HEADER ANTITUMOR PROTEIN 10-OCT-06 2IOL TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL MA3 DOMAIN OF PDCD4 (MOUSE); FORM TITLE 2 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 4, PDCD4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL MA3 DOMAIN, RESIDUES 323-448; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PDCD4, TIS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST14 KEYWDS ALPHA-HELICAL, ANTITUMOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.WLODAWER,N.A.LARONDE-LEBLANC REVDAT 5 20-NOV-24 2IOL 1 SEQADV LINK REVDAT 4 13-JUL-11 2IOL 1 VERSN REVDAT 3 24-FEB-09 2IOL 1 VERSN REVDAT 2 02-JAN-07 2IOL 1 JRNL REVDAT 1 14-NOV-06 2IOL 0 JRNL AUTH N.LARONDE-LEBLANC,A.N.SANTHANAM,A.R.BAKER,A.WLODAWER, JRNL AUTH 2 N.H.COLBURN JRNL TITL STRUCTURAL BASIS FOR INHIBITION OF TRANSLATION BY THE TUMOR JRNL TITL 2 SUPPRESSOR PDCD4. JRNL REF MOL.CELL.BIOL. V. 27 147 2007 JRNL REFN ISSN 0270-7306 JRNL PMID 17060447 JRNL DOI 10.1128/MCB.00867-06 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 25810 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) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1381 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1818 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2060 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : -0.04000 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): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.115 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2106 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2848 ; 1.482 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 252 ; 5.133 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;37.650 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 400 ;17.353 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;14.802 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 326 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1548 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1032 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1483 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 63 ; 0.177 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 53 ; 0.209 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.238 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1315 ; 0.932 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2072 ; 1.235 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 895 ; 2.354 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 776 ; 3.483 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 322 A 448 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2924 31.5836 29.6461 REMARK 3 T TENSOR REMARK 3 T11: -0.2442 T22: -0.2306 REMARK 3 T33: -0.2867 T12: 0.0076 REMARK 3 T13: 0.0425 T23: -0.0321 REMARK 3 L TENSOR REMARK 3 L11: 9.2594 L22: 4.4078 REMARK 3 L33: 3.8921 L12: -0.1430 REMARK 3 L13: 1.1465 L23: -1.3403 REMARK 3 S TENSOR REMARK 3 S11: -0.0114 S12: -0.1751 S13: -0.0983 REMARK 3 S21: -0.4087 S22: -0.0259 S23: -0.2686 REMARK 3 S31: 0.1158 S32: -0.1354 S33: 0.0373 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 322 B 448 REMARK 3 ORIGIN FOR THE GROUP (A): -2.6192 21.6605 54.3934 REMARK 3 T TENSOR REMARK 3 T11: -0.2066 T22: 0.1290 REMARK 3 T33: -0.1131 T12: -0.0198 REMARK 3 T13: -0.0641 T23: 0.1162 REMARK 3 L TENSOR REMARK 3 L11: 12.1877 L22: 6.0001 REMARK 3 L33: 7.0324 L12: 4.4424 REMARK 3 L13: 2.4187 L23: 1.9754 REMARK 3 S TENSOR REMARK 3 S11: 0.6824 S12: -0.1897 S13: -0.8935 REMARK 3 S21: 0.8927 S22: -0.2228 S23: -0.6667 REMARK 3 S31: 0.7149 S32: 0.0292 S33: -0.4595 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039822. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97174 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26640 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 1000, 0.1 M HEPES, 5% REMARK 280 GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.90000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 109.80000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 109.80000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.90000 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 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 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 GLY A 320 REMARK 465 GLN A 321 REMARK 465 SER A 449 REMARK 465 ARG A 450 REMARK 465 GLY A 451 REMARK 465 ARG A 452 REMARK 465 LYS A 453 REMARK 465 ARG A 454 REMARK 465 PHE A 455 REMARK 465 VAL A 456 REMARK 465 SER A 457 REMARK 465 GLU A 458 REMARK 465 GLY A 459 REMARK 465 ASP A 460 REMARK 465 GLY A 461 REMARK 465 GLY A 462 REMARK 465 ARG A 463 REMARK 465 LEU A 464 REMARK 465 LYS A 465 REMARK 465 PRO A 466 REMARK 465 GLU A 467 REMARK 465 SER A 468 REMARK 465 TYR A 469 REMARK 465 GLY B 320 REMARK 465 GLN B 321 REMARK 465 SER B 449 REMARK 465 ARG B 450 REMARK 465 GLY B 451 REMARK 465 ARG B 452 REMARK 465 LYS B 453 REMARK 465 ARG B 454 REMARK 465 PHE B 455 REMARK 465 VAL B 456 REMARK 465 SER B 457 REMARK 465 GLU B 458 REMARK 465 GLY B 459 REMARK 465 ASP B 460 REMARK 465 GLY B 461 REMARK 465 GLY B 462 REMARK 465 ARG B 463 REMARK 465 LEU B 464 REMARK 465 LYS B 465 REMARK 465 PRO B 466 REMARK 465 GLU B 467 REMARK 465 SER B 468 REMARK 465 TYR B 469 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 322 CG CD OE1 NE2 REMARK 470 GLN B 322 CG CD OE1 NE2 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 18 O HOH A 39 2.07 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 MSE B 333 CG MSE B 333 SE 0.218 REMARK 500 GLY B 342 C GLY B 342 O 0.169 REMARK 500 GLY B 342 C ASP B 343 N 0.159 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 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 444 NE - CZ - NH2 ANGL. DEV. = -3.2 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 HIS B 421 18.10 59.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ION RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C-TERMINAL MA3 DOMAIN OF PDCD4 (MOUSE); REMARK 900 FORM 2 REMARK 900 RELATED ID: 2IOS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C-TERMINAL MA3 DOMAIN OF PDCD4 (MOUSE); REMARK 900 FORM 3 DBREF 2IOL A 320 469 UNP Q61823 PDCD4_MOUSE 320 469 DBREF 2IOL B 320 469 UNP Q61823 PDCD4_MOUSE 320 469 SEQADV 2IOL MSE A 333 UNP Q61823 MET 333 MODIFIED RESIDUE SEQADV 2IOL MSE A 370 UNP Q61823 MET 370 MODIFIED RESIDUE SEQADV 2IOL MSE A 382 UNP Q61823 MET 382 MODIFIED RESIDUE SEQADV 2IOL MSE A 401 UNP Q61823 MET 401 MODIFIED RESIDUE SEQADV 2IOL MSE B 333 UNP Q61823 MET 333 MODIFIED RESIDUE SEQADV 2IOL MSE B 370 UNP Q61823 MET 370 MODIFIED RESIDUE SEQADV 2IOL MSE B 382 UNP Q61823 MET 382 MODIFIED RESIDUE SEQADV 2IOL MSE B 401 UNP Q61823 MET 401 MODIFIED RESIDUE SEQRES 1 A 150 GLY GLN GLN PRO VAL ASN HIS LEU VAL LYS GLU ILE ASP SEQRES 2 A 150 MSE LEU LEU LYS GLU TYR LEU LEU SER GLY ASP ILE SER SEQRES 3 A 150 GLU ALA GLU HIS CYS LEU LYS GLU LEU GLU VAL PRO HIS SEQRES 4 A 150 PHE HIS HIS GLU LEU VAL TYR GLU ALA ILE VAL MSE VAL SEQRES 5 A 150 LEU GLU SER THR GLY GLU SER ALA PHE LYS MSE ILE LEU SEQRES 6 A 150 ASP LEU LEU LYS SER LEU TRP LYS SER SER THR ILE THR SEQRES 7 A 150 ILE ASP GLN MSE LYS ARG GLY TYR GLU ARG ILE TYR ASN SEQRES 8 A 150 GLU ILE PRO ASP ILE ASN LEU ASP VAL PRO HIS SER TYR SEQRES 9 A 150 SER VAL LEU GLU ARG PHE VAL GLU GLU CYS PHE GLN ALA SEQRES 10 A 150 GLY ILE ILE SER LYS GLN LEU ARG ASP LEU CYS PRO SER SEQRES 11 A 150 ARG GLY ARG LYS ARG PHE VAL SER GLU GLY ASP GLY GLY SEQRES 12 A 150 ARG LEU LYS PRO GLU SER TYR SEQRES 1 B 150 GLY GLN GLN PRO VAL ASN HIS LEU VAL LYS GLU ILE ASP SEQRES 2 B 150 MSE LEU LEU LYS GLU TYR LEU LEU SER GLY ASP ILE SER SEQRES 3 B 150 GLU ALA GLU HIS CYS LEU LYS GLU LEU GLU VAL PRO HIS SEQRES 4 B 150 PHE HIS HIS GLU LEU VAL TYR GLU ALA ILE VAL MSE VAL SEQRES 5 B 150 LEU GLU SER THR GLY GLU SER ALA PHE LYS MSE ILE LEU SEQRES 6 B 150 ASP LEU LEU LYS SER LEU TRP LYS SER SER THR ILE THR SEQRES 7 B 150 ILE ASP GLN MSE LYS ARG GLY TYR GLU ARG ILE TYR ASN SEQRES 8 B 150 GLU ILE PRO ASP ILE ASN LEU ASP VAL PRO HIS SER TYR SEQRES 9 B 150 SER VAL LEU GLU ARG PHE VAL GLU GLU CYS PHE GLN ALA SEQRES 10 B 150 GLY ILE ILE SER LYS GLN LEU ARG ASP LEU CYS PRO SER SEQRES 11 B 150 ARG GLY ARG LYS ARG PHE VAL SER GLU GLY ASP GLY GLY SEQRES 12 B 150 ARG LEU LYS PRO GLU SER TYR MODRES 2IOL MSE A 333 MET SELENOMETHIONINE MODRES 2IOL MSE A 370 MET SELENOMETHIONINE MODRES 2IOL MSE A 382 MET SELENOMETHIONINE MODRES 2IOL MSE A 401 MET SELENOMETHIONINE MODRES 2IOL MSE B 333 MET SELENOMETHIONINE MODRES 2IOL MSE B 370 MET SELENOMETHIONINE MODRES 2IOL MSE B 382 MET SELENOMETHIONINE MODRES 2IOL MSE B 401 MET SELENOMETHIONINE HET MSE A 333 8 HET MSE A 370 8 HET MSE A 382 8 HET MSE A 401 8 HET MSE B 333 8 HET MSE B 370 8 HET MSE B 382 8 HET MSE B 401 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 HOH *50(H2 O) HELIX 1 1 ASN A 325 GLY A 342 1 18 HELIX 2 2 ASP A 343 LEU A 354 1 12 HELIX 3 3 GLU A 355 HIS A 358 5 4 HELIX 4 4 PHE A 359 SER A 374 1 16 HELIX 5 5 GLU A 377 SER A 393 1 17 HELIX 6 6 THR A 397 VAL A 419 1 23 HELIX 7 7 HIS A 421 ALA A 436 1 16 HELIX 8 8 SER A 440 CYS A 447 1 8 HELIX 9 9 ASN B 325 GLY B 342 1 18 HELIX 10 10 ASP B 343 GLU B 355 1 13 HELIX 11 11 VAL B 356 HIS B 358 5 3 HELIX 12 12 PHE B 359 SER B 374 1 16 HELIX 13 13 GLU B 377 SER B 393 1 17 HELIX 14 14 THR B 397 VAL B 419 1 23 HELIX 15 15 HIS B 421 ALA B 436 1 16 HELIX 16 16 SER B 440 LEU B 446 1 7 LINK C ASP A 332 N MSE A 333 1555 1555 1.34 LINK C MSE A 333 N LEU A 334 1555 1555 1.32 LINK C VAL A 369 N MSE A 370 1555 1555 1.33 LINK C MSE A 370 N VAL A 371 1555 1555 1.33 LINK C LYS A 381 N MSE A 382 1555 1555 1.32 LINK C MSE A 382 N ILE A 383 1555 1555 1.32 LINK C GLN A 400 N MSE A 401 1555 1555 1.34 LINK C MSE A 401 N LYS A 402 1555 1555 1.32 LINK C ASP B 332 N MSE B 333 1555 1555 1.33 LINK C MSE B 333 N LEU B 334 1555 1555 1.34 LINK C VAL B 369 N MSE B 370 1555 1555 1.33 LINK C MSE B 370 N VAL B 371 1555 1555 1.34 LINK C LYS B 381 N MSE B 382 1555 1555 1.33 LINK C MSE B 382 N ILE B 383 1555 1555 1.33 LINK C GLN B 400 N MSE B 401 1555 1555 1.33 LINK C MSE B 401 N LYS B 402 1555 1555 1.33 CRYST1 64.650 64.650 164.700 90.00 90.00 120.00 P 31 2 1 12 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 0.015468 0.008930 0.000000 0.00000 SCALE2 0.000000 0.017861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006072 0.00000