HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 09-JUN-10 3NEU TITLE THE CRYSTAL STRUCTURE OF A FUNCTIONALLY-UNKNOWN PROTEIN LIN1836 FROM TITLE 2 LISTERIA INNOCUA CLIP11262 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIN1836 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA INNOCUA; SOURCE 3 ORGANISM_TAXID: 1642; SOURCE 4 STRAIN: CLIP11262; SOURCE 5 GENE: LIN1836; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, MIDWEST KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, MCSG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,H.LI,M.GU,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 2 (MCSG) REVDAT 1 04-AUG-10 3NEU 0 JRNL AUTH K.TAN,H.LI,M.GU,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF A FUNCTIONALLY-UNKNOWN PROTEIN JRNL TITL 2 LIN1836 FROM LISTERIA INNOCUA CLIP11262 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 19100 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 973 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 28.2682 - 3.0206 0.94 2704 143 0.1942 0.2168 REMARK 3 2 3.0206 - 2.3979 1.00 2730 156 0.1881 0.2151 REMARK 3 3 2.3979 - 2.0949 0.99 2699 140 0.1782 0.2050 REMARK 3 4 2.0949 - 1.9034 0.99 2653 145 0.1866 0.2273 REMARK 3 5 1.9034 - 1.7670 0.96 2577 143 0.1854 0.2237 REMARK 3 6 1.7670 - 1.6629 0.92 2435 145 0.2127 0.2714 REMARK 3 7 1.6629 - 1.5796 0.86 2329 101 0.2629 0.3052 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 : 0.44 REMARK 3 B_SOL : 66.43 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.330 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) : -4.51200 REMARK 3 B22 (A**2) : 4.81110 REMARK 3 B33 (A**2) : -0.29900 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 : 0.006 1043 REMARK 3 ANGLE : 0.966 1415 REMARK 3 CHIRALITY : 0.066 154 REMARK 3 PLANARITY : 0.004 183 REMARK 3 DIHEDRAL : 17.082 423 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A RESID 2:76 REMARK 3 ORIGIN FOR THE GROUP (A): 7.1729 19.3027 -0.9768 REMARK 3 T TENSOR REMARK 3 T11: 0.2012 T22: 0.2028 REMARK 3 T33: 0.2188 T12: -0.0180 REMARK 3 T13: -0.0060 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 1.9194 L22: 0.5986 REMARK 3 L33: 1.7771 L12: 0.0862 REMARK 3 L13: -0.9840 L23: -0.2383 REMARK 3 S TENSOR REMARK 3 S11: -0.0175 S12: 0.1470 S13: 0.0651 REMARK 3 S21: -0.0350 S22: 0.0562 S23: -0.0107 REMARK 3 S31: 0.0151 S32: -0.0758 S33: -0.0643 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A RESID 77:102 REMARK 3 ORIGIN FOR THE GROUP (A): -3.0236 9.1819 14.1217 REMARK 3 T TENSOR REMARK 3 T11: 0.2580 T22: 0.2743 REMARK 3 T33: 0.2318 T12: -0.0269 REMARK 3 T13: -0.0011 T23: -0.0310 REMARK 3 L TENSOR REMARK 3 L11: 0.5797 L22: 0.2638 REMARK 3 L33: 1.0703 L12: -0.0776 REMARK 3 L13: -0.4573 L23: -0.3649 REMARK 3 S TENSOR REMARK 3 S11: 0.1378 S12: 0.0929 S13: 0.1388 REMARK 3 S21: 0.4110 S22: -0.0451 S23: 0.2541 REMARK 3 S31: 0.0312 S32: -0.0733 S33: -0.0253 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A RESID 103:120 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1328 -6.0168 23.1376 REMARK 3 T TENSOR REMARK 3 T11: 0.3695 T22: 0.2944 REMARK 3 T33: 0.2427 T12: 0.0068 REMARK 3 T13: -0.0145 T23: 0.0261 REMARK 3 L TENSOR REMARK 3 L11: 1.1504 L22: 0.4184 REMARK 3 L33: 1.0908 L12: 0.3586 REMARK 3 L13: -0.4636 L23: -0.3147 REMARK 3 S TENSOR REMARK 3 S11: 0.3214 S12: -0.0975 S13: 0.1114 REMARK 3 S21: 0.2753 S22: -0.3382 S23: -0.0312 REMARK 3 S31: 0.8258 S32: 0.1309 S33: 0.0883 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 3NEU COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-10. REMARK 100 THE RCSB ID CODE IS RCSB059740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19919 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 28.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.74700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD/MLPHARE/DM/ARP/WARP/HKL3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10%(W/V)PEG1000, 10%(W/V)PEG8000, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 20.91400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.02550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.91400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.02550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MSE A 1 REMARK 465 HIS A 121 REMARK 465 GLU A 122 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 31 -4.50 76.18 REMARK 500 MSE A 70 -1.35 -141.12 REMARK 500 ASP A 77 92.71 -163.51 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 123 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC88792 RELATED DB: TARGETDB DBREF 3NEU A 1 122 UNP Q92AT3 Q92AT3_LISIN 1 122 SEQADV 3NEU SER A -2 UNP Q92AT3 EXPRESSION TAG SEQADV 3NEU ASN A -1 UNP Q92AT3 EXPRESSION TAG SEQADV 3NEU ALA A 0 UNP Q92AT3 EXPRESSION TAG SEQRES 1 A 125 SER ASN ALA MSE ASN PRO THR PHE HIS ALA ASP LYS PRO SEQRES 2 A 125 ILE TYR SER GLN ILE SER ASP TRP MSE LYS LYS GLN MSE SEQRES 3 A 125 ILE THR GLY GLU TRP LYS GLY GLU ASP LYS LEU PRO SER SEQRES 4 A 125 VAL ARG GLU MSE GLY VAL LYS LEU ALA VAL ASN PRO ASN SEQRES 5 A 125 THR VAL SER ARG ALA TYR GLN GLU LEU GLU ARG ALA GLY SEQRES 6 A 125 TYR ILE TYR ALA LYS ARG GLY MSE GLY SER PHE VAL THR SEQRES 7 A 125 SER ASP LYS ALA LEU PHE ASP GLN LEU LYS LYS GLU LEU SEQRES 8 A 125 ALA ASP ALA ILE THR GLU ARG PHE LEU GLU GLU ALA LYS SEQRES 9 A 125 SER ILE GLY LEU ASP ASP GLN THR ALA ILE GLU LEU LEU SEQRES 10 A 125 ILE LYS ARG SER ARG ASN HIS GLU MODRES 3NEU MSE A 19 MET SELENOMETHIONINE MODRES 3NEU MSE A 23 MET SELENOMETHIONINE MODRES 3NEU MSE A 40 MET SELENOMETHIONINE MODRES 3NEU MSE A 70 MET SELENOMETHIONINE HET MSE A 19 8 HET MSE A 23 8 HET MSE A 40 8 HET MSE A 70 8 HET GOL A 123 6 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *98(H2 O) HELIX 1 1 PRO A 10 THR A 25 1 16 HELIX 2 2 SER A 36 ALA A 45 1 10 HELIX 3 3 ASN A 47 ALA A 61 1 15 HELIX 4 4 ASP A 77 ILE A 103 1 27 HELIX 5 5 ASP A 106 ARG A 119 1 14 SHEET 1 A 2 ILE A 64 LYS A 67 0 SHEET 2 A 2 GLY A 71 VAL A 74 -1 O PHE A 73 N TYR A 65 LINK C TRP A 18 N MSE A 19 1555 1555 1.33 LINK C MSE A 19 N LYS A 20 1555 1555 1.33 LINK C GLN A 22 N MSE A 23 1555 1555 1.33 LINK C MSE A 23 N ILE A 24 1555 1555 1.33 LINK C GLU A 39 N MSE A 40 1555 1555 1.33 LINK C MSE A 40 N GLY A 41 1555 1555 1.33 LINK C GLY A 69 N MSE A 70 1555 1555 1.33 LINK C MSE A 70 N GLY A 71 1555 1555 1.33 SITE 1 AC1 1 ALA A 79 CRYST1 41.828 88.051 38.341 90.00 90.00 90.00 P 21 21 2 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 0.023907 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011357 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026082 0.00000