HEADER UBIQUITIN 22-APR-05 2BPS TITLE UBIQUITIN-LIKE PROTEIN YUKD OF BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: YUKD PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PHIS17 KEYWDS YUKD, UBIQUITIN-LIKE PROTEIN, UBIQUITIN EXPDTA X-RAY DIFFRACTION AUTHOR F.VAN DEN ENT,J.LOWE REVDAT 3 24-JAN-18 2BPS 1 SOURCE JRNL REVDAT 2 24-FEB-09 2BPS 1 VERSN REVDAT 1 04-JUL-05 2BPS 0 JRNL AUTH F.VAN DEN ENT,J.LOWE JRNL TITL CRYSTAL STRUCTURE OF UBIQUITIN-LIKE PROTEIN YUKD FROM JRNL TITL 2 BACILLUS SUBTILIS JRNL REF FEBS LETT. V. 579 3837 2005 JRNL REFN ISSN 0014-5793 JRNL PMID 15978580 JRNL DOI 10.1016/J.FEBSLET.2005.06.002 REMARK 2 REMARK 2 RESOLUTION. 2.70 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 : MAXIMUM LIKELYHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 200.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 6703 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) : 0.241 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 654 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 13 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 451 REMARK 3 BIN R VALUE (WORKING SET) : 0.4030 REMARK 3 BIN FREE R VALUE : 0.4540 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 654 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -15.14900 REMARK 3 B22 (A**2) : -15.14900 REMARK 3 B33 (A**2) : 30.29700 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 29.02 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BPS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290023709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9700 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6767 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 87.55300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.16400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.16400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.77650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.16400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.16400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 131.32950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.16400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.16400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.77650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.16400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.16400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 131.32950 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 87.55300 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: PQS 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: PQS 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 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 9 42.17 -93.27 REMARK 500 TYR A 12 -122.86 -140.82 REMARK 500 MET A 42 -79.02 -117.51 REMARK 500 PRO A 43 -155.38 -90.12 REMARK 500 SER B 1 122.29 -176.08 REMARK 500 LEU B 9 42.82 -92.65 REMARK 500 TYR B 12 -121.41 -140.11 REMARK 500 SER B 41 -86.67 -59.41 REMARK 500 ASN B 54 4.62 -59.37 REMARK 500 CYS B 63 179.20 -49.37 REMARK 500 LEU B 65 -70.94 -29.20 REMARK 500 CYS B 68 3.24 -65.59 REMARK 500 THR B 71 -146.25 -115.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 2BPS A -1 1 PDB 2BPS 2BPS -1 1 DBREF 2BPS A 2 79 UNP P71071 P71071_BACSU 2 79 DBREF 2BPS B -1 1 PDB 2BPS 2BPS -1 1 DBREF 2BPS B 2 79 UNP P71071 P71071_BACSU 2 79 SEQRES 1 A 81 HIS GLY SER TYR ILE ASP ILE THR ILE ASP LEU LYS HIS SEQRES 2 A 81 TYR ASN GLY SER VAL PHE ASP LEU ARG LEU SER ASP TYR SEQRES 3 A 81 HIS PRO VAL LYS LYS VAL ILE ASP ILE ALA TRP GLN ALA SEQRES 4 A 81 GLN SER VAL SER MET PRO PRO ARG GLU GLY HIS TRP ILE SEQRES 5 A 81 ARG VAL VAL ASN LYS ASP LYS VAL PHE SER GLY GLU CYS SEQRES 6 A 81 LYS LEU SER ASP CYS GLY ILE THR ASN GLY ASP ARG LEU SEQRES 7 A 81 GLU ILE LEU SEQRES 1 B 81 HIS GLY SER TYR ILE ASP ILE THR ILE ASP LEU LYS HIS SEQRES 2 B 81 TYR ASN GLY SER VAL PHE ASP LEU ARG LEU SER ASP TYR SEQRES 3 B 81 HIS PRO VAL LYS LYS VAL ILE ASP ILE ALA TRP GLN ALA SEQRES 4 B 81 GLN SER VAL SER MET PRO PRO ARG GLU GLY HIS TRP ILE SEQRES 5 B 81 ARG VAL VAL ASN LYS ASP LYS VAL PHE SER GLY GLU CYS SEQRES 6 B 81 LYS LEU SER ASP CYS GLY ILE THR ASN GLY ASP ARG LEU SEQRES 7 B 81 GLU ILE LEU FORMUL 3 HOH *7(H2 O) HELIX 1 1 LYS A 28 GLN A 38 1 11 HELIX 2 2 ASN A 54 ASP A 56 5 3 HELIX 3 3 LEU A 65 GLY A 69 5 5 HELIX 4 4 LYS B 28 GLN B 38 1 11 HELIX 5 5 LEU B 65 GLY B 69 5 5 SHEET 1 AA10 LYS A 57 SER A 60 0 SHEET 2 AA10 TRP A 49 VAL A 52 -1 O ILE A 50 N PHE A 59 SHEET 3 AA10 ARG A 75 ILE A 78 -1 O GLU A 77 N ARG A 51 SHEET 4 AA10 TYR A 2 ASP A 8 1 O THR A 6 N LEU A 76 SHEET 5 AA10 VAL A 16 SER A 22 -1 O PHE A 17 N ILE A 7 SHEET 6 AA10 LYS B 57 PHE B 59 1 O VAL B 58 N ARG A 20 SHEET 7 AA10 ILE B 50 VAL B 52 -1 O ILE B 50 N PHE B 59 SHEET 8 AA10 ARG B 75 ILE B 78 -1 O GLU B 77 N ARG B 51 SHEET 9 AA10 TYR B 2 ASP B 8 1 O THR B 6 N LEU B 76 SHEET 10 AA10 VAL B 16 SER B 22 -1 O PHE B 17 N ILE B 7 CISPEP 1 MET A 42 PRO A 43 0 0.24 CRYST1 50.328 50.328 175.106 90.00 90.00 90.00 P 41 21 2 16 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 0.019870 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005711 0.00000