 157 GLU C 161 -1 N SER C 160 O SER C 174 SHEET 1 P 4 SER C 151 GLU C 152 0 SHEET 2 P 4 ASN C 143 ILE C 148 -1 N ILE C 148 O SER C 151 SHEET 3 P 4 SER C 189 THR C 195 -1 O GLU C 193 N LYS C 145 SHEET 4 P 4 ILE C 203 ASN C 208 -1 O LYS C 205 N CYS C 192 SHEET 1 Q 4 LYS D 3 GLU D 6 0 SHEET 2 Q 4 VAL D 18 SER D 25 -1 O SER D 25 N LYS D 3 SHEET 3 Q 4 THR D 77 LEU D 82 -1 O ALA D 78 N CYS D 22 SHEET 4 Q 4 ALA D 67 ASP D 72 -1 N THR D 70 O TYR D 79 SHEET 1 R 6 GLU D 10 VAL D 12 0 SHEET 2 R 6 VAL D 107 VAL D 111 1 O THR D 110 N VAL D 12 SHEET 3 R 6 ALA D 88 ALA D 97 -1 N ALA D 88 O VAL D 109 SHEET 4 R 6 TYR D 32 GLN D 39 -1 N GLN D 39 O VAL D 89 SHEET 5 R 6 GLU D 46 ILE D 51 -1 O GLU D 46 N LYS D 38 SHEET 6 R 6 THR D 57 TYR D 59 -1 O ASN D 58 N VAL D 50 SHEET 1 S 4 GLU D 10 VAL D 12 0 SHEET 2 S 4 VAL D 107 VAL D 111 1 O THR D 110 N VAL D 12 SHEET 3 S 4 ALA D 88 ALA D 97 -1 N ALA D 88 O VAL D 109 SHEET 4 S 4 TYR D 102 TRP D 103 -1 O TYR D 102 N ARG D 94 SHEET 1 T 4 SER D 120 LEU D 124 0 SHEET 2 T 4 VAL D 135 TYR D 144 -1 O LEU D 140 N TYR D 122 SHEET 3 T 4 LEU D 173 VAL D 182 -1 O VAL D 182 N VAL D 135 SHEET 4 T 4 VAL D 162 THR D 164 -1 N HIS D 163 O SER D 179 SHEET 1 U 4 SER D 120 LEU D 124 0 SHEET 2 U 4 VAL D 135 TYR D 144 -1 O LEU D 140 N TYR D 122 SHEET 3 U 4 LEU D 173 VAL D 182 -1 O VAL D 182 N VAL D 135 SHEET 4 U 4 VAL D 168 GLN D 170 -1 N GLN D 170 O LEU D 173 SHEET 1 V 3 THR D 150 TRP D 153 0 SHEET 2 V 3 THR D 193 HIS D 198 -1 O ASN D 195 N THR D 152 SHEET 3 V 3 THR D 203 LYS D 208 -1 O THR D 203 N HIS D 198 SSBOND 1 CYS A 23 CYS A 87 1555 1555 2.27 SSBOND 2 CYS A 132 CYS A 192 1555 1555 2.07 SSBOND 3 CYS B 22 CYS B 92 1555 1555 2.08 SSBOND 4 CYS B 139 CYS B 194 1555 1555 2.08 SSBOND 5 CYS C 23 CYS C 87 1555 1555 2.04 SSBOND 6 CYS C 132 CYS C 192 1555 1555 2.07 SSBOND 7 CYS D 22 CYS D 92 1555 1555 2.22 SSBOND 8 CYS D 139 CYS D 194 1555 1555 2.02 CISPEP 1 TYR A 138 PRO A 139 0 1.96 CISPEP 2 SER B 54 GLY B 55 0 -20.42 CISPEP 3 ALA B 127 ALA B 128 0 10.00 CISPEP 4 ALA B 130 ALA B 131 0 -20.44 CISPEP 5 PHE B 145 PRO B 146 0 -10.63 CISPEP 6 GLU B 147 PRO B 148 0 18.66 CISPEP 7 TRP B 187 PRO B 188 0 23.32 CISPEP 8 TRP I 6 GLY I 7 0 -6.09 CISPEP 9 TYR C 138 PRO C 139 0 5.13 CISPEP 10 ALA D 129 ALA D 130 0 -11.66 CISPEP 11 PHE D 145 PRO D 146 0 -10.12 CISPEP 12 GLU D 147 PRO D 148 0 19.99 CISPEP 13 TRP D 187 PRO D 188 0 25.96 CISPEP 14 TRP J 6 GLY J 7 0 -10.54 SITE 1 AC1 8 TYR A 90 ASN B 58 PRO B 100 THR B 100A SITE 2 AC1 8 TYR B 100B TYR B 100C ALA B 100D HOH I 101 SITE 1 AC2 13 TYR C 48 TRP C 49 TYR C 90 TYR D 32 SITE 2 AC2 13 ASN D 58 GLY D 96 ALA D 97 PRO D 100 SITE 3 AC2 13 THR D 100A TYR D 100B TYR D 100C ALA D 100D SITE 4 AC2 13 ASP D 101 CRYST1 65.415 71.567 207.592 90.00 90.00 90.00 P 21 2 21 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 0.015287 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013973 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004817 0.00000