HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 25-JUN-09 3I18 TITLE CRYSTAL STRUCTURE OF THE PDZ DOMAIN OF THE SDRC-LIKE PROTEIN (LMO2051) TITLE 2 FROM LISTERIA MONOCYTOGENES, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET LMR166B COMPND MOL_ID: 1; COMPND 2 MOLECULE: LMO2051 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES; SOURCE 3 ORGANISM_TAXID: 1639; SOURCE 4 STRAIN: EGD-E; SOURCE 5 GENE: LMO2051; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: BL21 KEYWDS ALPHA-BETA PROTEIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, UNKNOWN KEYWDS 3 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,S.LEW,J.SEETHARAMAN,J.JANJUA,R.XIAO,C.CICCOSANTI,L.ZHAO, AUTHOR 2 J.K.EVERETT,R.NAIR,T.B.ACTON,B.ROST,G.T.MONTELIONE,L.TONG,J.F.HUNT, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 2 24-JUL-19 3I18 1 REMARK LINK REVDAT 1 14-JUL-09 3I18 0 JRNL AUTH F.FOROUHAR,S.LEW,J.SEETHARAMAN,J.JANJUA,R.XIAO,C.CICCOSANTI, JRNL AUTH 2 L.ZHAO,J.K.EVERETT,R.NAIR,T.B.ACTON,B.ROST,G.T.MONTELIONE, JRNL AUTH 3 L.TONG,J.F.HUNT JRNL TITL NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LMR166B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 & XTALVIEW REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 586592.500 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.1 REMARK 3 NUMBER OF REFLECTIONS : 14838 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) : 0.193 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 735 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1022 REMARK 3 BIN R VALUE (WORKING SET) : 0.1710 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 71 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 735 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : -1.65000 REMARK 3 B33 (A**2) : 2.13000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.05 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 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 : 0.35 REMARK 3 BSOL : 33.42 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3I18 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053836. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-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) : 0.97947 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS 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 : 14872 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.1 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 32.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.08300 REMARK 200 R SYM FOR SHELL (I) : 0.10600 REMARK 200 FOR SHELL : 9.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5), RESERVOIR SOLUTION: 30% W/V REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2K AND 150MM POTASSIUM REMARK 280 BROMIDE, MICROBATCH, UNDER OIL, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 25.90550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.90550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 17.85250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.23750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.85250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.23750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.90550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.85250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.23750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.90550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.85250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.23750 REMARK 290 SMTRY3 8 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 1 REMARK 465 GLU A 94 REMARK 465 HIS A 95 REMARK 465 HIS A 96 REMARK 465 HIS A 97 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 VAL A 23 -58.16 -132.13 REMARK 500 ASP A 65 37.08 -140.79 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 BR A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: LMR166B RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 LEU134 WAS MUTATED TO MET SO THAT THE STRUCTURE COULD BE DETERMINED REMARK 999 USING SE ANOMALOUS SIGNAL. DBREF 3I18 A 2 92 UNP Q8Y5K8 Q8Y5K8_LISMO 124 214 SEQADV 3I18 MSE A 1 UNP Q8Y5K8 INITIATING METHIONINE SEQADV 3I18 MSE A 12 UNP Q8Y5K8 LEU 134 SEE REMARK 999 SEQADV 3I18 LEU A 93 UNP Q8Y5K8 EXPRESSION TAG SEQADV 3I18 GLU A 94 UNP Q8Y5K8 EXPRESSION TAG SEQADV 3I18 HIS A 95 UNP Q8Y5K8 EXPRESSION TAG SEQADV 3I18 HIS A 96 UNP Q8Y5K8 EXPRESSION TAG SEQADV 3I18 HIS A 97 UNP Q8Y5K8 EXPRESSION TAG SEQADV 3I18 HIS A 98 UNP Q8Y5K8 EXPRESSION TAG SEQADV 3I18 HIS A 99 UNP Q8Y5K8 EXPRESSION TAG SEQADV 3I18 HIS A 97 UNP Q8Y5K8 EXPRESSION TAG SEQRES 1 A 100 MSE VAL LYS VAL THR TYR ASP GLY VAL TYR VAL MSE SER SEQRES 2 A 100 VAL LYS ASP ASP VAL PRO ALA ALA ASP VAL LEU HIS ALA SEQRES 3 A 100 GLY ASP LEU ILE THR GLU ILE ASP GLY ASN ALA PHE LYS SEQRES 4 A 100 SER SER GLN GLU PHE ILE ASP TYR ILE HIS SER LYS LYS SEQRES 5 A 100 VAL GLY ASP THR VAL LYS ILE ASN TYR LYS HIS GLY ASP SEQRES 6 A 100 LYS ASN GLU GLN ALA ASP ILE LYS LEU THR ALA ILE ASP SEQRES 7 A 100 LYS LYS GLY THR PRO GLY ILE GLY ILE THR LEU VAL ASP SEQRES 8 A 100 ASP LEU GLU HIS HIS HIS HIS HIS HIS MODRES 3I18 MSE A 12 MET SELENOMETHIONINE HET MSE A 12 8 HET BR A 101 1 HETNAM MSE SELENOMETHIONINE HETNAM BR BROMIDE ION FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 BR BR 1- FORMUL 3 HOH *122(H2 O) HELIX 1 1 VAL A 18 VAL A 23 5 6 HELIX 2 2 SER A 40 SER A 50 1 11 HELIX 3 3 ASP A 91 LEU A 93 5 3 SHEET 1 A 5 LYS A 66 LYS A 73 0 SHEET 2 A 5 THR A 56 HIS A 63 -1 N TYR A 61 O GLU A 68 SHEET 3 A 5 LEU A 29 ILE A 33 -1 N THR A 31 O ASN A 60 SHEET 4 A 5 VAL A 9 VAL A 14 -1 N VAL A 9 O ILE A 30 SHEET 5 A 5 ILE A 87 LEU A 89 -1 O THR A 88 N MSE A 12 SHEET 1 B 2 THR A 75 ALA A 76 0 SHEET 2 B 2 PRO A 83 GLY A 84 -1 O GLY A 84 N THR A 75 LINK C VAL A 11 N MSE A 12 1555 1555 1.33 LINK C MSE A 12 N SER A 13 1555 1555 1.33 SITE 1 AC1 3 VAL A 9 TYR A 10 ASP A 91 CRYST1 35.705 90.475 51.811 90.00 90.00 90.00 C 2 2 21 8 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 0.028007 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019301 0.00000