PDB Short entry for 1Z2M HEADER SIGNALING PROTEIN 08-MAR-05 1Z2M TITLE CRYSTAL STRUCTURE OF ISG15, THE INTERFERON-INDUCED UBIQUITIN CROSS TITLE 2 REACTIVE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERFERON, ALPHA-INDUCIBLE PROTEIN (CLONE IFI-15K); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ISG15; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PED11D KEYWDS ISG15, UBIQUITIN CROSS REACTIVE PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.NARASIMHAN,M.WANG,Z.FU,J.M.KLEIN,A.L.HAAS,J.J.KIM REVDAT 5 20-OCT-21 1Z2M 1 REMARK SEQADV REVDAT 4 24-FEB-09 1Z2M 1 VERSN REVDAT 3 09-AUG-05 1Z2M 3 HETATM REVDAT 2 02-AUG-05 1Z2M 1 JRNL REVDAT 1 24-MAY-05 1Z2M 0 JRNL AUTH J.NARASIMHAN,M.WANG,Z.FU,J.M.KLEIN,A.L.HAAS,J.J.KIM JRNL TITL CRYSTAL STRUCTURE OF THE INTERFERON-INDUCED UBIQUITIN-LIKE JRNL TITL 2 PROTEIN ISG15. JRNL REF J.BIOL.CHEM. V. 280 27356 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15917233 JRNL DOI 10.1074/JBC.M502814200 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 142510.370 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 5624 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 SET) : 0.206 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 603 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 454 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.045 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1173 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.32 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.860 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.480 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.590 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.120 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.310 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 56.95 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1Z2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5624 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.19200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIR REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL BUFFER, PEG4K, MGCL2, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 27.89500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.47000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.86000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.89500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.47000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.86000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.89500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.47000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.86000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.89500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 28.47000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.86000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 ARG A 155 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 ASN A 13 -96.73 -116.59 REMARK 500 SER A 21 -93.85 -125.51 REMARK 500 MET A 23 75.33 63.76 REMARK 500 SER A 62 31.31 -77.79 REMARK 500 SER A 78 138.18 -31.34 REMARK 500 ASP A 79 49.93 -149.68 REMARK 500 LEU A 145 18.89 59.40 REMARK 500 ARG A 153 44.31 -78.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OS4 A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB REMARK 900 UBIQUITIN DBREF 1Z2M A 1 155 UNP P05161 UCRP_HUMAN 0 154 SEQADV 1Z2M SER A 78 UNP P05161 CYS 77 ENGINEERED MUTATION SEQRES 1 A 155 MET GLY TRP ASP LEU THR VAL LYS MET LEU ALA GLY ASN SEQRES 2 A 155 GLU PHE GLN VAL SER LEU SER SER SER MET SER VAL SER SEQRES 3 A 155 GLU LEU LYS ALA GLN ILE THR GLN LYS ILE GLY VAL HIS SEQRES 4 A 155 ALA PHE GLN GLN ARG LEU ALA VAL HIS PRO SER GLY VAL SEQRES 5 A 155 ALA LEU GLN ASP ARG VAL PRO LEU ALA SER GLN GLY LEU SEQRES 6 A 155 GLY PRO GLY SER THR VAL LEU LEU VAL VAL ASP LYS SER SEQRES 7 A 155 ASP GLU PRO LEU SER ILE LEU VAL ARG ASN ASN LYS GLY SEQRES 8 A 155 ARG SER SER THR TYR GLU VAL ARG LEU THR GLN THR VAL SEQRES 9 A 155 ALA HIS LEU LYS GLN GLN VAL SER GLY LEU GLU GLY VAL SEQRES 10 A 155 GLN ASP ASP LEU PHE TRP LEU THR PHE GLU GLY LYS PRO SEQRES 11 A 155 LEU GLU ASP GLN LEU PRO LEU GLY GLU TYR GLY LEU LYS SEQRES 12 A 155 PRO LEU SER THR VAL PHE MET ASN LEU ARG LEU ARG HET OS4 A 400 1 HETNAM OS4 OSMIUM 4+ ION FORMUL 2 OS4 OS 4+ FORMUL 3 HOH *39(H2 O) HELIX 1 1 SER A 24 GLY A 37 1 14 HELIX 2 2 HIS A 39 PHE A 41 5 3 HELIX 3 3 LEU A 60 GLY A 64 5 5 HELIX 4 4 THR A 103 GLY A 116 1 14 HELIX 5 5 GLN A 118 ASP A 120 5 3 HELIX 6 6 PRO A 136 GLY A 141 5 6 SHEET 1 A 4 GLU A 14 SER A 18 0 SHEET 2 A 4 ASP A 4 MET A 9 -1 N VAL A 7 O PHE A 15 SHEET 3 A 4 THR A 70 VAL A 75 1 O VAL A 71 N LYS A 8 SHEET 4 A 4 GLN A 43 HIS A 48 -1 N ALA A 46 O LEU A 72 SHEET 1 B 5 SER A 93 VAL A 98 0 SHEET 2 B 5 LEU A 82 ARG A 87 -1 N LEU A 82 O VAL A 98 SHEET 3 B 5 THR A 147 LEU A 152 1 O VAL A 148 N LEU A 85 SHEET 4 B 5 PHE A 122 PHE A 126 -1 N THR A 125 O PHE A 149 SHEET 5 B 5 LYS A 129 PRO A 130 -1 O LYS A 129 N PHE A 126 CISPEP 1 HIS A 48 PRO A 49 0 0.14 SITE 1 AC1 4 MET A 9 GLY A 12 ASN A 13 HOH A 526 CRYST1 55.790 56.940 103.720 90.00 90.00 90.00 I 2 2 2 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 0.017924 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009641 0.00000