PDB Short entry for 2Y4U HEADER CHAPERONE 10-JAN-11 2Y4U TITLE CRYSTAL STRUCTURE OF HUMAN P58(IPK) IN SPACE GROUP P312 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNAJ HOMOLOG SUBFAMILY C MEMBER 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 35-461; COMPND 5 SYNONYM: INTERFERON-INDUCED\,DOUBLE-STRANDED RNA-ACTIVATED PROTEIN COMPND 6 KINASE INHIBITOR, PROTEIN KINASE INHIBITOR OF 58 KDA, PROTEIN KINASE COMPND 7 INHIBITOR P58IPK; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PNIC28-BSA4; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: P58IPK_6 KEYWDS CHAPERONE, ENDOPLASMIC RETICULUM, PROTEIN FOLDING, KEYWDS 2 TETRATRICOPEPTIDEREPEAT, J DOMAIN, UNFOLDED PROTEIN RESPONSE EXPDTA X-RAY DIFFRACTION AUTHOR M.SVARD,E.I.BITEROVA,J.-M.BOURHIS,J.E.GUY REVDAT 2 20-DEC-23 2Y4U 1 LINK REVDAT 1 10-AUG-11 2Y4U 0 JRNL AUTH M.SVARD,E.I.BITEROVA,J.BOURHIS,J.E.GUY JRNL TITL THE CRYSTAL STRUCTURE OF THE HUMAN CO-CHAPERONE P58IPK JRNL REF PLOS ONE V. 6 22337 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 21799829 JRNL DOI 10.1371/JOURNAL.PONE.0022337 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12967 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) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 677 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 938 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3429 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 118.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.56000 REMARK 3 B22 (A**2) : 1.56000 REMARK 3 B33 (A**2) : -2.35000 REMARK 3 B12 (A**2) : 0.78000 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): 0.899 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.479 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.435 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 56.174 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3481 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4668 ; 1.259 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 423 ; 4.986 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;36.549 ;25.169 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 698 ;18.785 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;15.157 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 504 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2597 ; 0.006 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 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 32 A 455 REMARK 3 ORIGIN FOR THE GROUP (A): -34.6234 -32.9860 -22.5066 REMARK 3 T TENSOR REMARK 3 T11: 0.3079 T22: 0.3633 REMARK 3 T33: 0.3016 T12: -0.0805 REMARK 3 T13: 0.1064 T23: 0.1218 REMARK 3 L TENSOR REMARK 3 L11: 0.2456 L22: 0.7900 REMARK 3 L33: 0.0340 L12: 0.0587 REMARK 3 L13: -0.0135 L23: 0.0719 REMARK 3 S TENSOR REMARK 3 S11: -0.0013 S12: 0.2734 S13: 0.0402 REMARK 3 S21: 0.0171 S22: -0.0606 S23: -0.2108 REMARK 3 S31: 0.0336 S32: -0.0127 S33: 0.0619 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. U VALUES WITH TLS ADDED. REMARK 4 REMARK 4 2Y4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290046956. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12967 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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 3IEG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.5, 1.3 M SUCCINIC REMARK 280 ACID, 1% (W/V) PEG MME 2000. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -Y,-X,-Z REMARK 290 5555 -X+Y,Y,-Z REMARK 290 6555 X,X-Y,-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 -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 0.00000 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 0.00000 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 0.00000 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 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 67440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.8 KCAL/MOL 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 BIOMT1 2 -0.500000 -0.866025 0.000000 -124.62000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -62.31000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -107.92409 REMARK 350 BIOMT3 3 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 MSE A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 SER A 19 REMARK 465 SER A 20 REMARK 465 GLY A 21 REMARK 465 VAL A 22 REMARK 465 ASP A 23 REMARK 465 LEU A 24 REMARK 465 GLY A 25 REMARK 465 THR A 26 REMARK 465 GLU A 27 REMARK 465 ASN A 28 REMARK 465 LEU A 29 REMARK 465 TYR A 30 REMARK 465 PHE A 31 REMARK 465 LYS A 456 REMARK 465 LYS A 457 REMARK 465 PHE A 458 REMARK 465 ASP A 459 REMARK 465 ASP A 460 REMARK 465 GLY A 461 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 PHE A 81 O MSE A 84 2.15 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 A 421 CE2 TRP A 421 CD2 -0.092 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 A 455 NE - CZ - NH2 ANGL. DEV. = -3.4 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 MSE A 34 32.70 -91.39 REMARK 500 LEU A 53 -73.99 60.76 REMARK 500 LYS A 101 71.54 -113.34 REMARK 500 PHE A 104 101.26 -58.93 REMARK 500 GLU A 138 -145.05 39.72 REMARK 500 CYS A 184 78.92 -102.99 REMARK 500 GLU A 203 67.29 -118.66 REMARK 500 ASN A 219 -44.41 68.19 REMARK 500 ASP A 237 65.57 -68.31 REMARK 500 MSE A 355 75.44 -110.13 REMARK 500 LEU A 399 -74.14 -148.72 REMARK 500 PRO A 423 -18.81 -41.18 REMARK 500 ASP A 451 -149.71 63.35 REMARK 500 MSE A 454 -34.76 99.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y4T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FULL-LENGTH HUMAN P58(IPK) DBREF 2Y4U A 35 461 UNP Q13217 DNJC3_HUMAN 35 461 SEQADV 2Y4U MSE A 12 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U HIS A 13 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U HIS A 14 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U HIS A 15 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U HIS A 16 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U HIS A 17 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U HIS A 18 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U SER A 19 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U SER A 20 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U GLY A 21 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U VAL A 22 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U ASP A 23 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U LEU A 24 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U GLY A 25 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U THR A 26 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U GLU A 27 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U ASN A 28 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U LEU A 29 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U TYR A 30 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U PHE A 31 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U GLN A 32 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U SER A 33 UNP Q13217 EXPRESSION TAG SEQADV 2Y4U MSE A 34 UNP Q13217 EXPRESSION TAG SEQRES 1 A 450 MSE HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 450 GLY THR GLU ASN LEU TYR PHE GLN SER MSE ALA ASP VAL SEQRES 3 A 450 GLU LYS HIS LEU GLU LEU GLY LYS LYS LEU LEU ALA ALA SEQRES 4 A 450 GLY GLN LEU ALA ASP ALA LEU SER GLN PHE HIS ALA ALA SEQRES 5 A 450 VAL ASP GLY ASP PRO ASP ASN TYR ILE ALA TYR TYR ARG SEQRES 6 A 450 ARG ALA THR VAL PHE LEU ALA MSE GLY LYS SER LYS ALA SEQRES 7 A 450 ALA LEU PRO ASP LEU THR LYS VAL ILE GLN LEU LYS MSE SEQRES 8 A 450 ASP PHE THR ALA ALA ARG LEU GLN ARG GLY HIS LEU LEU SEQRES 9 A 450 LEU LYS GLN GLY LYS LEU ASP GLU ALA GLU ASP ASP PHE SEQRES 10 A 450 LYS LYS VAL LEU LYS SER ASN PRO SER GLU ASN GLU GLU SEQRES 11 A 450 LYS GLU ALA GLN SER GLN LEU ILE LYS SER ASP GLU MSE SEQRES 12 A 450 GLN ARG LEU ARG SER GLN ALA LEU ASN ALA PHE GLY SER SEQRES 13 A 450 GLY ASP TYR THR ALA ALA ILE ALA PHE LEU ASP LYS ILE SEQRES 14 A 450 LEU GLU VAL CYS VAL TRP ASP ALA GLU LEU ARG GLU LEU SEQRES 15 A 450 ARG ALA GLU CYS PHE ILE LYS GLU GLY GLU PRO ARG LYS SEQRES 16 A 450 ALA ILE SER ASP LEU LYS ALA ALA SER LYS LEU LYS ASN SEQRES 17 A 450 ASP ASN THR GLU ALA PHE TYR LYS ILE SER THR LEU TYR SEQRES 18 A 450 TYR GLN LEU GLY ASP HIS GLU LEU SER LEU SER GLU VAL SEQRES 19 A 450 ARG GLU CYS LEU LYS LEU ASP GLN ASP HIS LYS ARG CYS SEQRES 20 A 450 PHE ALA HIS TYR LYS GLN VAL LYS LYS LEU ASN LYS LEU SEQRES 21 A 450 ILE GLU SER ALA GLU GLU LEU ILE ARG ASP GLY ARG TYR SEQRES 22 A 450 THR ASP ALA THR SER LYS TYR GLU SER VAL MSE LYS THR SEQRES 23 A 450 GLU PRO SER ILE ALA GLU TYR THR VAL ARG SER LYS GLU SEQRES 24 A 450 ARG ILE CYS HIS CYS PHE SER LYS ASP GLU LYS PRO VAL SEQRES 25 A 450 GLU ALA ILE ARG VAL CYS SER GLU VAL LEU GLN MSE GLU SEQRES 26 A 450 PRO ASP ASN VAL ASN ALA LEU LYS ASP ARG ALA GLU ALA SEQRES 27 A 450 TYR LEU ILE GLU GLU MSE TYR ASP GLU ALA ILE GLN ASP SEQRES 28 A 450 TYR GLU THR ALA GLN GLU HIS ASN GLU ASN ASP GLN GLN SEQRES 29 A 450 ILE ARG GLU GLY LEU GLU LYS ALA GLN ARG LEU LEU LYS SEQRES 30 A 450 GLN SER GLN LYS ARG ASP TYR TYR LYS ILE LEU GLY VAL SEQRES 31 A 450 LYS ARG ASN ALA LYS LYS GLN GLU ILE ILE LYS ALA TYR SEQRES 32 A 450 ARG LYS LEU ALA LEU GLN TRP HIS PRO ASP ASN PHE GLN SEQRES 33 A 450 ASN GLU GLU GLU LYS LYS LYS ALA GLU LYS LYS PHE ILE SEQRES 34 A 450 ASP ILE ALA ALA ALA LYS GLU VAL LEU SER ASP PRO GLU SEQRES 35 A 450 MSE ARG LYS LYS PHE ASP ASP GLY MODRES 2Y4U MSE A 34 MET SELENOMETHIONINE MODRES 2Y4U MSE A 84 MET SELENOMETHIONINE MODRES 2Y4U MSE A 102 MET SELENOMETHIONINE MODRES 2Y4U MSE A 154 MET SELENOMETHIONINE MODRES 2Y4U MSE A 295 MET SELENOMETHIONINE MODRES 2Y4U MSE A 335 MET SELENOMETHIONINE MODRES 2Y4U MSE A 355 MET SELENOMETHIONINE MODRES 2Y4U MSE A 454 MET SELENOMETHIONINE HET MSE A 34 8 HET MSE A 84 8 HET MSE A 102 8 HET MSE A 154 8 HET MSE A 295 8 HET MSE A 335 8 HET MSE A 355 8 HET MSE A 454 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 8(C5 H11 N O2 SE) HELIX 1 1 MSE A 34 GLY A 51 1 18 HELIX 2 2 LEU A 53 ASP A 67 1 15 HELIX 3 3 ASN A 70 MSE A 84 1 15 HELIX 4 4 LYS A 86 LYS A 101 1 16 HELIX 5 5 PHE A 104 GLN A 118 1 15 HELIX 6 6 LYS A 120 SER A 134 1 15 HELIX 7 7 SER A 137 GLY A 168 1 32 HELIX 8 8 ASP A 169 CYS A 184 1 16 HELIX 9 9 ASP A 187 GLU A 201 1 15 HELIX 10 10 GLU A 203 ASN A 219 1 17 HELIX 11 11 ASN A 221 LEU A 235 1 15 HELIX 12 12 ASP A 237 ASP A 252 1 16 HELIX 13 13 HIS A 255 ASP A 281 1 27 HELIX 14 14 ARG A 283 GLU A 298 1 16 HELIX 15 15 ILE A 301 ASP A 319 1 19 HELIX 16 16 LYS A 321 GLU A 336 1 16 HELIX 17 17 ASN A 339 GLU A 354 1 16 HELIX 18 18 MSE A 355 GLU A 368 1 14 HELIX 19 19 ASP A 373 LYS A 392 1 20 HELIX 20 20 LYS A 406 TRP A 421 1 16 HELIX 21 21 HIS A 422 PHE A 426 5 5 HELIX 22 22 ASN A 428 SER A 450 1 23 SSBOND 1 CYS A 248 CYS A 258 1555 1555 2.08 SSBOND 2 CYS A 313 CYS A 329 1555 1555 2.06 LINK C SER A 33 N MSE A 34 1555 1555 1.34 LINK C MSE A 34 N ALA A 35 1555 1555 1.34 LINK C ALA A 83 N MSE A 84 1555 1555 1.33 LINK C MSE A 84 N GLY A 85 1555 1555 1.32 LINK C LYS A 101 N MSE A 102 1555 1555 1.36 LINK C MSE A 102 N ASP A 103 1555 1555 1.33 LINK C GLU A 153 N MSE A 154 1555 1555 1.33 LINK C MSE A 154 N GLN A 155 1555 1555 1.33 LINK C VAL A 294 N MSE A 295 1555 1555 1.33 LINK C MSE A 295 N LYS A 296 1555 1555 1.32 LINK C GLN A 334 N MSE A 335 1555 1555 1.33 LINK C MSE A 335 N GLU A 336 1555 1555 1.33 LINK C GLU A 354 N MSE A 355 1555 1555 1.33 LINK C MSE A 355 N TYR A 356 1555 1555 1.32 LINK C GLU A 453 N MSE A 454 1555 1555 1.34 LINK C MSE A 454 N ARG A 455 1555 1555 1.36 CRYST1 124.620 124.620 92.220 90.00 90.00 120.00 P 3 1 2 6 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 0.008024 0.004633 0.000000 0.00000 SCALE2 0.000000 0.009266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010844 0.00000