HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 13-OCT-05 2BA2 TITLE CRYSTAL STRUCTURE OF THE DUF16 DOMAIN OF MPN010 FROM TITLE 2 MYCOPLASMA PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL UPF0134 PROTEIN MPN010; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: DUF16 DOMAIN, RESIDUES 46-130; COMPND 5 SYNONYM: D12_ORF131; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 2104; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834(DE3), PSJS1244; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PB3, PET21A DERIVED KEYWDS DUF16, MPN010, HYPOTHETICAL PROTEIN, COILED-COIL, STUTTER, KEYWDS 2 STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 BERKELEY STRUCTURAL GENOMICS CENTER, BSGC, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR D.H.SHIN,J.-S.KIM,H.YOKOTA,R.KIM,S.-H.KIM,BERKELEY AUTHOR 2 STRUCTURAL GENOMICS CENTER (BSGC) REVDAT 4 24-FEB-09 2BA2 1 VERSN REVDAT 3 18-APR-06 2BA2 1 JRNL REVDAT 2 28-MAR-06 2BA2 1 JRNL REVDAT 1 07-MAR-06 2BA2 0 JRNL AUTH D.H.SHIN,J.-S.KIM,H.YOKOTA,R.KIM,S.-H.KIM JRNL TITL CRYSTAL STRUCTURE OF THE DUF16 DOMAIN OF MPN010 JRNL TITL 2 FROM MYCOPLASMA PNEUMONIAE. JRNL REF PROTEIN SCI. V. 15 921 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16522803 JRNL DOI 10.1110/PS.051993506 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 215255.050 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 79.5 REMARK 3 NUMBER OF REFLECTIONS : 16591 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) : 0.229 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1651 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 21.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 671 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 58 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.042 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1970 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.82000 REMARK 3 B22 (A**2) : 5.82000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.09 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.80 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 15.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.62 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 67.63 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_REP.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 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BA2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-05. REMARK 100 THE RCSB ID CODE IS RCSB034863. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97938 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 13.0 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: 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 (%): 33.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 25% PEG3350, REMARK 280 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 19.43700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 VAL A 1 REMARK 465 LYS A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 VAL B 101 REMARK 465 LYS B 102 REMARK 465 THR B 103 REMARK 465 PRO B 104 REMARK 465 GLY B 105 REMARK 465 VAL C 201 REMARK 465 LYS C 202 REMARK 465 THR C 203 REMARK 465 PRO C 204 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 539 DISTANCE = 6.30 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BSGCAIR30905 RELATED DB: TARGETDB DBREF 2BA2 A 1 85 UNP P75103 Y010_MYCPN 46 130 DBREF 2BA2 B 101 185 UNP P75103 Y010_MYCPN 46 130 DBREF 2BA2 C 201 285 UNP P75103 Y010_MYCPN 46 130 SEQRES 1 A 85 VAL LYS THR PRO GLY THR ARG TYR VAL THR HIS LYS GLN SEQRES 2 A 85 LEU ASP GLU LYS LEU LYS ASN PHE VAL THR LYS THR GLU SEQRES 3 A 85 PHE LYS GLU PHE GLN THR VAL VAL MET GLU SER PHE ALA SEQRES 4 A 85 VAL GLN ASN GLN ASN ILE ASP ALA GLN GLY GLU GLN ILE SEQRES 5 A 85 LYS GLU LEU GLN VAL GLU GLN LYS ALA GLN GLY LYS THR SEQRES 6 A 85 LEU GLN LEU ILE LEU GLU ALA LEU GLN GLY ILE ASN LYS SEQRES 7 A 85 ARG LEU ASP ASN LEU GLU SER SEQRES 1 B 85 VAL LYS THR PRO GLY THR ARG TYR VAL THR HIS LYS GLN SEQRES 2 B 85 LEU ASP GLU LYS LEU LYS ASN PHE VAL THR LYS THR GLU SEQRES 3 B 85 PHE LYS GLU PHE GLN THR VAL VAL MET GLU SER PHE ALA SEQRES 4 B 85 VAL GLN ASN GLN ASN ILE ASP ALA GLN GLY GLU GLN ILE SEQRES 5 B 85 LYS GLU LEU GLN VAL GLU GLN LYS ALA GLN GLY LYS THR SEQRES 6 B 85 LEU GLN LEU ILE LEU GLU ALA LEU GLN GLY ILE ASN LYS SEQRES 7 B 85 ARG LEU ASP ASN LEU GLU SER SEQRES 1 C 85 VAL LYS THR PRO GLY THR ARG TYR VAL THR HIS LYS GLN SEQRES 2 C 85 LEU ASP GLU LYS LEU LYS ASN PHE VAL THR LYS THR GLU SEQRES 3 C 85 PHE LYS GLU PHE GLN THR VAL VAL MET GLU SER PHE ALA SEQRES 4 C 85 VAL GLN ASN GLN ASN ILE ASP ALA GLN GLY GLU GLN ILE SEQRES 5 C 85 LYS GLU LEU GLN VAL GLU GLN LYS ALA GLN GLY LYS THR SEQRES 6 C 85 LEU GLN LEU ILE LEU GLU ALA LEU GLN GLY ILE ASN LYS SEQRES 7 C 85 ARG LEU ASP ASN LEU GLU SER FORMUL 4 HOH *190(H2 O) HELIX 1 1 THR A 10 LYS A 19 1 10 HELIX 2 2 THR A 23 GLU A 84 1 62 HELIX 3 3 THR B 110 LYS B 119 1 10 HELIX 4 4 THR B 123 SER B 185 1 63 HELIX 5 5 THR C 210 LYS C 219 1 10 HELIX 6 6 THR C 223 GLU C 284 1 62 CRYST1 42.559 38.874 68.734 90.00 99.21 90.00 P 1 21 1 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 0.023497 0.000000 0.003808 0.00000 SCALE2 0.000000 0.025724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014739 0.00000