HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 01-SEP-10 3OPN TITLE THE CRYSTAL STRUCTURE OF A PUTATIVE HEMOLYSIN FROM LACTOCOCCUS LACTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE HEMOLYSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. LACTIS; SOURCE 3 ORGANISM_COMMON: STREPTOCOCCUS LACTIS; SOURCE 4 ORGANISM_TAXID: 1360; SOURCE 5 STRAIN: LACTIS (LL); SOURCE 6 GENE: L814, L81441, LL0858, YIIB; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) - CODON+RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: BC - PSGX3 (BC) KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NEW YORK KEYWDS 2 SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGXRC, SGX, PSI, KEYWDS 3 UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHANG,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 2 10-FEB-21 3OPN 1 AUTHOR JRNL REMARK LINK REVDAT 1 13-OCT-10 3OPN 0 JRNL AUTH Z.ZHANG,S.K.BURLEY,S.SWAMINATHAN JRNL TITL THE CRYSTAL STRUCTURE OF A PUTATIVE HEMOLYSIN FROM JRNL TITL 2 LACTOCOCCUS LACTIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 625 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 43.1719 - 3.2539 1.00 3039 162 0.1757 0.2308 REMARK 3 2 3.2539 - 2.5828 1.00 2929 143 0.1931 0.2242 REMARK 3 3 2.5828 - 2.2563 1.00 2873 152 0.1795 0.2439 REMARK 3 4 2.2563 - 2.0500 1.00 2851 168 0.1654 0.2445 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 : 0.37 REMARK 3 B_SOL : 35.68 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.22830 REMARK 3 B22 (A**2) : -0.54360 REMARK 3 B33 (A**2) : -3.08830 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 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 : 0.007 1641 REMARK 3 ANGLE : 1.030 2209 REMARK 3 CHIRALITY : 0.065 255 REMARK 3 PLANARITY : 0.005 283 REMARK 3 DIHEDRAL : 17.494 610 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 3OPN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS 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 : 12358 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 70.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 0.11700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.50 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 (%): 31.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M REMARK 280 CACODYLATE TRIHYDRATE PH 6.5, 30% W/V PEG 400, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 24.35800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.32150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.26150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.32150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.35800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.26150 REMARK 290 SMTRY3 4 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: 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 MSE A 20 REMARK 465 SER A 21 REMARK 465 LEU A 22 REMARK 465 ASP A 23 REMARK 465 GLY A 24 REMARK 465 THR A 25 REMARK 465 GLU A 26 REMARK 465 LEU A 27 REMARK 465 ARG A 28 REMARK 465 LEU A 29 REMARK 465 LYS A 30 REMARK 465 GLY A 31 REMARK 465 GLU A 32 REMARK 465 LYS A 169 REMARK 465 GLU A 242 REMARK 465 LEU A 243 REMARK 465 GLU A 244 REMARK 465 GLY A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 241 CG CD OE1 OE2 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 SER A 66 -128.97 51.29 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 GOL A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-11117L RELATED DB: TARGETDB DBREF 3OPN A 23 243 UNP Q9CH80 Q9CH80_LACLA 23 243 SEQADV 3OPN MSE A 20 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN SER A 21 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN LEU A 22 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN GLU A 244 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN GLY A 245 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN HIS A 246 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN HIS A 247 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN HIS A 248 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN HIS A 249 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN HIS A 250 UNP Q9CH80 EXPRESSION TAG SEQADV 3OPN HIS A 251 UNP Q9CH80 EXPRESSION TAG SEQRES 1 A 232 MSE SER LEU ASP GLY THR GLU LEU ARG LEU LYS GLY GLU SEQRES 2 A 232 LYS LEU ARG TYR VAL SER ARG GLY GLY LEU LYS LEU GLU SEQRES 3 A 232 LYS ALA LEU LYS GLU PHE HIS LEU GLU ILE ASN GLY LYS SEQRES 4 A 232 THR CYS LEU ASP ILE GLY SER SER THR GLY GLY PHE THR SEQRES 5 A 232 ASP VAL MSE LEU GLN ASN GLY ALA LYS LEU VAL TYR ALA SEQRES 6 A 232 LEU ASP VAL GLY THR ASN GLN LEU ALA TRP LYS ILE ARG SEQRES 7 A 232 SER ASP GLU ARG VAL VAL VAL MSE GLU GLN PHE ASN PHE SEQRES 8 A 232 ARG ASN ALA VAL LEU ALA ASP PHE GLU GLN GLY ARG PRO SEQRES 9 A 232 SER PHE THR SER ILE ASP VAL SER PHE ILE SER LEU ASP SEQRES 10 A 232 LEU ILE LEU PRO PRO LEU TYR GLU ILE LEU GLU LYS ASN SEQRES 11 A 232 GLY GLU VAL ALA ALA LEU ILE LYS PRO GLN PHE GLU ALA SEQRES 12 A 232 GLY ARG GLU GLN VAL GLY LYS ASN GLY ILE ILE ARG ASP SEQRES 13 A 232 PRO LYS VAL HIS GLN MSE THR ILE GLU LYS VAL LEU LYS SEQRES 14 A 232 THR ALA THR GLN LEU GLY PHE SER VAL LYS GLY LEU THR SEQRES 15 A 232 PHE SER PRO ILE LYS GLY GLY ALA GLY ASN VAL GLU PHE SEQRES 16 A 232 LEU VAL HIS LEU LEU LYS ASP GLY LYS ALA GLU ILE ALA SEQRES 17 A 232 GLN GLN VAL ASN ILE GLU SER VAL LEU GLN LYS GLU SER SEQRES 18 A 232 GLU GLU LEU GLU GLY HIS HIS HIS HIS HIS HIS MODRES 3OPN MSE A 74 MET SELENOMETHIONINE MODRES 3OPN MSE A 105 MET SELENOMETHIONINE MODRES 3OPN MSE A 181 MET SELENOMETHIONINE HET MSE A 74 8 HET MSE A 105 8 HET MSE A 181 8 HET GOL A 2 6 HET SO4 A 1 5 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 GOL C3 H8 O3 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *153(H2 O) HELIX 1 1 GLY A 40 PHE A 51 1 12 HELIX 2 2 GLY A 68 ASN A 77 1 10 HELIX 3 3 ALA A 93 SER A 98 1 6 HELIX 4 4 ASN A 109 ALA A 113 5 5 HELIX 5 5 VAL A 114 PHE A 118 5 5 HELIX 6 6 SER A 134 LEU A 137 5 4 HELIX 7 7 ILE A 138 LEU A 146 1 9 HELIX 8 8 LYS A 157 ALA A 162 1 6 HELIX 9 9 GLY A 163 GLY A 168 1 6 HELIX 10 10 ASP A 175 GLY A 194 1 20 HELIX 11 11 ASN A 231 GLU A 241 1 11 SHEET 1 A 7 VAL A 102 MSE A 105 0 SHEET 2 A 7 LEU A 81 LEU A 85 1 N ALA A 84 O VAL A 103 SHEET 3 A 7 THR A 59 ILE A 63 1 N CYS A 60 O LEU A 81 SHEET 4 A 7 PHE A 125 ILE A 128 1 O SER A 127 N ILE A 63 SHEET 5 A 7 GLU A 151 ILE A 156 1 O ALA A 153 N THR A 126 SHEET 6 A 7 PHE A 214 LEU A 219 -1 O PHE A 214 N ILE A 156 SHEET 7 A 7 SER A 196 PHE A 202 -1 N SER A 196 O LEU A 219 LINK C VAL A 73 N MSE A 74 1555 1555 1.33 LINK C MSE A 74 N LEU A 75 1555 1555 1.33 LINK C VAL A 104 N MSE A 105 1555 1555 1.33 LINK C MSE A 105 N GLU A 106 1555 1555 1.33 LINK C GLN A 180 N MSE A 181 1555 1555 1.33 LINK C MSE A 181 N THR A 182 1555 1555 1.34 SITE 1 AC1 9 LYS A 33 LEU A 34 ARG A 35 TYR A 36 SITE 2 AC1 9 SER A 38 ARG A 39 GLN A 237 HOH A 278 SITE 3 AC1 9 HOH A 372 SITE 1 AC2 9 SER A 38 GLY A 40 SER A 65 SER A 66 SITE 2 AC2 9 THR A 67 GLY A 68 GLY A 69 HOH A 265 SITE 3 AC2 9 HOH A 336 CRYST1 48.716 54.523 70.643 90.00 90.00 90.00 P 21 21 21 4 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 0.020527 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018341 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014156 0.00000