HEADER LIPID BINDING PROTEIN 08-OCT-09 3K63 TITLE X-RAY STRUCTURE OF THE PF04200 DOMAIN FROM Q9PRA0_UREPA PROTEIN OF TITLE 2 UREAPLASMA PARVUM. NESG TARGET UUR17A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL MEMBRANE LIPOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIPOPROTEIN_17 DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UREAPLASMA PARVUM; SOURCE 3 ORGANISM_COMMON: UREAPLASMA UREALYTICUM BIOTYPE 1; SOURCE 4 ORGANISM_TAXID: 134821; SOURCE 5 STRAIN: ATCC 700970 / SEROVAR 3; SOURCE 6 GENE: UU045; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) +MAGIC; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET 21-23C KEYWDS LIPOPROTEIN-17, Q9PRA0, PF04200, DUF1976, UUR17A, NESG., STRUCTURAL KEYWDS 2 GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL KEYWDS 3 GENOMICS CONSORTIUM, LIPOPROTEIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VOROBIEV,H.NEELY,J.SEETHARAMAN,D.LEE,C.CICCOSANTI,L.MAO,R.XIAO, AUTHOR 2 T.B.ACTON,G.T.MONTELIONE,L.TONG,J.F.HUNT,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 2 25-OCT-17 3K63 1 REMARK REVDAT 1 20-OCT-09 3K63 0 JRNL AUTH S.VOROBIEV,H.NEELY,J.SEETHARAMAN,D.LEE,C.CICCOSANTI,L.MAO, JRNL AUTH 2 R.XIAO,T.B.ACTON,G.T.MONTELIONE,L.TONG,J.F.HUNT JRNL TITL X-RAY STRUCTURE OF THE PF04200 DOMAIN FROM Q9PRA0_UREPA JRNL TITL 2 PROTEIN OF UREAPLASMA PARVUM. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 9232 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 426 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.5397 - 3.5958 0.99 2939 133 0.1852 0.1996 REMARK 3 2 3.5958 - 2.8550 1.00 2912 152 0.2322 0.3074 REMARK 3 3 2.8550 - 2.4944 0.99 2955 141 0.2851 0.3652 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.29 REMARK 3 B_SOL : 27.65 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1006 REMARK 3 ANGLE : 1.639 1357 REMARK 3 CHIRALITY : 0.112 143 REMARK 3 PLANARITY : 0.009 178 REMARK 3 DIHEDRAL : 21.267 374 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3K63 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-09 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 : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97908 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9252 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.494 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.8000 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.81200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.650 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX D/E, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 8000, 0.1M KBR, 0.1M HEPES PH REMARK 280 7.5, MICROBATCH UNDER PARAFFIN OIL, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 43.14400 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 21.57200 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 21.57200 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 43.14400 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 300 REMARK: MONOMER ACCORDING TO GEL-FILTRATION 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: PISA 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 HIS A 252 REMARK 465 HIS A 253 REMARK 465 HIS A 254 REMARK 465 HIS A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 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 GLU A 133 134.27 -179.91 REMARK 500 LYS A 136 -5.83 -54.59 REMARK 500 LYS A 145 -6.96 70.91 REMARK 500 ASP A 146 -80.12 -114.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3JVC RELATED DB: PDB REMARK 900 THE SAME PROTEIN CRYSTALLIZED IN DIFFERENT SPACE GROUP W/ BETTER REMARK 900 RESOLUTION REMARK 900 RELATED ID: UUR17A RELATED DB: TARGETDB DBREF 3K63 A 133 249 UNP Q9PRA0 Q9PRA0_UREPA 133 249 SEQADV 3K63 MSE A 132 UNP Q9PRA0 EXPRESSION TAG SEQADV 3K63 LEU A 250 UNP Q9PRA0 EXPRESSION TAG SEQADV 3K63 GLU A 251 UNP Q9PRA0 EXPRESSION TAG SEQADV 3K63 HIS A 252 UNP Q9PRA0 EXPRESSION TAG SEQADV 3K63 HIS A 253 UNP Q9PRA0 EXPRESSION TAG SEQADV 3K63 HIS A 254 UNP Q9PRA0 EXPRESSION TAG SEQADV 3K63 HIS A 255 UNP Q9PRA0 EXPRESSION TAG SEQADV 3K63 HIS A 256 UNP Q9PRA0 EXPRESSION TAG SEQADV 3K63 HIS A 257 UNP Q9PRA0 EXPRESSION TAG SEQRES 1 A 126 MSE GLU ASP PHE LYS LYS ILE VAL ASN ASN ILE ARG LEU SEQRES 2 A 126 LYS ASP THR PHE ASP PHE LYS LEU ALA ALA PHE PRO ASN SEQRES 3 A 126 GLN ASN TYR ASP GLN LEU LEU PRO SER GLN ILE TYR LYS SEQRES 4 A 126 ASN TYR TYR GLN GLY ILE GLU ILE GLN GLN HIS LYS TYR SEQRES 5 A 126 GLN ASN GLU LEU ASP ILE LYS ILE ILE ASN PHE LEU TYR SEQRES 6 A 126 PRO ASP GLY ASP PHE GLY SER ALA ASN LYS ASN GLY THR SEQRES 7 A 126 LEU LYS LEU SER LEU MSE LEU THR ASP LYS LYS ASN ASN SEQRES 8 A 126 GLN VAL TYR TYR LYS LEU LEU GLU VAL SER GLY PHE LYS SEQRES 9 A 126 SER ASN PRO TYR GLY VAL ASP GLU ASN GLY THR ILE PRO SEQRES 10 A 126 GLY LEU GLU HIS HIS HIS HIS HIS HIS MODRES 3K63 MSE A 132 MET SELENOMETHIONINE MODRES 3K63 MSE A 215 MET SELENOMETHIONINE HET MSE A 132 8 HET MSE A 215 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *14(H2 O) HELIX 1 1 ASP A 134 VAL A 139 1 6 HELIX 2 2 ASN A 140 ILE A 142 5 3 HELIX 3 3 ASN A 159 LEU A 163 5 5 HELIX 4 4 LEU A 164 TYR A 172 1 9 HELIX 5 5 ASP A 200 GLY A 208 1 9 SHEET 1 A 2 PHE A 148 LEU A 152 0 SHEET 2 A 2 ILE A 176 GLN A 180 -1 O GLU A 177 N LYS A 151 SHEET 1 B 3 LEU A 187 LEU A 195 0 SHEET 2 B 3 LEU A 210 ASP A 218 -1 O LYS A 211 N LEU A 195 SHEET 3 B 3 VAL A 224 VAL A 231 -1 O TYR A 225 N LEU A 216 LINK C MSE A 132 N GLU A 133 1555 1555 1.32 LINK C LEU A 214 N MSE A 215 1555 1555 1.33 LINK C MSE A 215 N LEU A 216 1555 1555 1.33 CRYST1 60.557 60.557 64.716 90.00 90.00 120.00 P 32 2 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 0.016513 0.009534 0.000000 0.00000 SCALE2 0.000000 0.019068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015452 0.00000 HETATM 1 N MSE A 132 -0.346 -33.968 -27.625 1.00 96.27 N HETATM 2 CA MSE A 132 -1.743 -33.452 -27.702 1.00 94.10 C HETATM 3 C MSE A 132 -1.758 -31.989 -28.103 1.00 90.99 C HETATM 4 O MSE A 132 -2.449 -31.587 -29.040 1.00 90.60 O HETATM 5 CB MSE A 132 -2.441 -33.662 -26.352 1.00 89.86 C HETATM 6 CG MSE A 132 -1.506 -33.615 -25.149 1.00 93.80 C HETATM 7 SE MSE A 132 -2.190 -34.648 -23.646 1.00117.21 SE HETATM 8 CE MSE A 132 -0.663 -34.484 -22.441 1.00 80.38 C